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    Publication numberUS20140178866 A1
    Publication typeApplication
    Application numberUS 13/781,963
    Publication date26 Jun 2014
    Filing date1 Mar 2013
    Priority date21 Dec 2012
    Also published asCA2893975A1, US20160130671, WO2014100229A1
    Publication number13781963, 781963, US 2014/0178866 A1, US 2014/178866 A1, US 20140178866 A1, US 20140178866A1, US 2014178866 A1, US 2014178866A1, US-A1-20140178866, US-A1-2014178866, US2014/0178866A1, US2014/178866A1, US20140178866 A1, US20140178866A1, US2014178866 A1, US2014178866A1
    InventorsJoshua M. Shendelman, John B. Woodward, Meizhu Yang
    Original AssigneePioneer Hi-Bred International, Inc.
    Export CitationBiBTeX, EndNote, RefMan
    External Links: USPTO, USPTO Assignment, Espacenet
    Genetic loci associated with soybean cyst nematode resistance and methods of use
    US 20140178866 A1
    Abstract
    Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with resistance or improved resistance to soybean cyst nematode. In certain embodiments, the method comprises detecting at least one marker locus that is associated with resistance to soybean cyst nematode. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with resistance to soybean cyst nematode. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with resistance or improved resistance to soybean cyst nematode.
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    Claims(20)
    That which is claimed:
    1. A method of identifying a first soybean plant or a first soybean germplasm that displays resistance or improved resistance to soybean cyst nematode, the method comprising detecting in the genome of said first soybean plant or in the genome of said first soybean germplasm at least one marker locus that is associated with the resistance, wherein the at least one marker locus comprises
    (a) S07160-1 or a marker closely linked thereto on linkage group A2; or
    (b) Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linked thereto.
    2. The method of claim 1, wherein at least two marker loci are detected.
    3. The method of claim 2, wherein the at least two marker loci comprise a haplotype that is associated with said resistance.
    4. The method of claim 1, wherein the germplasm is a soybean variety.
    5. The method of claim 1, wherein the method further comprises selecting the first soybean plant or first soybean germplasm or a progeny thereof having the at least one marker locus.
    6. The method of claim 5, further comprising crossing the selected first soybean plant or first soybean germplasm with a second soybean plant or second soybean germplasm.
    7. The method of claim 6, wherein the second soybean plant or second soybean germplasm comprises an exotic soybean strain or an elite soybean strain.
    8. The method of claim 1, wherein the detecting comprises DNA sequencing of at least one of said marker loci.
    9. The method of claim 1, wherein the detecting comprises amplifying at least one of said marker loci and detecting the resulting amplified marker amplicon.
    10. The method of claim 9, wherein the amplifying comprises:
    a) admixing an amplification primer or amplification primer pair for each marker locus being amplified with a nucleic acid isolated from the first soybean plant or the first soybean germplasm, wherein the primer or primer pair is complementary or partially complementary to a variant or fragment of the genomic locus comprising the marker locus, and is capable of initiating DNA polymerization by a DNA polymerase using the soybean nucleic acid as a template; and
    b) extending the primer or primer pair in a DNA polymerization reaction comprising a DNA polymerase and a template nucleic acid to generate at least one amplicon.
    11. The method of claim 10, wherein said method comprises amplifying a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379 or 380.
    12. The method of claim 10, wherein said primer or primer pair comprises a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380 or complements thereof.
    13. The method of claim 12, wherein said primer or primer pair comprises a nucleic acid sequence comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8 or variants or fragments thereof.
    14. The method of claim 13, wherein said primer pair comprises SEQ ID NO: 1 and SEQ ID NO: 2.
    15. The method of claim 10, wherein the method further comprises providing one or more labeled nucleic acid probes suitable for detection of each marker locus being amplified.
    16. The method of claim 15, wherein said labeled nucleic acid probe comprises a nucleic acid sequence comprising a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380 or complements thereof.
    17. The method of claim 16, wherein the labeled nucleic acid probe comprises a nucleic acid sequence comprising SEQ ID NOs: 9 or 10.
    18. An isolated polynucleotide capable of detecting a marker locus of the soybean genome comprising
    (a) S07160-1 or a marker closely linked thereto on linkage group A2; or
    (b) Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linked thereto.
    19. The isolated polynucleotide of claim 18, wherein the polynucleotide comprises:
    (a) a polynucleotide comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, or 8;
    (b) a polynucleotide comprising SEQ ID NOs: 9 or 10;
    (c) a polynucleotide having at least 90% sequence identity to the polynucleotides set forth in parts (a) or (b); or
    (d) a polynucleotide comprising at least 10 contiguous nucleotides of the polynucleotides set forth in parts (a) or (b).
    20. A kit for detecting or selecting at least one soybean plant or soybean germplasm with resistance or improved resistance to soybean cyst nematode, the kit comprising:
    a) primers or probes for detecting one or more marker loci associated with resistance to soybean cyst nematode, wherein the primers or probes are capable of detecting a marker locus comprising
    (i) S07160-1 or a marker closely linked thereto; or
    (ii) Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linked thereto; and
    b) instructions for using the primers or probes for detecting the one or more marker loci and correlating the detected marker loci with predicted resistance to soybean cyst nematode.
    Description
      CROSS-REFERENCE TO RELATED APPLICATIONS
    • [0001]
      This application claims the benefit of U.S. Provisional Application No. 61/740,567, filed Dec. 21, 2012, which is hereby incorporated herein in its entirety by reference.
    • FIELD OF THE INVENTION
    • [0002]
      This invention relates to methods of identifying and/or selecting soybean plants or germplasm that display resistance or improved resistance to Soybean Cyst Nematode.
    • REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA EFS-WEB
    • [0003]
      The official copy of the sequence listing is submitted concurrently with the specification as a text file via EFS-Web, in compliance with the American Standard Code for Information Interchange (ASCII), with a file name of 430267seqlist.txt, a creation date of Feb. 21, 2013 and a size of 229 KB. The sequence listing filed via EFS-Web is part of the specification and is hereby incorporated in its entirety by reference herein.
    • BACKGROUND
    • [0004]
      Soybeans (Glycine max L. Merr.) are a major cash crop and investment commodity in North America and elsewhere. Soybean oil is one of the most widely used edible oils, and soybeans are used worldwide both in animal feed and in human food production. Additionally, soybean utilization is expanding to industrial, manufacturing, and pharmaceutical applications.
    • [0005]
      Soybean Cyst Nematode (SCN) is a parasitic pest which has threatened soybean production in the U.S. for more than fifty years. Soybean cyst nematode resistance is an economically important trait as infection can substantially reduce yields. Molecular characterization of soybean cyst nematode resistance would have important implications for soybean cultivar improvement.
    • [0006]
      There remains a need for soybean plants with improved resistance to soybean cyst nematode and methods for identifying and selecting such plants.
    • SUMMARY
    • [0007]
      Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with resistance or improved resistance to soybean cyst nematode. In certain embodiments, the method comprises detecting at least one marker locus that is associated with resistance to soybean cyst nematode. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with resistance to soybean cyst nematode. In further embodiments, the method comprises crossing a selected soybean plant with a second soybean plant. Further provided are markers, primers, probes and kits useful for identifying and/or selecting soybean plants or soybean germplasm with resistance or improved resistance to soybean cyst nematode.
    • BRIEF DESCRIPTION OF THE FIGURES
    • [0008]
      FIG. 1 A-D provides a genetic map for loci on linkage group A2.
    • DETAILED DESCRIPTION
    • [0009]
      Before describing the present invention in detail, it is to be understood that this invention is not limited to particular embodiments, which can, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting.
    • [0010]
      Certain definitions used in the specification and claims are provided below. In order to provide a clear and consistent understanding of the specification and claims, including the scope to be given such terms, the following definitions are provided:
    • [0011]
      As used in this specification and the appended claims, terms in the singular and the singular forms “a,” “an,” and “the,” for example, include plural referents unless the content clearly dictates otherwise. Thus, for example, reference to “plant,” “the plant,” or “a plant” also includes a plurality of plants; also, depending on the context, use of the term “plant” can also include genetically similar or identical progeny of that plant; use of the term “a nucleic acid” optionally includes, as a practical matter, many copies of that nucleic acid molecule; similarly, the term “probe” optionally (and typically) encompasses many similar or identical probe molecules.
    • [0012]
      Additionally, as used herein, “comprising” is to be interpreted as specifying the presence of the stated features, integers, steps, or components as referred to, but does not preclude the presence or addition of one or more features, integers, steps, or components, or groups thereof. Thus, for example, a kit comprising one pair of oligonucleotide primers may have two or more pairs of oligonucleotide primers. Additionally, the term “comprising” is intended to include examples encompassed by the terms “consisting essentially of” and “consisting of.” Similarly, the term “consisting essentially of” is intended to include examples encompassed by the term “consisting of.”
    • [0013]
      “Agronomics,” “agronomic traits,” and “agronomic performance” refer to the traits (and underlying genetic elements) of a given plant variety that contribute to yield over the course of a growing season. Individual agronomic traits include emergence vigor, vegetative vigor, stress tolerance, disease resistance or tolerance, insect resistance or tolerance, herbicide resistance, branching, flowering, seed set, seed size, seed density, standability, threshability, and the like.
    • [0014]
      “Allele” means any of one or more alternative forms of a genetic sequence. In a diploid cell or organism, the two alleles of a given sequence typically occupy corresponding loci on a pair of homologous chromosomes. With regard to a SNP marker, allele refers to the specific nucleotide base present at that SNP locus in that individual plant.
    • [0015]
      The term “amplifying” in the context of nucleic acid amplification is any process whereby additional copies of a selected nucleic acid (or a transcribed form thereof) are produced. An “amplicon” is an amplified nucleic acid, e.g., a nucleic acid that is produced by amplifying a template nucleic acid by any available amplification method.
    • [0016]
      An “ancestral line” is a parent line used as a source of genes, e.g., for the development of elite lines.
    • [0017]
      An “ancestral population” is a group of ancestors that have contributed the bulk of the genetic variation that was used to develop elite lines.
    • [0018]
      “Backcrossing” is a process in which a breeder crosses a progeny variety back to one of the parental genotypes one or more times.
    • [0019]
      The term “chromosome segment” designates a contiguous linear span of genomic DNA that resides in planta on a single chromosome. “Chromosome interval” refers to a chromosome segment defined by specific flanking marker loci.
    • [0020]
      “Cultivar” and “variety” are used synonymously and mean a group of plants within a species (e.g., Glycine max) that share certain genetic traits that separate them from other possible varieties within that species. Soybean cultivars are inbred lines produced after several generations of self-pollinations. Individuals within a soybean cultivar are homogeneous, nearly genetically identical, with most loci in the homozygous state.
    • [0021]
      An “elite line” is an agronomically superior line that has resulted from many cycles of breeding and selection for superior agronomic performance. Numerous elite lines are available and known to those of skill in the art of soybean breeding.
    • [0022]
      An “elite population” is an assortment of elite individuals or lines that can be used to represent the state of the art in terms of agronomically superior genotypes of a given crop species, such as soybean.
    • [0023]
      An “exotic soybean strain” or an “exotic soybean germplasm” is a strain or germplasm derived from a soybean not belonging to an available elite soybean line or strain of germplasm. In the context of a cross between two soybean plants or strains of germplasm, an exotic germplasm is not closely related by descent to the elite germplasm with which it is crossed. Most commonly, the exotic germplasm is not derived from any known elite line of soybean, but rather is selected to introduce novel genetic elements (typically novel alleles) into a breeding program.
    • [0024]
      A “genetic map” is a description of genetic association or linkage relationships among loci on one or more chromosomes (or linkage groups) within a given species, generally depicted in a diagrammatic or tabular form.
    • [0025]
      “Genotype” is a description of the allelic state at one or more loci.
    • [0026]
      “Germplasm” means the genetic material that comprises the physical foundation of the hereditary qualities of an organism. As used herein, germplasm includes seeds and living tissue from which new plants may be grown; or, another plant part, such as leaf, stem, pollen, or cells, that may be cultured into a whole plant. Germplasm resources provide sources of genetic traits used by plant breeders to improve commercial cultivars.
    • [0027]
      An individual is “homozygous” if the individual has only one type of allele at a given locus (e.g., a diploid individual has a copy of the same allele at a locus for each of two homologous chromosomes). An individual is “heterozygous” if more than one allele type is present at a given locus (e.g., a diploid individual with one copy each of two different alleles). The term “homogeneity” indicates that members of a group have the same genotype at one or more specific loci. In contrast, the term “heterogeneity” is used to indicate that individuals within the group differ in genotype at one or more specific loci.
    • [0028]
      “Introgression” means the entry or introduction of a gene, QTL, haplotype, marker profile, trait, or trait locus from the genome of one plant into the genome of another plant.
    • [0029]
      The terms “label” or “detectable label” refer to a molecule capable of detection. A detectable label can also include a combination of a reporter and a quencher, such as are employed in FRET probes or TaqMan™ probes. The term “reporter” refers to a substance or a portion thereof which is capable of exhibiting a detectable signal, which signal can be suppressed by a quencher. The detectable signal of the reporter is, e.g., fluorescence in the detectable range. The term “quencher” refers to a substance or portion thereof which is capable of suppressing, reducing, inhibiting, etc., the detectable signal produced by the reporter. As used herein, the terms “quenching” and “fluorescence energy transfer” refer to the process whereby, when a reporter and a quencher are in close proximity, and the reporter is excited by an energy source, a substantial portion of the energy of the excited state non-radiatively transfers to the quencher where it either dissipates non-radiatively or is emitted at a different emission wavelength than that of the reporter.
    • [0030]
      A “line” or “strain” is a group of individuals of identical parentage that are generally inbred to some degree and that are generally homozygous and homogeneous at most loci (isogenic or near isogenic). A “subline” refers to an inbred subset of descendants that are genetically distinct from other similarly inbred subsets descended from the same progenitor. Traditionally, a subline has been derived by inbreeding the seed from an individual soybean plant selected at the F3 to F5 generation until the residual segregating loci are “fixed” or homozygous across most or all loci. Commercial soybean varieties (or lines) are typically produced by aggregating (“bulking”) the self-pollinated progeny of a single F3 to F5 plant from a controlled cross between 2 genetically different parents. While the variety typically appears uniform, the self-pollinating variety derived from the selected plant eventually (e.g., F8) becomes a mixture of homozygous plants that can vary in genotype at any locus that was heterozygous in the originally selected F3 to F5 plant. Marker-based sublines that differ from each other based on qualitative polymorphism at the DNA level at one or more specific marker loci are derived by genotyping a sample of seed derived from individual self-pollinated progeny derived from a selected F3-F5 plant. The seed sample can be genotyped directly as seed, or as plant tissue grown from such a seed sample. Optionally, seed sharing a common genotype at the specified locus (or loci) are bulked providing a subline that is genetically homogenous at identified loci important for a trait of interest (e.g., yield, tolerance, etc.).
    • [0031]
      “Linkage” refers to the tendency for alleles to segregate together more often than expected by chance if their transmission was independent. Typically, linkage refers to alleles on the same chromosome. Genetic recombination occurs with an assumed random frequency over the entire genome. Genetic maps are constructed by measuring the frequency of recombination between pairs of traits or markers, the lower the frequency of recombination, and the greater the degree of linkage. “Linkage disequilibrium” is a non-random association of alleles at two or more loci and can occur between unlinked markers. It is based on allele frequencies within a population and is influenced by but not dependent on linkage.
    • [0032]
      “Linkage group” (LG) refers to traits or markers that generally co-segregate. A linkage group generally corresponds to a chromosomal region containing genetic material that encodes the traits or markers.
    • [0033]
      “Locus” is a defined segment of DNA.
    • [0034]
      A “map location” or “map position” is an assigned location on a genetic map relative to linked genetic markers where a specified marker can be found within a given species. Map positions are generally provided in centimorgans (cM), unless otherwise indicated, genetic positions provided are based on the Glycine max consensus map v 4.0 as provided by Hyten et al. (2010) Crop Sci 50:960-968. A “physical position” or “physical location” or “physical map location” is the position, typically in nucleotides bases, of a particular nucleotide, such as a SNP nucleotide, on a chromosome. Unless otherwise indicated, the physical position within the soybean genome provided is based on the Glyma 1.0 genome sequence described in Schmutz et al. (2010) Nature 463:178-183, available from the Phytozome website (phytozome-dot-net/soybean).
    • [0035]
      “Mapping” is the process of defining the association and relationships of loci through the use of genetic markers, populations segregating for the markers, and standard genetic principles of recombination frequency.
    • [0036]
      “Marker” or “molecular marker” or “marker locus” is a term used to denote a nucleic acid or amino acid sequence that is sufficiently unique to characterize a specific locus on the genome. Any detectable polymorphic trait can be used as a marker so long as it is inherited differentially and exhibits linkage disequilibrium with a phenotypic trait of interest.
    • [0037]
      “Marker assisted selection” refers to the process of selecting a desired trait or traits in a plant or plants by detecting one or more nucleic acids from the plant, where the nucleic acid is linked to the desired trait, and then selecting the plant or germplasm possessing those one or more nucleic acids.
    • [0038]
      “Haplotype” refers to a combination of particular alleles present within a particular plant's genome at two or more linked marker loci, for instance at two or more loci on a particular linkage group. For instance, in one example, two specific marker loci on LG-A2 are used to define a haplotype for a particular plant. In still further examples, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more linked marker loci are used to define a haplotype for a particular plant.
    • [0039]
      As used herein, a “marker profile” means a combination of particular alleles present within a particular plant's genome at two or more marker loci which are not linked, for instance two or more loci on two or more different linkage groups or two or more chromosomes. For instance, in one example, a particular combination of marker loci or a particular combination of haplotypes define the marker profile of a particular plant.
    • [0040]
      The term “plant” includes reference to an immature or mature whole plant, including a plant from which seed or grain or anthers have been removed. Seed or embryo that will produce the plant is also considered to be the plant.
    • [0041]
      “Plant parts” means any portion or piece of a plant, including leaves, stems, buds, roots, root tips, anthers, seed, grain, embryo, pollen, ovules, flowers, cotyledons, hypocotyls, pods, flowers, shoots, stalks, tissues, tissue cultures, cells and the like.
    • [0042]
      “Polymorphism” means a change or difference between two related nucleic acids. A “nucleotide polymorphism” refers to a nucleotide that is different in one sequence when compared to a related sequence when the two nucleic acids are aligned for maximal correspondence.
    • [0043]
      “Polynucleotide,” “polynucleotide sequence,” “nucleic acid,” “nucleic acid molecule,” “nucleic acid sequence,” “nucleic acid fragment,” and “oligonucleotide” are used interchangeably herein to indicate a polymer of nucleotides that is single- or multi-stranded, that optionally contains synthetic, non-natural, or altered RNA or DNA nucleotide bases. A DNA polynucleotide may be comprised of one or more strands of cDNA, genomic DNA, synthetic DNA, or mixtures thereof.
    • [0044]
      “Primer” refers to an oligonucleotide which is capable of acting as a point of initiation of nucleic acid synthesis or replication along a complementary strand when placed under conditions in which synthesis of a complementary strand is catalyzed by a polymerase. Typically, primers are about 10 to 30 nucleotides in length, but longer or shorter sequences can be employed. Primers may be provided in double-stranded form, though the single-stranded form is more typically used. A primer can further contain a detectable label, for example a 5′ end label.
    • [0045]
      “Probe” refers to an oligonucleotide that is complementary (though not necessarily fully complementary) to a polynucleotide of interest and forms a duplexed structure by hybridization with at least one strand of the polynucleotide of interest. Typically, probes are oligonucleotides from 10 to 50 nucleotides in length, but longer or shorter sequences can be employed. A probe can further contain a detectable label.
    • [0046]
      “Quantitative trait loci” or “QTL” refer to the genetic elements controlling a quantitative trait.
    • [0047]
      “Recombination frequency” is the frequency of a crossing over event (recombination) between two genetic loci. Recombination frequency can be observed by following the segregation of markers and/or traits during meiosis.
    • [0048]
      “Resistance and “improved resistance” are used interchangeably herein and refer to any type of increase in resistance or tolerance to, or any type of decrease in susceptibility. A “resistant plant” or “resistant plant variety” need not possess absolute or complete resistance. Instead, a “resistant plant,” “resistant plant variety,” or a plant or plant variety with “improved resistance” will have a level of resistance or tolerance which is higher than that of a comparable susceptible plant or variety.
    • [0049]
      “Self-crossing” or “self-pollination” or “selfing” is a process through which a breeder crosses a plant with itself; for example, a second generation hybrid F2 with itself to yield progeny designated F2:3.
    • [0050]
      “SNP” or “single nucleotide polymorphism” means a sequence variation that occurs when a single nucleotide (A, T, C, or G) in the genome sequence is altered or variable. “SNP markers” exist when SNPs are mapped to sites on the soybean genome.
    • [0051]
      The term “yield” refers to the productivity per unit area of a particular plant product of commercial value. For example, yield of soybean is commonly measured in bushels of seed per acre or metric tons of seed per hectare per season. Yield is affected by both genetic and environmental factors.
    • [0052]
      As used herein, an “isolated” or “purified” polynucleotide or polypeptide, or biologically active portion thereof, is substantially or essentially free from components that normally accompany or interact with the polynucleotide or polypeptide as found in its naturally occurring environment. Typically, an “isolated” polynucleotide is free of sequences (optimally protein encoding sequences) that naturally flank the polynucleotide (i.e., sequences located at the 5′ and 3′ ends of the polynucleotide) in the genomic DNA of the organism from which the polynucleotide is derived. For example, the isolated polynucleotide can contain less than about 5 kb, 4 kb, 3 kb, 2 kb, 1 kb, 0.5 kb, or 0.1 kb of nucleotide sequence that naturally flank the polynucleotide in genomic DNA of the cell from which the polynucleotide is derived. A polypeptide that is substantially free of cellular material includes preparations of polypeptides having less than about 30%, 20%, 10%, 5%, or 1% (by dry weight) of contaminating protein, culture media or other chemical components.
    • [0053]
      Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described more fully in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, 1989 (hereinafter “Sambrook”).
    • [0054]
      Methods are provided for identifying and/or selecting a soybean plant or soybean germplasm that displays resistance or improved resistance to soybean cyst nematode. The method comprises detecting in the soybean plant or germplasm, or a part thereof, at least one marker locus associated with resistance to soybean cyst nematode. Also provided are isolated polynucleotides and kits for use in identifying and/or detecting a soybean plant or soybean germplasm that displays resistance or improved resistance to soybean cyst nematode, and soybean plants, cells, and/or seeds comprising at least one marker locus conferring improved resistance to soybean cyst nematode.
    • [0055]
      Provided herein, marker loci associated with soybean cyst nematode resistance have been identified and mapped to the rhg4 (resistance to Heterodera glycines 4) locus on linkage group A2 on chromosome 8. Examples of soybean lines known to comprise the rhg4 resistance locus include, for example, Peking and PI437654.
    • [0056]
      These findings have important implications for soybean production, as identifying markers that can be used for selection of soybean cyst nematode resistance will greatly expedite the development of soybean cyst nematode resistance into elite cultivars.
    • [0057]
      Marker loci, haplotypes and marker profiles associated with resistance to soybean cyst nematode, are provided. Further provided are genomic loci that are associated with soybean resistance to soybean cyst nematode.
    • [0058]
      In certain embodiments, soybean plants or germplasm are identified that have at least one favorable allele, marker locus, haplotype or marker profile that positively correlates with resistance or improved resistance to soybean cyst nematode. However, in other embodiments, it is useful for exclusionary purposes during breeding to identify alleles, marker loci, haplotypes, or marker profiles that negatively correlate with resistance, for example, to eliminate such plants or germplasm from subsequent rounds of breeding.
    • [0059]
      In one embodiment, marker loci useful for identifying a first soybean plant or first soybean germplasm that displays resistance or improved resistance to soybean cyst nematode are associated with the rhg4 locus on linkage group A2 on chromosome 8. In another embodiment, the marker locus comprises: (a) S07160-1 or a closely linked marker on linkage group A2; or (b) Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linked thereto.
    • [0060]
      In certain embodiments, multiple marker loci that collectively make up a soybean cyst nematode resistance haplotype of interest are investigated. For example, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more of the various marker loci provided herein can comprise a soybean cyst nematode resistance haplotype. In some embodiments, the haplotype comprises: (a) two or more marker loci associated with the Rhg4 locus on linkage group A2; or (b) two or more marker loci comprising S07160-1, Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linked thereto.
    • [0061]
      In one embodiment, the method of identifying a first soybean plant or a first soybean germplasm that displays resistance or improved resistance to soybean cyst nematode comprises detecting in the genome of the first soybean plant or in the genome of the first soybean germplasm at least one haplotype that is associated with the resistance, wherein the at least one haplotype comprises at least two of the various marker loci provided herein.
    • [0062]
      In certain embodiments, two or more marker loci or haplotypes can collectively make up a marker profile. The marker profile can comprise any two or more marker loci comprising: (a) marker loci comprising S07160-1 on linkage group A2, or a closely linked marker; (b) marker loci comprising Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linked thereto; (c) any marker loci associated with the rhg4 locus on linkage group A2; (d) any marker loci associated with the rhg1 locus on linkage group G, or a closely linked marker; (e) any marker loci associated with the rhg2 locus on linkage group M; and/or (f) any marker loci associated with resistance to soybean cyst nematode.
    • [0063]
      Any of the marker loci in any of the genomic loci disclosed herein can be combined in the marker profile. For example, the marker profile can comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more marker loci or haplotypes associated with resistance to soybean cyst nematode.
    • [0064]
      In one embodiment, a method of identifying a first soybean plant or a first soybean germplasm that displays resistance or improved resistance to soybean cyst nematode comprises detecting in the genome of the first soybean plant or in the genome of the first soybean germplasm at least one marker profile that is associated with the resistance, wherein the at least one marker profile comprises the marker locus provided herein.
    • [0065]
      Not only can one detect the various markers provided herein, it is recognized that one could detect any markers that are closely linked to the various markers discussed herein. Non-limiting examples of closely linked markers on linkage group A2 are provided in FIG. 1 A-D.
    • [0066]
      In addition to the markers discussed herein, information regarding useful soybean markers can be found, for example, on the USDA's Soybase website, available at www.soybase.org. One of skill in the art will recognize that the identification of favorable marker alleles may be germplasm-specific. The determination of which marker alleles correlate with resistance (or susceptibility) is determined for the particular germplasm under study. One of skill will also recognize that methods for identifying the favorable alleles are routine and well known in the art, and furthermore, that the identification and use of such favorable alleles is well within the scope of the invention.
    • [0067]
      Various methods are provided to identify soybean plants and/or germplasm with resistance or improved resistance to soybean cyst nematode. In one embodiment, the method of identifying comprises detecting at least one marker locus associated with resistance to soybean cyst nematode. The term “associated with” in connection with a relationship between a marker locus and a phenotype refers to a statistically significant dependence of marker frequency with respect to a quantitative scale or qualitative gradation of the phenotype. Thus, an allele of a marker is associated with a trait of interest when the allele of the marker locus and the trait phenotypes are found together in the progeny of an organism more often than if the marker genotypes and trait phenotypes segregated separately.
    • [0068]
      Any combination of the marker loci provided herein can be used in the methods to identify a soybean plant or soybean germplasm that displays resistance or improved resistance to soybean cyst nematode. Any one marker locus or any combination of the markers set forth herein, or any closely linked marker can be used to aid in identifying and selecting soybean plants or soybean germplasm with resistance or improved resistance to soybean cyst nematode.
    • [0069]
      In one embodiment, a method of identifying a first soybean plant or a first soybean germplasm that displays resistance or improved resistance to soybean cyst nematode is provided. The method comprises detecting in the genome of the first soybean plant or first soybean germplasm at least one marker locus that is associated with resistance. In such a method, the at least one marker locus: (a) can comprise the marker locus S07160-1 on linkage group A2, or a closely linked marker; (b) can comprise the marker loci Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linked thereto; or (c) can be any marker associated with the rhg4 locus on linkage group A2.
    • [0070]
      In other embodiments, two or more marker loci are detected in the method. In a specific embodiment, the germplasm is a soybean variety.
    • [0071]
      In other embodiments, the method further comprises crossing the selected first soybean plant or first soybean germplasm with a second soybean plant or second soybean germplasm. In a further embodiment of the method, the second soybean plant or second soybean germplasm comprises an exotic soybean strain or an elite soybean strain.
    • [0072]
      In specific embodiments, the first soybean plant or first soybean germplasm comprises a soybean variety. Any soybean line known to the art or disclosed herein may be used. Non-limiting examples of soybean varieties and their associated soybean cyst nematode resistance alleles encompassed by the methods provided herein include, for example, Peking and PI437654.
    • [0073]
      In another embodiment, the detection method comprises amplifying at least one marker locus and detecting the resulting amplified marker amplicon. In such a method, amplifying comprises (a) admixing an amplification primer or amplification primer pair for each marker locus being amplified with a nucleic acid isolated from the first soybean plant or the first soybean germplasm such that the primer or primer pair is complementary or partially complementary to a variant or fragment of the genomic locus comprising the marker locus and is capable of initiating DNA polymerization by a DNA polymerase using the soybean nucleic acid as a template; and (b) extending the primer or primer pair in a DNA polymerization reaction comprising a DNA polymerase and a template nucleic acid to generate at least one amplicon. In such a method, the primer or primer pair can comprise a variant or fragment of one or more of the genomic loci provided herein.
    • [0074]
      In one embodiment, the method involves amplifying a variant or fragment of one or more polynucleotides comprising SEQ ID NOS: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380 or variants or fragments thereof.
    • [0075]
      In one embodiment, the primer or primer pair can comprise a variant or fragment of one or more polynucleotides comprising SEQ ID NOS: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380 or complements thereof.
    • [0076]
      In specific embodiments, the primer or primer pair comprises a nucleic acid sequence comprising SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8 or variants or fragments thereof.
    • [0077]
      In a specific embodiment, the primer pair comprises SEQ ID NO:1 and SEQ ID NO:2.
    • [0078]
      In another embodiment, the method further comprises providing one or more labeled nucleic acid probes suitable for detection of each marker locus being amplified. In such a method, the labeled nucleic acid probe can comprise a sequence comprising a variant or fragment of one or more of the genomic loci provided herein. In one embodiment, the labeled nucleic acid probe can comprise a sequence comprising a variant or fragment of one or more polynucleotides comprising SEQ ID NOS: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380 or complements thereof.
    • [0079]
      In specific embodiments, the labeled nucleic acid probe comprises a nucleic acid sequence comprising SEQ ID NOS: 9, 10 or variants or fragments thereof.
    • [0080]
      Non-limiting examples of primers, probes, genomic loci and amplicons that can be used in the methods and compositions provided herein are summarized in Tables 1, 2, 3A, 3B and 4, respectively.
    • [0000]
      TABLE 1 
      Non-Limiting Examples of Primer Sequences.
      Linkage SEQ
      Marker Group Marker Primer ID Allele
      position (ch) Name Name NO Primer Sequence (R/S)
      8300131 A2 S07160-1 136868 1 TGTGTTGTGTTTGACTGCCATA C/A
      (Gm08)
      8300131 A2 S07160-1 136869 2 CATTTCCCAAGCCTCTTGAT C/A
      (Gm08)
      8300131 A2 S07160-1 100532 3 TCTAGCTCTGACATATTGATGA C/A
      (Gm08) TTCTTTTGTGTTGT
      8300131 A2 S07160-1 80588  4 AAGCCTCTTGATAAGACAGTGT C/A
      (Gm08) CTTCCAAATC
      8300131 A2 S07160-1 136870 5 TCTTTTGTGTTGTGTTTGACTGC C/A
      (Gm08)
      8300131 A2 S07160-1 136871 6 TGAGGCTTTCCAGCATCTAAC C/A
      (Gm08)
      8300131 A2 S07160-1 136872 7 GGACTGGATCATGAGAATTGG C/A
      (Gm08)
      8300131 A2 S07160-1 136873 8 AAGCAGAAGGAGCATTGAGG C/A
      (Gm08)
      R=Resistant; S=Susceptible
    • [0000]
      TABLE 2 
      Non-Limiting Examples of Probe Sequences.
      Linkage
      Marker Group Marker Probe 1* Probe 2**
      Position (ch) Name Name Probe 1 Sequence Name Probe 2 Sequence
      8300131 A2 S07160-1 102389 ATTCCTAAAGATAGT 102390 CTAAAGATACATGCA
      (Gm08) CCAAT (SEQ IDNO: 9) AGTC (SEQ ID NO: 10)
      *Probe 1 detects the susceptible allele.
      **Probe 2 detects the resistant allele.
    • [0000]
      TABLE 3A 
      Non-Limiting Examples of Genomic Loci Comprising the Various Marker
      Loci Provided Herein.
      Resistant
      Marker (R) or
      Marker SEQ Susceptible
      Position Name NO ID (S) Allele Reference Sequence
      8300131 S07160-1 13 R TGGAATCTGAGAAGAGACTTGAGAAATGGTACTCTTTGAATCCATGTAAGG
      TAATCATTGCCACTGGATTCATTGCAAGCACACCTCAAAACATTCCTACCAC
      ACTGAAGAGAGATGGAAGTGACTTCTCGGCAGCAATTATGGGTGCTCTATT
      TAAGGCTCGTCAGGTCACAATTTGGACAGATGTTGATGGTGTGTATAGTGC
      AGATCCTAGAAAAGGTTTGTTATGCTTCGTACTCTGTCTCTGAGTTAAACAA
      TGAGTGGACTGGATCATGAGAATTGGTTTTTAGTAACCAGAGGGAGTTCTA
      GCTCTGACATATTGATGATTCTTTTGTGTTGTGTTTGACTGCCATAACATGA
      TGTTTGGATTAAATATAAACAATAATATCCTATGCAGTTAGTGAGGCTGTG
      ATTTGGAAGACACTGTCTTATCAAGAGGCTTGGGAAATGGTGAGTTAGATG
      CTGGAAAGCCTCAATGCTCCTTCTGCTTGTAAAATTAAGGAGATTAACTTGC
      AAATTGTCTGTTGTACAGTCTTATTTGGGTGCCAATGTCTTGCATCCCCGCA
      CAATTATTCCTGTGATGCGATATGGCATACCCATTATGATAAGGAACATTCC
      CA
      8300131 S07160-1 14 S TGGAATCTGAGAAGAGACTTGAGAAATGGTACTCTTTGAATCCATGTAAGG
      TAATCATTGCCACTGGATTCATTGCAAGCACACCTCAAAACATTCCTACCAC
      ACTGAAGAGAGATGGAAGTGACTTCTCGGCAGCAATTATGGGTGCTCTATT
      TAAGGCTCGTCAGGTCACAATTTGGACAGATGTTGATGGTGTGTATAGTGC
      AGATCCTAGAAAAGGTTTGTTATGCTTCGTACTCTGTCTCTGAGTTAAACAA
      TGAGTGGACTGGATCATGAGAATTGGTTTTTAGTAACCAGAGGGAGTTCTA
      GCTCTGACATATTGATGATTCTTTTGTGTTGTGTTTGACTGCCATAACATGA
      TGTTTGGATTAAATATAAACAATAATATCATATGCAGTTAGTGAGGCTGTG
      ATTTGGAAGACACTGTCTTATCAAGAGGCTTGGGAAATGGTGAGTTAGATG
      CTGGAAAGCCTCAATGCTCCTTCTGCTTGTAAAATTAAGGAGATTAACTTGC
      AAATTGTCTGTTGTACAGTCTTATTTGGGTGCCAATGTCTTGCATCCCCGCA
      CAATTATTCCTGTGATGCGATATGGCATACCCATTATGATAAGGAACATTCC
      CA
    • [0000]
      TABLE 3B 
      Non-Limiting Examples of Genomic Loci Comprising the Various Marker
      Loci Provided Herein.
      SEQ SEQ
      SNP ID ID Consensus Reference Sequence
      Marker SNP SNP NO NO r2 with r2 with (200 by flanking SNP)
      Name Position [S/R] [S] [R] 8357600 8356824 [S/R]
      8356824 [C/G] 15 198 0.857 GCCGGGCAACCGCTACTACGGCGGCAATGAATA
      CATCGACCAGATCGAAAACCTCTGCCGCTCACGC
      Gm08:85 GCCCTCCAAGCCTTCCACCTCGACGCCCAATCCT
      6824 GGGGCGTCAACGTCCAGCCCTACTCCGGCTCCCC
      (Rhg4 GGCCAACTTCGCCGCCTACACCGCCGTCCTCAAC
      mutation CCCCACGACCGCATCATGGGGCTAGATCTCC +C/G
      from Liu +CTCCGGCGGCCACCTCACCCACGGCTACTACAC
      et al CTCCGGCGGAAAGAAGATCTCCGCCACCTCCATT
      Nature TACTTCGAGAG TCTCCCTTACAAGGTAAACTCCA
      2012*) CCACCGGCTACATCGACTAYGACCGCTTGGAAGA
      AAAAGCCCTAGACTTCAGGCCAAAACTCATAATC
      TGCGGTGGCAGCGCGTACCCTCGCGA TTGGG
      CCGTTGCGCTTGGAAAATACTTGATGGGGAAAGG
      GTACAGCCTTGTCACTGGCGGAACGGAGAACCAT
      G08:835 CTTGTTTTGTGGGATCTGAGACCTCTTGGATTGAC
      7600 TGGTAATATATATAGGATTGGATCTCTACCTTCT
      (Rhg4 8357600 [A/T] 16 199 0.857 GGTTTTGATTTGTTACAAATGTCTATAAATCTGAC
      mutation TTGTTCGTTGTGTGATTGTTTTGCAGGG+AfI+ATA
      from Liu AGGTGGAGAAACTCTGTGATCTCTGTAACATTAC
      et al. TGTTAACAAGAACGCTGTTTTTGGTGATAGCAGT
      Nature GCCTTGGCCCCTGGTGGAGTGCGAATTGGTAACG
      2012) ATCTTACTTCTCTTTTATATGCTACAATACAAATC
      TTGCTTTACTAACTCAATTGGAAACAAGATCTCA
      TTTATAAGATTATAAAAATGATTTCC
      CATATCGCATCACAGGAATAATTGTGCGGGGATG
      CAAGACATTGGCACCAAAATAAGACTGTACAAC
      AGACAATTTGCAAGTTAATCTCCTTAATTTTACA
      AGCAGAAGGAGCATTGAGGCTTTCCAGCATCTAA
      Gm08:830 CTCACCATTTCCCAAGCCTCTTGATAAGACAGTG
      0131 8300131 [A/C] 17 200 0.818 0.738 TCTTCAAAATCACAGCCTCACTAACTGCATA[A/C]
      (S07160- GATATTATTGTTTATATTTAATCAAAACATCATGT
      1) TATGGCAGTCAAACACAACACAAAAGAATCATC
      AATATGTCAGAGCTAGAACTCCCTCTGGTTACTA
      AAAACCAATTCTCATGATCCAGTCCACTCATTGT
      TTAACTCAGAGACAGAGTACGAAGCATAACAAA
      CCTTTTCTAGGATCTGCACTATACACACCAT
      TAGGATGTTTTTCAAATACACTCTTTTCTCGCTGT
      TTAAAAAAAAAAATACACTCTCTTCTAATAATTA
      AAAGTTATTAAAAATCATAAATTTGAATGGATCT
      CATTTTTCATTGAGTAACTCTCTCTCGTGATTTTA
      TATTATCTCTGTGCTTTTTATTTTTTATTTTTAAAA
      Gm08:825 8257778 [A/T] 18 201 0.857 0.679 AATATGTAAAAACCAAGAAACATAAT[A/T]AATG
      7778 TGSTTCATCTTAATAAAACACTTCTTTCATCCTTA
      AATATAAGACTTTTATAATTAATTCACACTTATTA
      ATAAAATTACAAAGACTTTTATAATTAATTCACA
      CTTATTAATAAAATTGCTCGATTTAGTTAGTAATT
      AACATTATATTTGTTTGTAATTTTAATATTTTTTA
      AGATTATCTTTAAAATTATTCA
      TTTTTCAAATACACTCTTTTCTCGCTGTTTAAAAA
      AAAAAATACACTCTCTTCTAATAATTAAAAGTTA
      TTAAAAATCATAAATTTGAATGGATCTCATTTTTC
      ATTGAGTAACTCTCTCTCGTGATTTTATATTATCT
      CTGTGCTTTTTATTTTTTATTTTTAAAAAATATGT
      AAAAACCAAGAAACATAATWAATGTG[C/G]TTCA
      Gm08:825 8257785 [C/G] 19 202 0.848 0.68
      7785 TCTTAATAAAACACTTCTTTCATCCTTAAATATAA
      GACTTTTATAATTAATTCACACTTATTAATAAAAT
      TACAAAGACTTTTATAATTAATTCACACTTATTA
      ATAAAATTGCTCGATTTAGTTAGTAATTAACATT
      ATATTTGTTTGTAATTTTAATATTTTTTAAGATTA
      TCTTTAAAATTATTCAGACTAAA
      TCTTTAAAATTATTCAGACTAAATATATATTTTTT
      TCATTTAATTATTTTCTACCCAAACAATTAACATA
      TGAAAAGAGAATAATAGTAGTCGAGTTTTAATTT
      TAAAATTAAATCCTTCAATTCTCCAATCCTCCCAC
      GAAAGAGAAAATGACAATTCATAGCAATTRTTAT
      Gm08:825 TTATAGACTACAACAACTAGGGGTATT[A/C]TAGT
       8163 8258163 [C/A] 20 203 0.843 0.681
      AAAAAGAAAAACAAGTAATGCAAGAAAGAAGTC
      TTATACAAAAGAACAAAGAATTTTTTAAATAATG
      TCTTATATTCATAGACGAAAGAAACAATTGATCC
      TTTATCATTTTTATTAAACAATAAATGCATAGAT
      GTAAATAAATTAAAGATTAGAAAAAAGTAAGAA
      CATAATTGGCAAAAAAATAATTAATGTC
      TAAAAAAAGAAAACGTGGGAGAGTGCAATTAGG
      ATAAAGGGATTGGATTACTTGAAGAAAAAAARA
      ATAAAGGGGTTAGAAAAAGACCCTCTAGAAGTA
      TACGACAGCCTAAATTGAAATTGGGATACATAGT
      TTGGACTGTAATAGAATTGTGGATCTGTTTGCTC
      Gm08:825 GTTTTATTTCAAAATAAAACAAAATAAAGAACT+
      8688 8258688 [C/G] 21 204 0.895 0.688
      C/G+ CTAGCATRACAACAAAAAGTACTAATTTTTA
      ATCTCAAKGATC RGAAC TTTGC RTTTC TTTC CC GT
      ATCTTGTCGAATTTTYATTGTAAGAAATATTCTTT
      GTGGGTTCAGTTATTCACCATTATTATTTCAGAG
      GGAGCGATGGGWGGAATTATAATACTTCTTCATC
      AGATTCAATTTTGATAAAGAAAATCATTCAA
      AAGAAAAAAARAATAAAGGGGTTAGAAAAAGAC
      CC TCTAGAAGTATAC GACAGCC TAAATTGAAATT
      GGGATACATAGTTTGGACTGTAATAGAATTGTGG
      ATCTGTTTGCTCGTTTTATTTCAAAATAAAACAA
      AATAAAGAACTSCTAGCATRACAACAAAAAGTA
      Gm08:825 8258742 [G/A] 22 205 1 0.587 CTAATTTTTAATCTCAAKGATCRGAACTTTGC +A/
      8742 G+ TTTCTTTCCCGTATCTTGTCGAATTTTYATTGTA
      AGAAATATTCTTTGTGGGTTCAGTTATTCACCATT
      ATTATTTCAGAGGGAGCGATGGGWGGAATTATA
      ATACTTCTTCATCAGATTCAATTTTGATAAAGAA
      AATCATTCAAATAAGAGACTTTATTATCTTCAAA
      AAGCTAAGTACGGAAGATGCCAAAAAGAAA
      TTGGATCATTTAATTTATGAGGTGTGTGATTTTGT
      TTCCTAGTTTTTAATTTTGCAAATTGGATCATTTA
      AGTATTACAGGAATCCAATTTACTCAATTGAATT
      CTGAAAGATCAAAATTAAATAAATGCAATACCTA
      AGAGACAAAAAATAATTAATCTATTTTTTTAAAG
      Gm08:825 8259928 [C/T] 23 206 0.896 0.688 AAAATACTACTATCAGATATGGAAGCAC [C/T]AA
      9928 CAAAACCAGTCCAGGAGAGACATCAGCACCTAC
      CTACGCACCCCAAAATCAGATACAACTTTAAGCT
      TACAACATCACCTATAGTAACCTAATATTGCTCA
      AAATGGAAGCAACCATTCCACAACCAATACAAC
      AAACAAAATCAATAAATTTACTACAAACTAGTCG
      AAC CGTAC CTC GTTAATGCCATAAACC TAG
      AC TAAGC TACACAAAC TGAATCAC GTC TAAGAC G
      CTCTAAAAACAAAATCAGGAGGCAGGTTCCGCA
      AAATAGGACTGGATAATGATGTTGAAGCAGTAA
      TTTCTATCAAAATTAACAGGAAAAACTCTAAAAA
      AATCAGC CC CRGGAGAAATTTATATATATTTTTT
      Gm08:826 8260451 [C/T] 24 207 0.818 0.622 GTAGATAAAAATTTAAATTAGGGGAAGACACG+C
      0451 /T+ CTTCTTGTAAAACTACAAGAAAAATTAACAAC
      ATCAGCATTATAAAATTTATACATCGCATAACAA
      TATGCAAAATCCAAAAATCAATAAACCTAAATTA
      TTGCTGGTATAACTATTTGACTAAATGTGCCATT
      GTTGS CCAGAGAATATTAAAATGTAATGAAATAA
      AGTATTTTAAATTAATTGACTAAGAATTGGCA
      GC CC CRGGAGAAATTTATATATATTTTTTGTAGA
      TAAAAATTTAAATTAGGGGAAGACAC GYCTTC TT
      GTAAAACTACAAGAAAAATTAACAACATCAGCA
      TTATAAAATTTATACATCGCATAACAATATGCAA
      AATCCAAAAATCAATAAACCTAAATTATTGCTGG
      Gm08:826 8260590 [G/C] 25 208 0.918 0.772 TATAACTATTTGACTAAATGTGCCATTGTTG[C/G]
      0590 CCAGAGAATATTAAAATGTAATGAAATAAAGTA
      TTTTAAATTAATTGACTAAGAATTGGCATGGC TA
      TGAGAAATCATGCACTAATTGAGCAAAGATATG
      ATATATTTTTTATACTTGTCCTAACAATGTACTCC
      CACTAATTAAGTTACTAATTGAGCACTCCATAAT
      TTTTTTTGGAAGATGTTCTTTGGACACTGTG
      TCATGTCTACCAAGTCCGACTAACTTWTCCGTCC
      ATCAACCATTTTTTAACTGAGAATTGGTATGATA
      TCAAGAGTTAAGAGTTGTGACTGTATTTGGAAAA
      ATATTTCTTAAAATAAAATGATATTCAAAAAATA
      TATTTTTAATAGTTTTTTCTGCTGATTTTCAGTCT
      Gm08:826 8261480 26 209 1 0.856 ATAATTAAACGAATTTAGATACTCTATAT[G/T]AA
      1480 AAAAGAGAAAATCATTTTTTCAATAACAGTCCCA
      AAACTTTTAAATTAAAAAAAATAAAGTAAAATTT
      ATCTTTTATTTTGAATTAAATCAAGACATACTACT
      ATACCTGATCAGTCCTGGATCGAATTCTCCCAAC
      CAAATCAACTCGCCATAAATACCCTCTTATATCC
      AGTTAATTAATGGTCCATCTCGTTTTG
      AAAGAGAAAATCATTTTTTCAATAACAGTCCCAA
      AACTTTTAAATTAAAAAAAATAAAGTAAAATTTA
      TCTTTTATTTTGAATTAAATCAAGACATACTACTA
      TACCTGATCAGTCCTGGATCGAATTCTCCCAACC
      AAATCAACTCGCCATAAATACCCTCTTATATCCA
      Gm08:826 8261684 [A/T] 27 210 1 0.791 GTTAATTAATGGTCCATCTCGTTTTGAAA[A/T]TT
      1684 TTTTAACCATGAAGTTTTTTTTTAGTTACATGAGG
      AAAAGAAAGACAAGGGACAACCAAAAAAACTAC
      ACGTACTACTAAATTAAGGCAGATCACACTGCCA
      CTCCCTCTGCACAAAAACTGGTGGCCTCTGCCAG
      ACCACAGCATCAGAACTCAGAAGCATTGGTTGCA
      TCAGAGTTTTGTTATGGTGTATTTAGAA
      CCAATCCCGACACAACCAGCTCGAAATTTTCCGC
      ACCGCAGAATGTCGTGATTCTTGTGGCAACCAGA
      GTTGTTGTTCTTGCTAGCTCTATATTCTTCTCCTG
      TGTGGCAGTATTGCATCAATGCTACCATGCAGTG
      TCTAACAAGACTATATCATATATTTATGATAGTC
      Gm08:826 8262165 28 211 0.919 0.918 TCTAATCAATTTTTGAAAAAATTAGAGTC[A/T]TA
      2165 ATATTTATACATCTCATTTTCTTATAATTCACTTG
      CATCTTATTTCATTTTTTCCCCTATCATATAACAT
      ATCATATTTATTACATTCTCTCTATTTTTATTTTTA
      TTTCTCTCTCCATCTCTCTTCTCTTTTCACCCTAAA
      ATGGGGGTGAACACTCAACATGTTTTGAAAAATT
      ATTATTAGATTAATATGTATTG
      GGGTCATCCTTTCACTTGTTTGGTCTACACCACAC
      TCTTGTCTTGGGTCGCTGAGGTGGCGCGTGAGTT
      TCACCTCCCAACAGCGATGCTGTGGACTCAACCA
      GCTACGATACTCGACATCTTCTATTACTACTTTCA
      CGAACACGGTGAATACATCAAAGACAAAATCAA
      Gm08:826 8263213 [G/C] 29 212 0.913 0.09 AGACCCCTCGTGTTTCATTGAATTACCAG[C/G]AT
      3213 TGCCATTGTTGCTTGCACCACGGGACCTACCCTC
      YTTTTTATTGGGTTCAAACCCTACTATTGACTCTT
      TCATTGTCCCAATGTTTGAAAAGATGTTTTATGAT
      CTTGACGTGGAGACAAAGCCCAGAATACTTGTCA
      ACACCTTCGAAGCCTTGGAAGCGGAGGCTCTCAG
      AGCCGTTGATAAGTTCAACATGATCC
      TTGTCTTGGGTCGCTGAGGTGGCGCGTGAGTTTC
      ACCTCCCAACAGCGATGCTGTGGACTCAACCAGC
      TACGATACTCGACATCTTCTATTACTACTTTCACG
      AACACGGTGAATACATCAAAGACAAAATCAAAG
      ACCCCTCGTGTTTCATTGAATTACCAGSATTGCCA
      Gm08:826 8263250 30 213 1 0.678 TTGTTGCTTGCACCACGGGACCTACCCTC[C/T]TT
      3250 TTTATTGGGTTCAAACCCTACTATTGACTCTTTCA
      TTGTCCCAATGTTTGAAAAGATGTTTTATGATCTT
      GACGTGGAGACAAAGCCCAGAATACTTGTCAAC
      ACCTTCGAAGCCTTGGAAGCGGAGGCTCTCAGAG
      CCGTTGATAAGTTCAACATGATCCCAATCGGGCC
      GTTGATTCCCTCGGCTTTCTTGGATGG
      TCC CAATC GGGC CGTTGATTC CC TCGGCTTTC TTG
      GATGGGAAAGATMCTAATGATACTTCATTTGGCG
      GTGACATCTTC C GC CTC TCTAATGGTTGCAGC GA
      ATGGTTGGACTCGAAGCCAGAGATGTCGGTGGTT
      TATGTCTCGTTTGGTAGCCTTTGCGTGTTGCCTAA
      Gm08:826 8263611 [C/T] 31 214 0.924 0.682 GAC GCAAATGGAGGAAC TTGCACGTGC G[C/T] TA
      3611 TTAGATTGTGGAAGTCCTTTCCTGTGGGTCATTA
      AAGAAAAAGAAAATAAGTCACAAGTGGAAGGAA
      AAGAGGAGCTGAGCTGCATAGAGGAATTGGAAC
      AGAAGGGGAAGATAGTAAACTGGTGTTCTCAAG
      TGGAGGTTCTTTCACATGGTTCTGTGGGTTGTTTT
      GTTACACACTGTGGTTGGAATTCAACCATG
      AAATGAAGAAATTAGGCGGTGTTTGGAAGAGGT
      GATGGGGAGTGGAGAGAAAGGACAAGAATTGAG
      AAACAATGCAGAAAAGTGGAGGGGACTGGCCAG
      GGAAGCTGTCAAGGAAGGTGGCTCTTCGGATAA
      GAATCTAAGGGCTTTTTTAGATGATGTTGAAGTT
      Gm08:826 TGACCATATGGCTGTCACATCAGCTTTTCCGTTT+
      4149 8264149 [C/T] 32 215 0.933 0.702 C/T+TGAATTTTCCTGTCCGTTTCATTTTTCTTTTCT
      ATTATTGCATTTGCATGACTGAGAATCAAGTGAA
      ATTTCTTCTATATTAGTTTGAAATTTAAAAATATC
      TAAATGAGCCATGACTCCATGAGTAGTAATTTTG
      TGTTATAATTGATATATATATTTTCTCTTAAGTAG
      TGGCCAAAAATTTAATCTTTATGTAGATG
      ATGCATC TGGATCTGGTTTC CC TATTCATATTTC C
      AAAGCTTGCATGCTTTCTGGTTTCCTTGCCAATCA
      CTGCATGGAACAATCTTACCATCATAGGGCATGC
      TTCTTTTTTTAAGCTCGCTTGTGGTCTTCTTTTGGT
      ACATATGC TC CC CTCC CCCC TTTTTGTTTATTTTT
      Gm08:826 8265227 [C/T] 33 216 0.933 0.736 GTTTTATGGTTCATAATAGAGTTTA[C/T] TGATGA
      5227 AATAGCCAAATCATAGAATTAGTAAAATATCATG
      TACAAGGTCAAAATAGTATTTTTAGTAACCATCT
      TTTTTTTCTCGTACCTTACATAGAAGCTGACTCAA
      TGATAAAGGAAACCTAAAAATTAGTTTWAAAAA
      AACCTTTTGGCCTTTTTGACATMATATATGATATT
      TTTGTCAAAATATGAGACTTTTT
      GGTACATATGC TCC CC TCCCC CCTTTTTGTTTATT
      TTTGTTTTATGGTTCATAATAGAGTTTAYTGATGA
      AATAGCCAAATCATAGAATTAGTAAAATATCATG
      TACAAGGTCAAAATAGTATTTTTAGTAACCATCT
      TTTTTTTCTCGTACCTTACATAGAAGCTGACTCAA
      Gm08:826 8265364 [A/T] 34 217 1 0.824 TGATAAAGGAAACCTAAAAATTAGTTT[A/T]AAA
      5364 AAAACCTTTTGGCCTTTTTGACATMATATATGAT
      ATTTTTGTCAAAATATGAGACTTTTTTTTTATAAA
      AAC TAATAAAAAAATATTTTTTATTGGTAAAC CT
      AGAAC TTAAATTTTAGTTATTTTATTCTTAGAS AA
      AC CTTACC TAACAAATAATTTAATTCAAATATTT
      GC CTTTCATTC TATTTTATTTCAC C
      ATATGAGACTTTTTTTTTATAAAAACTAATAAAA
      AAATATTTTTTATTGGTAAACCTAGAACTTAAAT
      TTTAGTTATTTTATTCTTAGASAAACCTTACCTAA
      CAAATAATTTAATTCAAATATTTGCCTTTCATTCT
      ATTTTATTTCACCTTAACAACTTCCCTGGCCACAA
      Gm08:826 8265614 [G/A] 35 218 0.838 0.8 CATGTTGGATCTCAGTAAAAATTGATG[A/G]TGTA
      5614 AGATCATTCCATTAC GAAGAGATGCATGGCC TAT
      TATTCTTTCTCCATCCAAGAAAAAAATACATTTA
      TTCTTGCTTCCTGTTAAAACATAAAAAGACGTTTT
      AC CTTAGTATGATAACC TTCATAAATAGTTAAAT
      ATAGCATTGTCTTGAACTTTGAAATAAATTATGT
      TTAATTAGAACTTATAACTATAAGT
      ATATGTCAAGTATTATAATAAATATTTAATTATA
      TAAATAAATAATTTTATTCTTAAATATAAACATTT
      ACAAAGTTAAAGTAACAAAAAAGTAAGTTTTTA
      ATTCTCTTAATAATGTCATATCCTAATTTCGTACT
      AGGACTATCATTCGTCAACGTTTTGATTCTCCATT
      Gm08:826 8266183 36 219 0.924 0.773 GTCAAATTGAATTGTTCGACACCAGTTG[C/T] TRT
      6183 GTAAGACGGAAGATTATTCGACATTTCAGTAAAG
      AATGCAAAAAATGCCCAAATGGAAGGACAAAAG
      GATCATTTTRAGGC TTTTTCAGACCC CTGACTC GC
      TCAGGC TAGTC TCTGGC TCAC CTAGGC CC CTAAA
      TAGTTTAGGGGTGAAGTAACTAGCTCGYCTGGAC
      GAGCAAGGTTACTTCAGGTTGAAGCAA
      ATGTCAAGTATTATAATAAATATTTAATTATATA
      AATAAATAATTTTATTCTTAAATATAAACATTTA
      CAAAGTTAAAGTAACAAAAAAGTAAGTTTTTAAT
      TCTCTTAATAATGTCATATCCTAATTTCGTACTAG
      GACTATCATTCGTCAACGTTTTGATTCTCCATTGT
      Gm08:826 CAAATTGAATTGTTC GACACCAGTTGYT [A/G] TGT
      6185 8266185 [G/A] 37 220 0.924 0.773 AAGACGGAAGATTATTCGACATTTCAGTAAAGA
      ATGCAAAAAATGCCCAAATGGAAGGACAAAAGG
      ATCATTTTRAGGCTTTTTCAGACCCCTGACTCGCT
      CAGGCTAGTCTC TGGC TCAC CTAGGCC CC TAAAT
      AGTTTAGGGGTGAAGTAACTAGCTCGYCTGGACG
      AGCAAGGTTACTTCAGGTTGAAGCAACA
      GTAACAAAAAAGTAAGTTTTTAATTCTCTTAATA
      ATGTCATATCCTAATTTCGTACTAGGACTATCATT
      CGTCAACGTTTTGATTCTCCATTGTCAAATTGAAT
      TGTTCGACACCAGTTGYTRTGTAAGACGGAAGAT
      TATTCGACATTTCAGTAAAGAATGCAAAAAATGC
      Gm08:826 8266263 [A/G] 38 221 0.904 0.816 CCAAATGGAAGGACAAAAGGATCATTTT [A/G] AG
      6263 GC TTTTTCAGACC CC TGAC TC GC TCAGGC TAGTC T
      CTGGC TCACC TAGGCC CC TAAATAGTTTAGGGGT
      GAAGTAACTAGCTCGYCTGGACGAGCAAGGTTA
      CTTCAGGTTGAAGCAACARCTC GC TTGGGTGAGC
      TCCAGATCAAC TAAGTC CC CTCATTTCC TATAAA
      TAGGCATGAGGGGCTGAAAGAAAGGGTT
      CCATTGTCAAATTGAATTGTTCGACACCAGTTGY
      TRTGTAAGACGGAAGATTATTCGACATTTCAGTA
      AAGAATGCAAAAAATGCCCAAATGGAAGGACAA
      AAGGATCATTTTRAGGC TTTTTCAGAC CC CTGAC
      TCGC TCAGGC TAGTC TCTGGC TCACC TAGGC CC C
      Gm08:826 8266350 39 222 1 0.895 TAAATAGTTTAGGGGTGAAGTAACTAGCTCG+C/T
      6350 +CTGGACGAGCAAGGTTACTTCAGGTTGAAGCAA
      CARCTCGCTTGGGTGAGCTCCAGATCAACTAAGT
      CCCCTCATTTCCTATAAATAGGCATGAGGGGCTG
      AAAGAAAGGGTTCARCCTTCARATATTGAAAGG
      ATTTAGTGAAATTTGAAGAAAAGAAGAARAAAT
      AAAGGAAAAACAAGGTCGAGGTGCTACCGAATC
      TGTAAGACGGAAGATTATTCGACATTTCAGTAAA
      GAATGCAAAAAATGCCCAAATGGAAGGACAAAA
      GGATCATTTTRAGGC TTTTTCAGAC CC CTGACTC G
      CTCAGGC TAGTC TC TGGCTCACC TAGGC CC CTAA
      ATAGTTTAGGGGTGAAGTAACTAGCTCGYCTGGA
      Gm08:826 8266386 [A/G] 40 223 1 0.824 CGAGCAAGGTTACTTCAGGTTGAAGCAACA[A/G]
      6386 CTC GC TTGGGTGAGC TCCAGATCAAC TAAGTC CC
      CTCATTTCCTATAAATAGGCATGAGGGGCTGAAA
      GAAAGGGTTCARCCTTCARATATTGAAAGGATTT
      AGTGAAATTTGAAGAAAAGAAGAARAAATAAAG
      GAAAAACAAGGTCGAGGTGCTACCGAATCACGA
      TCGTAATCGATTTTCACATCGTTCTTCGTTCG
      CAGACCCCTGACTCGCTCAGGCTAGTCTCTGGCT
      CACCTAGGCCCCTAAATAGTTTAGGGGTGAAGTA
      ACTAGCTCGYCTGGACGAGCAAGGTTACTTCAGG
      TTGAAGCAACARCTCGCTTGGGTGAGCTCCAGAT
      CAACTAAGTCCCCTCATTTCCTATAAATAGGCAT
      Gm08:826 8266473 [G/A] 41 224 0.918 08 GAGGGGCTGAAAGAAAGGGTTCARCCTTCA[A/G]
      6473 ATATTGAAAGGATTTAGTGAAATTTGAAGAAAA
      GAAGAARAAATAAAGGAAAAACAAGGTCGAGGT
      GCTACCGAATCACGATCGTAATCGATTTTCACAT
      CGTTCTTCGTTCGTCATCCGGTTAGTATTTATTTT
      AAGTATTTCAATTCAATCTATGCACCCATAAGGG
      TCTTCTTTGTCGATTCATGCATCTTCATCTC
      TGTAATCTATTTTCTTTTGGTAAAGTGAGTTTTGA
      CCGGTCATTTACGTCACCAAACATCTTTTAATTA
      GTTTGAAGTTTAATAAGTGAAATCAAGTTAAAAT
      CAACATGTAACCGAGCTTTTTATCCGCAAAATTC
      ACTTAAATCCGTTCAAGGTCCAAGGCCTTAATGG
      Gm08:826 TCTCTTTTATTTTTGTTGGTTCGAATGAA[C/T]TTT
      6888 8266888 42 225 0.924 0.08 TCAAAAGTTTAAAATCAACTCGACACGCAATTTT
      CTTGTTTTAAGAACTATGTAGGTCTGAGTTTCTCA
      TCGCAMTTGAGGATACGTAGGAGCAAGGGCAAC
      GCCTTTGTCGACCCGAAAAAATAAAGAAGCATA
      AAAAGGGAAAATAAGTAATATTGAAGTCACGTT
      TTTGCACATTCGATTAAAGGTTGTCRTCC
      GAAYTTTTCAAAAGTTTAAAATCAACTCGACACG
      CAATTTTCTTGTTTTAAGAACTATGTAGGTCTGAG
      TTTCTCATCGCAMTTGAGGATACGTAGGAGCAAG
      GGCAACGCCTTTGTCGACCCGAAAAAATAAAGA
      AGCATAAAAAGGGAAAATAAGTAATATTGAAGT
      Gm08:826 8267085 [A/G] 43 226 0.912 0.808 CACGTTTTTGCACATTCGATTAAAGGTTGTC[A/G]
      7085 TCCCCTGTGACGAAYACGTGGGGTGTTAATACCT
      TTTTCGCTCGTAAATAACTCCCGTACCCTTATTTT
      CAAAATTCGCAKATCCCCCTTTTTGGTTTTTCTAA
      CGTTTTCCTCGAATAAACGTTGGTGGCGACTCCC
      GCGTGTTTTTCTTTTTGGAAGACGCATCCTTGAGT
      CTCGCCTCACCCCTCCCGTCGAAGGGT
      MTTGAGGATACGTAGGAGCAAGGGCAACGCCTT
      TGTCGACCCGAAAAAATAAAGAAGCATAAAAAG
      GGAAAATAAGTAATATTGAAGTCACGTTTTTGCA
      CATTCGATTAAAGGTTGTCRTCCCCTGTGACGAA
      YACGTGGGGTGTTAATACCTTTTTCGCTCGTAAA
      Gm08:826 8267166 44 227 1 0.836 TAACTCCCGTACCCTTATTTTCAAAATTCGCA+G/T
      7166 +ATCCCCCTTTTTGGTTTTTCTAACGTTTTCCTCGA
      ATAAACGTTGGTGGCGACTCCCGCGTGTTTTTCTT
      TTTGGAAGACGCATCCTTGAGTCTCGCCTCACCC
      CTCCCGTCGAAGGGTAGGTTGCAACAGATAATAA
      TAAAAAAATTCAACCATGATATTCGCAACAATAA
      ATTAAATGCACACATACATATATATAGT
      GAATTAGTGTGAGTCTCAGATTCTTCAAATGGTC
      TATGAGTTCATATTCATGCAGTAAYGTCTCACTG
      CTTTTCTTATCATATATGAAAGTATTCAAAATCTC
      TTCTTCATCCTAGATGGAGGTATCTATAACTTCAT
      CTCCATCCCAAATGAAGGTGTCTCGTACATATTC
      Gm08:826 8267721 [C/T] 45 228 0.817 0.772 AATTCTCAAAATAAAACATAAATTGTCA[C/T]TAC
      7721 TTCCTAAAGGATGATAACCAATTCACACATATTT
      ATAAAATATCATTTCAAATAACTATCAAATAAAT
      ACTTTAATTCCATATACACTAATTAATAACTTGSA
      AGGTCATACCTTAGTTATAGCATCACGTAAGTCA
      ATTTATAATTAACTATGAAATAAAACATACACAC
      AAATTAAAATATATTTTAGTTGCTAT
      CTTCATCCTAGATGGAGGTATCTATAACTTCATCT
      CCATCCCAAATGAAGGTGTCTCGTACATATTCAA
      TTCTCAAAATAAAACATAAATTGTCAYTACTTCC
      TAAAGGATGATAACCAATTCACACATATTTATAA
      AATATCATTTCAAATAAC TATCAAATAAATAC TT
      Gm08:826 8267826 [G/C] 46 229 0.831 0.824 TAATTC CATATACAC TAATTAATAAC TTG[C/G]AA
      7826 GGTCATACCTTAGTTATAGCATCACGTAAGTCAA
      TTTATAATTAACTATGAAATAAAACATACACACA
      AATTAAAATATATTTTAGTTGCTATATATGATAG
      CTAAACACAAAATCCAAACAAGCTGATTGATGA
      ATTTTCAAATAAATTTTAAGATTGAATATGCAAC
      TAGTGAATATTTGTACATTGTAATACCTT
      ATCTAGTTTCTATCGTGCATATTTGTTGAAGTTAA
      ACACAAGATCCAAGYAAGCACATATGATGCATT
      ATAATTGCAC TAAAATTTGAATATAGTTTC TATA
      TATCGTGCATGTTTGTTGGCTCTCCTTGACAAGCA
      TATCTATTTAATTTATACAAGTAGTAAATAAAAT
      Gm08:826 GATAAGACTAAATGATGAGTTCACATATA[C/T] TT
      8336 8268336 [C/T] 47 230 0.829 0.561 TATTTGTACTCWTATATATATATATATATATAATT
      CTTGGATGGAAAGGAC CC CGAAGATAC TTC CTTG
      GGTGGTGACTTGTTACCGGTTTCAAATGGTTACG
      TTGAGTGGCTTGACTCAAAGGAAGACAAGTCCGT
      GGTTTACATTTCATTTGGGAGCTACTTTGTGTTGT
      CTAAGAGACAAACGGAGGAAATTGCA
      CAGGTGGAGGTTCAGTGGGTTGTTTTGTGACGCA
      CTGTGGTTGGAATTCGACCATGGAGAGCTAGGTT
      TCGGGGGTGCCCATGGTGGTGTTTCCTCAGTGGT
      CGTACCAAAAGACAAATGCTAAACTGATAGAAA
      ATGTGTGGAAGATAGGGGTGAGGGTGGATCATG
      Gm08:826 8268861 [A/C] 48 231 1 0.722 AGGATGGGAAAGTAGAAGGAGAAAGAGATTAA+
      8861 A/C+ AAGTGTTC GGAAGAGGTGATGGGGAGTGGA
      GAGTTGAGAATGAATGTAAAGAAATGGAAGGGT
      TTGGCCAGGGAGGCAGC CAAGGAAGGTGGTC CT
      TCAGATTTCTTGATGCCATGACGTTGCAGAATCG
      ATAATCAATGCACGTGTTTGCCAAATAATTGACT
      TGGATTCCCGTGTTCTCAGTTCTTCCATGCTAAAT
      T
      AGGTGGTC CTTCAGATTTC TTGATGCCATGAC GT
      TGCAGAATCGATAATCAATGCACGTGTTTGCCAA
      ATAATTGACTTGGATTCCCGTGTTCTCAGTTCTTC
      CATGC TAAATTATTC TTTTTC TGCTTC TWTTTC TT
      TTTCCAATCAATTGATTCTATGTTTAAGATTTTTA
      Gm08:826 8269148 49 232 0.842 0.627 TTATTTAGAACAATTAAATTATTATTG[C/T]TTTA
      9148 AGAGATAGTATTATTTTAAGTTTAAATGTATATTT
      TTTATTCATAATTATATCTCTATTTAATCTGGTAT
      AC TCC TTAAAATTAC TTTTATTTAATTATGTTTTT
      TTTTAAAATAATCAAATTATTCAATCTTATTGATA
      AGTGGTTTGTATCAAATGCTCACCTAAAAAAGAT
      AAATAGACTCCCAAATATTAGA
      AGATAATTAATTTCTTTTAAATGGATGTAGGAAG
      AGACTAAATTATTACTAATCTTATTGCTTTATATT
      TTTTATAGTTATCTTTCCACTCCTACAGTACGAAA
      CACATGTAATAAATCAGTGCCATTAACATACAAC
      TCGACCTAATTGTAATTTGTAGTAACTTAGATAG
      Gm08:826 TTTAGATTTTTTTTTTGTTATGGTATTA[C/T] GTAT
      9785 8269785 [T/C] 50 233 0.912 0.808
      TTCATAAAAATTTATATTAATTTTCTTTTGAAAAA
      TATTATACWTCATATTGTCTTCTTGCCTTTGTAAA
      ATAAAAGTGTTAAAATATCAATACTYATGTTTAT
      TTGAACAAGTGAGATGCATGTAATC RC TATCATT
      ATTTAGGAATGYTAATGAACCTACTTGTTGCACT
      AATTAAGCYTGTTTCAACCTGTAA
      TATTGTCTTCTTGCCTTTGTAAAATAAAAGTGTTA
      AAATATCAATACTYATGTTTATTTGAACAAGTGA
      GATGCATGTAATC RC TATCATTATTTAGGAATGY
      TAATGAACCTACTTGTTGCACTAATTAAGCYTGT
      TTCAACCTGTAAAAAAAAGTCTGTTTCAAAATTA
      Gm08:827 8270037 [G/T] 51 234 0.924 0.823 TTTTTTATGCATTTTACTTAAAAAAATTA[G/T] AC
      0037 CTAATGAATTTTGAATATTGATTTGATTTTTTTAA
      GAGAATATATTTTTGAGTTATATATATATATATTA
      GTAGTCCTACCTCGTTCTAATATTTTATATTTTTT
      TAATAAAATATACAAATTTTTAAACAATTTTGTA
      TTAAGGAAAAATTAATCATTTTATTMTTATAATT
      ATACAAAATTTAGCTTTGAATGACC
      AATGAAAGTTTGAATATAAAAGGTTACTTTGTTT
      AAACTTAAAAAAAAATTCTAAAAAATATTTTTTA
      AGAAGTAAATATGATTTATTTATTAACAAGACAT
      TTTTCTATTTTTAAGAAAAAAATACATAAAAAAT
      AATTATTTTATTAAAAAATGATC CAAAC CC TTCA
      Gm08:827 8270562 [C/A] 52 235 1 0.704 TCATTAATGTTAATGATTAATCTATTAATT [A/C] A
      0562 TGTTTAATTTATTATATTATAATTATAATAGATTA
      TACAAAAAGCAATTATACGATTTAATGTTTTATA
      TATTTAATTTTATATTTAARATGTGGAAGATGC GT
      TAGCAAGTATTAAGATATTGACTAAAAAAGAAA
      ATTAAAAAATATATAATTAAAACTAAAGCATTTT
      CTATAAATAAAAAATATAAGACTTTTTT
      TTAACAAGACATTTTTCTATTTTTAAGAAAAAAA
      TACATAAAAAATAATTATTTTATTAAAAAATGAT
      CCAAACCCTTCATCATTAATGTTAATGATTAATCT
      ATTAATTMATGTTTAATTTATTATATTATAATTAT
      AATAGATTATACAAAAAGCAATTATACGATTTAA
      Gm08:827 8270652 [A/G] 53 236 1 1 TGTTTTATATATTTAATTTTATATTTAA[A/G]ATGT
      0652 GGAAGATGCGTTAGCAAGTATTAAGATATTGACT
      AAAAAAGAAAATTAAAAAATATATAATTAAAAC
      TAAAGCATTTTCTATAAATAAAAAATATAAGACT
      TTTTTTTTACATGACATATAAAACTTACTCTATTC
      AATATTAAAATTGTTAAAGATTTAACTGGTATAT
      AC TAATAGTGTAAATATATTTTACAC
      TCAMATATTGATTCATCATGTAGTGAAAAACTAA
      TCWCTTTTACTCAACCTAAS CTGTATCGATGYTA
      ATCATTGCTCTTAGTACATTGATTATAAAAAAAA
      TACTAGAAAGATAAAGTTTTTGTTAGAAATCATT
      TGCGAGTATATTTTAAAATAATTGAAGAATACAT
      Gm08:827 8271540 54 237 1 0.419 TTTTATGCATTATATAGTTAAAGTGTTTTT [G/T] TT
      1540 TTCCTTTTTTCACTTCCTCTATTTTAACCACTATTT
      TCTTTCTACACAMAAAAAAAAATCCATCATTTTT
      CTTTTATCCTTTTAACAAATTTTGGTTTTGGACAG
      TRAACACACACAAAATATATATTTYTCTTCTAAT
      ATGATTTGTTTTATTTTTGATGCCAATATGTTATG
      ATTGTTTGATAATGTAAAAAATAT
      AAS CTGTATCGATGYTAATCATTGCTCTTAGTAC
      ATTGATTATAAAAAAAATACTAGAAAGATAAAG
      TTTTTGTTAGAAATCATTTGCGAGTATATTTTAAA
      ATAATTGAAGAATACATTTTTATGCATTATATAG
      TTAAAGTGTTTTTKTTTTCCTTTTTTCACTTCCTCT
      Gm08:827 8271591 [C/A] 55 238 0.919 0.625 ATTTTAACCACTATTTTCTTTCTACACA[A/C]AAA
      1591 AAAAAATCCATCATTTTTCTTTTATCCTTTTAACA
      AATTTTGGTTTTGGACAGTRAACACACACAAAAT
      ATATATTTYTCTTCTAATATGATTTGTTTTATTTTT
      GATGCCAATATGTTATGATTGTTTGATAATGTAA
      AAAATATTAS AC TAATAATGC GTAGTAC TAGYAA
      TTAACCTCATTTTTWAAATAGTTA
      AAGATAAAGTTTTTGTTAGAAATCATTTGCGAGT
      ATATTTTAAAATAATTGAAGAATACATTTTTATG
      CATTATATAGTTAAAGTGTTTTTKTTTTCCTTTTTT
      CACTTCCTCTATTTTAACCACTATTTTCTTTCTAC
      ACAMAAAAAAAAATCCATCATTTTTCTTTTATCC
      Gm08:827 8271649 [A/G] 56 239 1 0.895 TTTTAACAAATTTTGGTTTTGGACAGT[A/G]AACA
      1649 CACACAAAATATATATTTYTCTTCTAATATGATTT
      GTTTTATTTTTGATGCCAATATGTTATGATTGTTT
      GATAATGTAAAAAATATTASACTAATAATGCGTA
      GTACTAGYAATTAACCTCATTTTTWAAATAGTTA
      AAAGAACTTGCTCATTCATTATTAATTTTTCATTA
      AAAATATTGTACCGGCCACTTTA
      CATTTGCGAGTATATTTTAAAATAATTGAAGAAT
      ACATTTTTATGCATTATATAGTTAAAGTGTTTTTK
      TTTTCCTTTTTTCACTTCCTCTATTTTAACCACTAT
      TTTCTTTCTACACAMAAAAAAAAATCCATCATTT
      TTCTTTTATCCTTTTAACAAATTTTGGTTTTGGAC
      Gm08:827 8271672 57 240 1 0.824 AGTRAACACACACAAAATATATATTT[C/T]TCTTC
      1672 TAATATGATTTGTTTTATTTTTGATGCCAATATGT
      TATGATTGTTTGATAATGTAAAAAATATTASACT
      AATAATGCGTAGTACTAGYAATTAACCTCATTTT
      TWAAATAGTTAAAAGAACTTGCTCATTCATTATT
      AATTTTTCATTAAAAATATTGTACCGGCCACTTTA
      ATTTATTTTCAAATGCTATTAAA
      GTAGTACTAGYAATTAACCTCATTTTTWAAATAG
      TTAAAAGAACTTGCTCATTCATTATTAATTTTTCA
      TTAAAAATATTGTACCGGCCACTTTAATTTATTTT
      CAAATGCTATTAAAATAAAGCAATGAGTTAATGA
      CATTAATTAAGAAATGCATTTAAAATTTTATTAA
      Gm08:827 8271955 58 241 0.09 0.847 TATTAAGGATCTTGTTAATTAATGTTTT[C/T]CCCC
      1955 CACAAGTCTTCTCTTTCAAAGGCCTAATGTACAT
      TAGGACACTAAATGTCACCCCTTTAAATGAATAT
      TCAAACATTGATTCATCACTTAGTGAAAARTTAA
      TCTCTTCCACTTGACTCAACCGGTGCTGATGTTAA
      CCATTGCTCTTAATATTGGTTATAAAAAATAATA
      AAAAGATAAAGTTTTTGTTAGAAAT
      ACCCAACGGTGCTTGTGAACACCTTTGAAGCTTT
      GGAAGAAGAAGCGTTGAGGGCCATTGATAAGAT
      CAACATGATCCCCATCGGGCCGTTGATTCCTTCT
      GCGTTCTTGGACGGGAATGACCCAACTGATACTT
      CGTTTGGTGGGGACATTTTTCAAGTCTCAAATGA
      Gm08:827 8273257 [G/A] 59 242 0.933 0.721 TTACGTTGAATGGCTTGACTCAAAGGAAGAG+A/G
      3257 +ATTCGGTGGTTTACGTTTCATTTGGTAGCTACTT
      TGAGCTTTCTAAGAGACAAATGGAGGAAATTGC
      ACGTGGGTTATTAGATTGTGGACGTCCATTYTTG
      TGGGTCGTTAGAGAAAAGGTAATTAATGGAAAA
      AAAGAAGAGGAGGAGGAGCTTTGTTGTTTCAGA
      GAGGAATTGGAGAAGTGGGGGAAGATAGTGACA
      TCTGCGTTCTTGGACGGGAATGACCCAACTGATA
      CTTCGTTTGGTGGGGACATTTTTCAAGTCTCAAAT
      GATTACGTTGAATGGCTTGACTCAAAGGAAGAGR
      ATTCGGTGGTTTACGTTTCATTTGGTAGCTACTTT
      GAGCTTTCTAAGAGACAAATGGAGGAAATTGCA
      Gm08:827 8273355 60 243 0.854 0.825 CGTGGGTTATTAGATTGTGGACGTCCATT[C/T]TT
      3355 GTGGGTCGTTAGAGAAAAGGTAATTAATGGAAA
      AAAAGAAGAGGAGGAGGAGCTTTGTTGTTTCAG
      AGAGGAATTGGAGAAGTGGGGGAAGATAGTGAC
      ATGGTGTTCTCAGGTGGAGGTTCTTTCGCATTCTT
      CTGTGGGTTGTTTTTTAACACACTGTGGGTGGAA
      TTCGACCATGGAAAGCCTTGTTTCTGGGGT
      GCGAAAGAAGGTGGCTCTTCAGAGAAGAATCTG
      AGGGCATTTGTGGATGATGTTAGACAAAAATTTA
      TGCATACACATGTGGGTGAATATTAATTAAGTTC
      GTCTCTAACTAGCTAGTAGTAAGCTGTAATGTGT
      TATTGTATGCTTATGATGCATGGCTTCAAACATT
      Gm08:827 8273979 [A/C] 61 244 0.87 0.734 GAAAGATGAACTGAAAAAATTAAGAAATTAT+A/
      3979 C+AGTCAGTTAATAAAAATGTGCGAAAATGGAAT
      ATCTTCAATAATAACATGTGCGTRTTGCTAAAAA
      ATGAGTTGTTGTCACGTTAGATGGTGGATGCCAT
      ATAACTGTCCAATATGTTGCCCAATTCGTCAGGA
      AAAGATAAATATTTTGATAAAGATTATTATTACA
      TTGTTGCTTTATACTCCCTTCCTTTCTTTTTA
      TGAAATGTCAATCAAAATATACAACAGTATGTGC
      ATGGATTCTTGATGACAATAATTCCAAAACCACA
      AATATGTATTTATAATCATCTTAAAAGCTCTAGT
      GAGACACTTAGCKGTACAAATTAAATTTTTTAAA
      TCGTTGGGCAAAGAATCATCAGCAAATGTAGTTT
      Gm08:827 8275766 62 245 0.928 0.903 TTTTTTTTTTTTGAGAAATCACCCAATGTA[G/T]TC
      5766 AATTGCGGAAGSAGGAGCTTGTCATTCCAGTAGT
      CCAATTTTTCAGTTATACTTTTGATTTTTATAGGG
      TAAGTACTAAGTAACCTAGCTAGTTTCTTAATCT
      CATGATCTCTTGGCTTATYTTTTTTTTTTTTWAAT
      TTGTGCTTGAGTCACTATACATATTTACTTGGTTG
      TCGAACAAAATTAAAATYTCTTCGT
      AAATATACAACAGTATGTGCATGGATTCTTGATG
      ACAATAATTCCAAAACCACAAATATGTATTTATA
      ATCATCTTAAAAGCTCTAGTGAGACACTTAGCKG
      TACAAATTAAATTTTTTAAATCGTTGGGCAAAGA
      ATCATCAGCAAATGTAGTTTTTTTTTTTTTTTGAG
      Gm08:827 8275780 [C/G] 63 246 0.924 0.823 AAATCACCCAATGTAKTCAATTGCGGAAG[C/G]A
      5780 GGAGCTTGTCATTCCAGTAGTCCAATTTTTCAGTT
      ATACTTTTGATTTTTATAGGGTAAGTACTAAGTA
      ACCTAGCTAGTTTCTTAATCTCATGATCTCTTGGC
      TTATYTTTTTTTTTTTTWAATTTGTGCTTGAGTCA
      CTATACATATTTACTTGGTTGTCGAACAAAATTA
      AAATYTCTTCGTACCTAAACAAAACC
      CAATGTAKTCAATTGCGGAAGSAGGAGCTTGTCA
      TTCCAGTAGTCCAATTTTTCAGTTATACTTTTGAT
      TTTTATAGGGTAAGTACTAAGTAACCTAGCTAGT
      TTCTTAATCTCATGATCTCTTGGCTTATYTTTTTTT
      TTTTTWAATTTGTGCTTGAGTCACTATACATATTT
      Gm08:827 8275959 64 247 0.929 0.837 ACTTGGTTGTCGAACAAAATTAAAAT[C/T]TCTTC
      5959 GTACCTAAACAAAACCTAACTTAAAGTCCCAGAC
      TAATTCAACAATAATCAACTCAATTTTTTTTTTTT
      TGCATGTTACATTTCATACATTAACTGTTGAGCTA
      CTTTATGGGTTCCCTCCCGTGTAGGGTTTGTTTAA
      TGATATTAGCTTGAAGTTTTCACTCTTTTGATCTT
      CAAGAAGAGTTAAAGGTGGAC
      GCAACTTGAGGCTGAACTCGGTCGTGCGGTCAAG
      CAAGACATTTCTGTGTACGTAGCTGTACAATAAT
      ATACAATGAATTAGAATAATAACAGATTATGTGG
      CATTAATTATTACAGCAGCAACTCATTCCTTGATT
      CTGGGAATTAGCAATTTCTTCCAGCTTATATATAT
      Gm08:827 8276701 65 248 0.874 0.923 ACCAGCATCTCAATCCTTGATTGTACGA[C/T]ATA
      6701 ATTTTGCAATTTGATCCAAATTTATTACAGCTAGT
      TAGGATACTACTCGTCTTACAATTTTTGACAAGG
      TTTTGTCAGCAATGTTGAGGATGTTTAAGCTGAA
      CACCGTCCGAGAAGTAAAATACTATTAAAGGAG
      GCTAAAGGRATATATTGGATTAGAATTTTAAAAG
      ATTATTTTAATATAAAAGGTTATATGA
      Gm08:827 8276849 [A/G] 66 249 0.904 0.79
      6849
      Gm08:827 8276913 67 250 0.684 0.827
      6913
      Gm08:827 8277162 [A/G] 68 251 0.904 0.655
      7162
      Gm08:827 8277227 69 252 0.918 0.743
      7227
      Gm08:827 8277248 [A/G] 70 253 1 0.824
      7248
      GTTATGGAATGCAATAATAAATATATACTAAAAA
      AGAGTAATAAGAGTGTGAAATTGGTAY[A/G]ASA
      71 254 1 0.756
      GTTATTAAGTCATGTGGATAATGAAATTAAGAGT
      AACATTTATGAAAATATTATATTGAGCAAGTTAT
      AAACATAATCAMTAAAACTCATCATAAGAAAAA
      AAACATGATTAGTCTTGACACATAAGATAAACAT
      TAATTTAATTTAAAAAACAAAGRAAAAAGTGTA
      GAGGGGAGACATATATTTGACATTTTTTA
      ATTCTCCTATATTAACCTTTCATGCAATAATATCT
      TCTCATTCTYACTTTTGAATTTGAACAATARATTT
      AAAATTATACATTGATTTTCTGATTTTTTTAATTA
      GTCTAATTATTTCATAATAAATATAATGACATGT
      TATGGAATGCAATAATAAATATATACTAAAAAA
      GAGTAATAAGAGTGTGAAATTGGTAYRA[C/G]AG
      72 255 1 0.755
      TTATTAAGTCATGTGGATAATGAAATTAAGAGTA
      ACATTTATGAAAATATTATATTGAGCAAGTTATA
      AACATAATCAMTAAAACTCATCATAAGAAAAAA
      AACATGATTAGTCTTGACACATAAGATAAACATT
      AATTTAATTTAAAAAACAAAGRAAAAAGTGTAG
      AGGGGAGACATATATTTGACATTTTTTATT
      ATATACTAAAAAAGAGTAATAAGAGTGTGAAAT
      TGGTAYRASAGTTATTAAGTCATGTGGATAATGA
      AATTAAGAGTAACATTTATGAAAATATTATATTG
      AGCAAGTTATAAACATAATCAMTAAAACTCATC
      ATAAGAAAAAAAACATGATTAGTCTTGACACAT
      AAGATAAACATTAATTTAATTTAAAAAACAAAG+
      73 256 0.862 0.648 A/G+AAAAAGTGTAGAGGGGAGACATATATTTGA
      CATTTTTTATTTCAAAAGAATAAGAGAAATATAT
      ATGGTGCTTGCATCTTGAWGAACATTAAATAGAT
      AARAAGATATGTGTGATAAAAGAAAAAAAAAAG
      TGTGGTAATCAATAGAAAAAAAAAAGAGWAAA
      ATCATTCAAATCATTCAATAGAAAAGTGTGGGGT
      TGT
      TATGAAAATATTATATTGAGCAAGTTATAAACAT
      AATCAMTAAAACTCATCATAAGAAAAAAAACAT
      GATTAGTCTTGACACATAAGATAAACATTAATTT
      AATTTAAAAAACAAAGRAAAAAGTGTAGAGGGG
      AGACATATATTTGACATTTTTTATTTCAAAAGAA
      TAAGAGAAATATATATGGTGCTTGCATCTTGA+A/
      74 257 0.895 0.622
      T+GAACATTAAATAGATAARAAGATATGTGTGAT
      AAAAGAAAAAAAAAAGTGTGGTAATCAATAGAA
      AAAAAAAAGAGWAAAATCATTCAAATCATTCAA
      TAGAAAAGTGTGGGGTTGTTTAATTGATGTTTTA
      TATTAAAAAATTAGATGAAATTCATCCAAATCAT
      TCTTAAAAAATAATGCATCAAAATTTGTATATTT
      AGCAAGTTATAAACATAATCAMTAAAACTCATC
      ATAAGAAAAAAAACATGATTAGTCTTGACACAT
      AAGATAAACATTAATTTAATTTAAAAAACAAAGR
      AAAAAGTGTAGAGGGGAGACATATATTTGACAT
      TTTTTATTTCAAAAGAATAAGAGAAATATATATG
      GTGCTTGCATCTTGAWGAACATTAAATAGATAA+
      75 258 0.87 0.53
      A/G+AAGATATGTGTGATAAAAGAAAAAAAAAAG
      TGTGGTAATCAATAGAAAAAAAAAAGAGWAAA
      ATCATTCAAATCATTCAATAGAAAAGTGTGGGGT
      TGTTTAATTGATGTTTTATATTAAAAAATTAGATG
      AAATTCATCCAAATCATTCTTAAAAAATAATGCA
      TCAAAATTTGTATATTTTTAAATATTAAAAGACTT
      TGGTAATCAATAGAAAAAAAAAAGAGWAAAATC
      ATTCAAATCATTCAATAGAAAAGTGTGGGGTTGT
      TTAATTGATGTTTTATATTAAAAAATTAGATGAA
      ATTCATCCAAATCATTCTTAAAAAATAATGCATC
      AAAATTTGTATATTTTTAAATATTAAAAGACTTTT
      Gm08:827 8277876 [C/T] 76 259 0.836 0.713 TTATAAGTTATAAAAAATTATAATTGAATA[C/T] C
      7876 ACMAAATTTTATTATTTTTCTTAAAAAATCTTAW
      ATGTTTTAATTGAATACCATAAGACTTTTTTATAT
      AAAAAHTATTTTAAAATCTTTTMAAATCTTAATC
      YAATATATCCACTAAGTTATYAAAGGCTAGGAG
      GAAACAAGTGGASCATGAGACAATACATATATA
      GGGGGGAATATATGGAAATTGAAAAAAAAA
      AATCAATAGAAAAAAAAAAGAGWAAAATCATTC
      AAATCATTCAATAGAAAAGTGTGGGGTTGTTTAA
      TTGATGTTTTATATTAAAAAATTAGATGAAATTC
      ATCCAAATCATTCTTAAAAAATAATGCATCAAAA
      TTTGTATATTTTTAAATATTAAAAGACTTTTTTAT
      Gm08:827 AAGTTATAAAAAATTATAATTGAATAYCAC [A/C]
      7880 8277880 [C/A] 77 260 0.809 0.673 AAATTTTATTATTTTTCTTAAAAAATCTTAWATGT
      TTTAATTGAATACCATAAGACTTTTTTATATAAA
      AAHTATTTTAAAATCTTTTMAAATCTTAATCYAA
      TATATC CAC TAAGTTATYAAAGGC TAGGAGGAA
      ACAAGTGGAS CATGAGACAATACATATATAGGG
      GGGAATATATGGAAATTGAAAAAAAAAAGAT
      TAGATGAAATTCATCCAAATCATTCTTAAAAAAT
      AATGCATCAAAATTTGTATATTTTTAAATATTAA
      AAGACTTTTTTATAAGTTATAAAAAATTATAATT
      GAATAYCACMAAATTTTATTATTTTTCTTAAAAA
      ATCTTAWATGTTTTAATTGAATACCATAAGAC TT
      Gm08:827 8277969 [C/A] 78 261 0.87 0.658 TTTTATATAAAAAHTATTTTAAAATCTTTT +A/C +A
      7969 AATCTTAATCYAATATATCCACTAAGTTATYAAA
      GGCTAGGAGGAAACAAGTGGAS CATGAGACAAT
      ACATATATAGGGGGGAATATATGGAAATTGAAA
      AAAAAAAGATGTGAAAAATAATAAATCTCAATA
      GAAAATGAAGGAAGCATAAATGAAATAAAAGTG
      AAATCAGGTGATGAGATAAAAAACAATTGTS TA
      ATAATGCATCAAAATTTGTATATTTTTAAATATTA
      AAAGACTTTTTTATAAGTTATAAAAAATTATAAT
      TGAATAYCACMAAATTTTATTATTTTTCTTAAAA
      AATCTTAWATGTTTTAATTGAATACCATAAGACT
      TTTTTATATAAAAAHTATTTTAAAATCTTTTMAA
      Gm08:827 8278001 79 262 0.884 0.741 ATCTTAATCYAATATATCCACTAAGTTAT[C/T]AA
      8001 AGGCTAGGAGGAAACAAGTGGASCATGAGACAA
      TACATATATAGGGGGGAATATATGGAAATTGAA
      AAAAAAAAGATGTGAAAAATAATAAATCTCAAT
      AGAAAATGAAGGAAGCATAAATGAAATAAAAGT
      GAAATCAGGTGATGAGATAAAAAACAATTGTS TA
      AAAAAATTGACGATAAGTCTATAATAAATAAA
      TTMAAATCTTAATCYAATATATCCACTAAGTTAT
      YAAAGGCTAGGAGGAAACAAGTGGASCATGAGA
      CAATACATATATAGGGGGGAATATATGGAAATT
      GAAAAAAAAAAGATGTGAAAAATAATAAATCTC
      AATAGAAAATGAAGGAAGCATAAATGAAATAAA
      AGTGAAATCAGGTGATGAGATAAAAAACAATTG
      Gm08:827 8278167 [C/G] 80 263 0.861 0.847 T[C/G]TAAAAAAATTGACGATAAGTCTATAATAA
      8167
      ATAAAAAGTGAGGTCATATACATATTCCCGATTT
      CTATAAAAAAAAATGAATATTTGAAAATCAATTC
      ATTTTCAATYTTTAAAAAATAAATAAAAAAGAAT
      TGAAGTTGTATATCAATCTATGGAGAATTAATTC
      AAAAAATGATTTATAGAAGTTAGCAATAGAAAA
      AT
      AAAAGATGTGAAAAATAATAAATCTCAATAGAA
      AATGAAGGAAGCATAAATGAAATAAAAGTGAAA
      TCAGGTGATGAGATAAAAAACAATTGTSTAAAAA
      AATTGACGATAAGTCTATAATAAATAAAAAGTG
      AGGTCATATACATATTC CC GATTTC TATAAAAAA
      Gm08:827 8278274 [C/T] 81 264 0.831 0.628 AAATGAATATTTGAAAATCAATTCATTTTCAAT+C
      8274 /T+ TTTAAAAAATAAATAAAAAAGAATTGAAGTTG
      TATATCAATCTATGGAGAATTAATTCAAAAAATG
      ATTTATAGAAGTTAGCAATAGAAAAATACGTACT
      AACATTATAAGAAAGAGAAAATATTTTAAGAGA
      TAAATAGCAAAATAATATTTATTTAAS TGAATGA
      GTATCTTAAACCATATATCAAAATTTACAACAC
      TAAAAAAAAATGAATATTTGAAAATCAATTCATT
      TTCAATYTTTAAAAAATAAATAAAAAAGAATTGA
      AGTTGTATATCAATCTATGGAGAATTAATTCAAA
      AAATGATTTATAGAAGTTAGCAATAGAAAAATA
      CGTACTAACATTATAAGAAAGAGAAAATATTTTA
      Gm08:827 AGAGATAAATAGCAAAATAATATTTATTTAA+C/G
      8434 8278434 [C/G] 82 265 0.858 0.647 + TGAATGAGTATCTTAAACCATATATCAAAATTTA
      CAACACATTAAAATGAAAAATCTTAAAAAGAAG
      GAACAACAAAACTTTTTATGAAAATTATAACCAA
      AAAAAAATAAAAATTAATATAAAGCTTAACATTT
      CTTTTGTTGAAGTACTAATATAAAGCTTAACATG
      ATAGCTAGGATAAGCACTATCC TATGGC CAC
      TTTTGGTAAACAGATTTAATTTGATGTAAATCAT
      ATTAACATAATTAATATTAGGTATTTTAATAATTT
      TTTATTATTTTATTTGTATTGTTCATTAWTTGTTR
      AATAATATATAAGATAAAAAACATTTTGTCATTT
      ATCTTTATCCTATCTTATTTTTTATCTTGTCTAATA
      Gm08:827 8279165 83 266 0.83 0.759 TCATATTTTTAACAAATCAAATWGGG[G/T] GTAA
      9165 GTGTTTGATAAATTTTTTCAAACAAATTACAAAT
      GTTAATATATTTTATTTTTTCAACAAKTAATATGT
      TAATCTTAATAAACAAATTCACATTTTATTTTTCA
      TTTACCAAAATAGATATATTATTTTTAAATATTGT
      TTGAAATAAATAATTTATAATTAATTWAAAAAA
      ATAAWAATTTCATTTCGTAACATA
      ATTTTTTATTATTTTATTTGTATTGTTCATTAWTT
      GTTRAATAATATATAAGATAAAAAACATTTTGTC
      ATTTATCTTTATCCTATCTTATTTTTTATCTTGTCT
      AATATCATATTTTTAACAAATCAAATWGGGKGTA
      AGTGTTTGATAAATTTTTTCAAACAAATTACAAA
      Gm08:827 8279230 84 267 0.903 0.797 TGTTAATATATTTTATTTTTTCAACAA [G/T] TAATA
      9230 TGTTAATCTTAATAAACAAATTCACATTTTATTTT
      TCATTTACCAAAATAGATATATTATTTTTAAATAT
      TGTTTGAAATAAATAATTTATAATTAATTWAAAA
      AAATAAWAATTTCATTTCGTAACATATTTTTCAC
      ATTGAAATAAACATGTACGACACACATATATACA
      TACATATATATATATATATATAT
      AAAAATAATTCATATTAATATACCAACTTAAGAA
      AGCTGTTAAATATATTAAAAAAAGGAAATATGTT
      ATTATTAAATCAAATTTTCATCAGTTAACAACCA
      ACATTTTAATCTAATTTAGTTGTTTAAACAAAATT
      TGTATGTATTATAAATTTTTAATATTATTTTTATT
      Gm08:827 TTTAAAAATAAAAAACAGTGAAAACAAT [A/C] AA
      9854 8279854 [A/C] 85 268 0.842 0.759
      CC TTGCATTATCATATATAGTCAATTAAAAAAAA
      GGAATGAGTGAAGGGGAAAAAGTGGAGGAAAA
      GGTAATGGATTCAATTCCTTCCATTAATATTTTAA
      ACAAAAATTAATAAATTAACATATTGGTAAAAA
      ATATAATATTAATTTCTTGAAAATTTGTATCCAGT
      AGTACAACATTATAAATTATTTTTTAGGT
      TTCTGCCAATGGAAGGGTATCCAATGCGATTCAT
      CCAGCCACGTGACCAGCATAAGCCTCGCTTCGCA
      KTCCCTCACCGGAACACTCCCCTCGGATCTCAAT
      TCCCTCTCTCAACTCCGCACTCTCTCCCTCCAAGA
      CAATTCCCTCACCGGCACCCTCCCTTCTCTCTCCA
      Gm08:828 8280901 [A/C] 86 269 0.929 0.848 ACCTTTCTTTCCTCCAAACCGTCTAC TT [A/C] AAC
      0901 CGCAACAACTTCTCCTCCGTGTCCCCCACCGCYT
      TCGCCTCCCTAACCTCCCTCCAAACCCTCAGCCTC
      GGCTCCAACCCTGCTCTCCAACCCTGGTCCTTCCC
      CACCGACCTCACTTCCTCCTCTAACCTAATCGAC
      CTCGACCTCGCCACCGTATCCCTCACCGGTCCC TT
      GCCGGACATTTTCGACAAATTCCC
      AGCCACGTGACCAGCATAAGCCTCGCTTCGCAKT
      CCCTCACCGGAACACTCCCCTCGGATCTCAATTC
      CC TCTC TCAACTCCGCAC TCTC TCCCTCCAAGACA
      ATTCCCTCACCGGCACCCTCCCTTCTCTCTCCAAC
      CTTTCTTTCCTCCAAACCGTCTACTTMAACCGCA
      Gm08:828 8280937 87 270 1 0.848 ACAACTTCTCCTCCGTGTCCCCCACCGC [C/T] TTC
      0937 GCCTCCCTAACCTCCCTCCAAACCCTCAGCCTCG
      GC TCCAACCC TGCTC TCCAACCC TGGTCC TTCCCC
      ACCGACCTCACTTCCTCCTCTAACCTAATCGACCT
      CGACCTCGCCACCGTATCCCTCACCGGTCCCTTG
      CCGGACATTTTCGACAAATTCCCTTCCCTTCAAC
      ACCTTCGCCTCTCTTACAACAACCT
      GTTCCCGCTTCATTGACAAGTCTTCCTAGTTTGAA
      GAAAGTTTCTCTGGATAATAATGAGCTTCAGGGG
      CC TGTGCCCGTGTTTGGGAAAGGTGTGAATGTTA
      CTCTCGATGGGATTAATAGTTTTTGTCTTGATACT
      CC TGGGAATTGTGATCCCAGGGTGATGGTTTTGC
      Gm08:828 8281564 [A/G] 88 271 0.924 0.824 TGCAGATTGCCGAGGCATTCGGGTATCC [A/G] ATT
      1564 CGGTYGGCAGAGTCGTGGAAGGGGAATGATCCG
      TGTGATGGTTGGAACTATGTTGTGTGTGCTGCCG
      GAAAGATTATTACTGTCAATTTCGAGAAACAGGG
      TTTGCAGGGTACCATCTCCCCTGCATTTGCCAATT
      TGACTGACTTGAGGACTTTGTTTCTCAATGGCAA
      TAATTTGATCGGTTCTATACCTGATAG
      AAGGTTGCTGATTTTGGGTTGGTTAAAAATGCAC
      CAGATGGGAAGTATTCTGTTGAGACACGGTTGGC
      TGGAACATTTGGATATCTTGCACCTGAGTATGCA
      GGTACAGAAAGCCTTTGATTTTAGTTTTGTACAA
      TTGTGCCTTAATTTTGAAGTTCATATTTTATATGC
      Gm08:828 8282902 89 272 1 0.848 TCGTATTTGGTGGTTATAGCTGTTGGTTA[G/T] TA
      2902 CTTCAATATCATGCTTCGGTGTTCAGCAAATTTA
      AGTAGTTCACCAGAGTAATCGCTCACATACAAAA
      AAAAAGTAGAAAGAGTTGAAGGGAAAATAATTG
      ATACTCAATTCCTAGATACATGGCTACTTCAAAA
      TTCTTTGTGGCTATTTCTTTGCAATGTTATATTTT
      GC TC TTTTCACGTGTTTTGTTGAGTTGG
      GGAGCAATGGAAACCTACTAGCCATGATGAAGA
      AGAGGAAGACGGCTCTGGCGGTGACCTTCATATG
      AGCCTTCCTCAAGCTCTACGAAGGTGGCAAGCCA
      ACGAAGGCACTTCCTCAATATTTAATGACATTTC
      CATCTCACAAACCCAATCAAGCATCTCCTCTAAA
      Gm08:828 8284027 90 273 0.863 0.744 CC TGCAGGGTTTGCAGAC TCC TTTGATTCAA [C/T]
      4027 GGATTGCCGTTAACCGAATTGATAAACGAGACA
      AC TATCCAAGGGCATCTTAGTCCATATGATAGTG
      GAAGGTTTAGTTGAGAATACCCAAGAAAACCAG
      AGGTTGTAAAGCTGTTTTGATCTATTAGCATCGC
      CAATTTCTTTGTAATTATTTATTATTGTTCAAAAT
      GTCATTTTTATGGTGTTCTTAAAATCTCCTC
      CAAGATTTGTAAGAGAAAAC TTC TTGGCTC TATA
      TTTAASAACAAAAAATCTAAGAKRAAATGGGATT
      KAATGGAAATGATCGGTCGCAAGCATATCTAAAT
      TTGACAGGAAATCCATAAATGAC TTGACCAC CAT
      TAACAAGATAAATATTGTGTGAGATCTTTAAAAR
      Gm08:828 8286864 [A/T] 91 274 1 0.687 TGAAGATTTTAC GGGTTTAACAGATTAAAA [A/T] C
      6864 TTTTACAATTTAATATCACATTCTTTTGAACACAT
      GAACACTTATTGATGATAGTTACATTCCATGCTT
      GC TTTCC TTGCAC TTTATTTTTTGTTGGAAATTGA
      TCTAYGGAGAGATC TTTCAAGGAACATTGGC TAT
      AGCTGACATGATGATWGRAGGAAAAATTACAAA
      CAATAATTTATACAAATTTTATGTTTCA
      TAMAATAGAAGAAACCAGTATCTTGACTTCTTGA
      GAAATGAGGACAAGGAGCAAAACTATGCTAAGA
      ATCTTGATGGCTGAACCASCCATTTCAGAAAATG
      TAAATACAAGCTTCGATTCTCGAATTGCATAGCT
      CTTATATGTCGCGTTATTTATAAATGAATTGTTGT
      Gm08:828 AATTTGTAAAACAATATGTTTTACGTTTCG[C/T] G
      7265 8287265 92 275 0.776 0.917 TGAAGAATATCRCATTTATGAATGACTGAATTTT
      TAAGACAATGAAACTGAAGTTAAAGAAACATAA
      ATTACTCTAAAAAAAATTAAATACAGTGAAATTG
      TATAGATTTGATAAATATTTTTTTAATAGTTGATA
      TGATTTTGTTTTGTTAGGAGAAAGCTATCATTTTG
      TTCTCCTATAGTTATS TTTAGYAAGTTA
      AC CAGTATCTTGACTTCTTGAGAAATGAGGACAA
      GGAGCAAAACTATGCTAAGAATCTTGATGGCTGA
      AC CAS C CATTTCAGAAAATGTAAATACAAGCTTC
      GATTCTCGAATTGCATAGCTCTTATATGTCGCGTT
      ATTTATAAATGAATTGTTGTAATTTGTAAAACAA
      Gm08:828 8287278 [A/G] 93 276 0.76 0.91 TATGTTTTACGTTTCGYGTGAAGAATATC [A/G] CA
      7278 TTTATGAATGACTGAATTTTTAAGACAATGAAAC
      TGAAGTTAAAGAAACATAAATTACTCTAAAAAA
      AATTAAATACAGTGAAATTGTATAGATTTGATAA
      ATATTTTTTTAATAGTTGATATGATTTTGTTTTGT
      TAGGAGAAAGCTATCATTTTGTTCTCCTATAGTT
      ATS TTTAGYAAGTTATTTTAATTAAATT
      TTTTACGTTTCGYGTGAAGAATATCRCATTTATG
      AATGACTGAATTTTTAAGACAATGAAACTGAAGT
      TAAAGAAACATAAATTACTCTAAAAAAAATTAA
      ATACAGTGAAATTGTATAGATTTGATAAATATTT
      TTTTAATAGTTGATATGATTTTGTTTTGTTAGGAG
      Gm08:828 8287453 [G/C] 94 277 1 0.738 AAAGCTATCATTTTGTTCTCCTATAGTTAT[C/G]TT
      7453 TAGYAAGTTATTTTAATTAAATTTTTTTATTAATT
      AAAAGATTTATTTGACTATTTGATAAATAATTTTT
      TTAAGTAATTTTTAATGTTTCTCTAGTATYTTTTA
      GTATTTTTTTAAAATATTATTTAAAATAACATTTT
      TTAAACACTAATTTTTAATTTTTAACCTTTTAATT
      TTATTCTCTTTATATCTTAAAAT
      GTTTCGYGTGAAGAATATCRCATTTATGAATGAC
      TGAATTTTTAAGACAATGAAACTGAAGTTAAAGA
      AACATAAATTACTCTAAAAAAAATTAAATACAGT
      GAAATTGTATAGATTTGATAAATATTTTTTTAATA
      GTTGATATGATTTTGTTTTGTTAGGAGAAAGC TA
      Gm08:828 8287459 95 278 1 0.591 TCATTTTGTTCTCCTATAGTTATSTTTAG[C/T]AAG
      7459 TTATTTTAATTAAATTTTTTTATTAATTAAAAGAT
      TTATTTGACTATTTGATAAATAATTTTTTTAAGTA
      ATTTTTAATGTTTCTCTAGTATYTTTTAGTATTTTT
      TTAAAATATTATTTAAAATAACATTTTTTAAACA
      CTAATTTTTAATTTTTAACCTTTTAATTTTATTCTC
      TTTATATCTTAAAATATTTAT
      TAACTTTTCAGTTTACTTTTGCAAATAAYATATTT
      CTTTCCTGGMATATKACAAAGCTAAACAATATTT
      CTTGAGTGTTTAATTGTTTTAAATTGAAATAGGA
      AGTGAGCATTTMCTAATATCTTAGCTCGAAACAT
      CTCTTTCATCTTTGTTGAAGTAAACCTCTGTATGG
      Gm08:828 8288039 [G/C] 96 279 0.884 0.584 TAAAATTAAGAGGAGAAAGAAAAATGAA[C/G]T
      8039 GGAGTAAGGTCTTGTTTGAAATTATTTTTTAATTT
      CAAAACTTGTTTTCAATATAATTTTTAGCTTTGTT
      ATATTTTAAAAATAAAATAAAAAGAAAAAAYAT
      TTGTTAAAATTCAAAAATAGATTTTTTTTAAAAA
      AATGTTCATAAAATATCAGCATYTGTCAATTGCA
      TGTTTATGAGGTAAAAAATTGCTTTATT
      AAGTGAGCATTTMCTAATATCTTAGCTCGAAACA
      TCTCTTTCATCTTTGTTGAAGTAAACCTCTGTATG
      GTAAAATTAAGAGGAGAAAGAAAAATGAAS TGG
      AGTAAGGTCTTGTTTGAAATTATTTTTTAATTTCA
      AAACTTGTTTTCAATATAATTTTTAGCTTTGTTAT
      Gm08:828 ATTTTAAAAATAAAATAAAAAGAAAAAA [C/T] AT
      8141 8288141 97 280 0.823 0.713 TTGTTAAAATTCAAAAATAGATTTTTTTTAAAAA
      AATGTTCATAAAATATCAGCATYTGTCAATTGCA
      TGTTTATGAGGTAAAAAATTGCTTTATTTATGAA
      AATATTTAGGATCCAAAACAAGAGTAGGAAAGT
      AATTTTTAAAAGACATTTTTTTCCAGCACTGCAAT
      TGTAGGAACAAGTTTTAAAATACAAATG
      CC TCTGTATGGTAAAATTAAGAGGAGAAAGAAA
      AATGAAS TGGAGTAAGGTCTTGTTTGAAATTATT
      TTTTAATTTCAAAACTTGTTTTCAATATAATTTTT
      AGCTTTGTTATATTTTAAAAATAAAATAAAAAGA
      AAAAAYATTTGTTAAAATTCAAAAATAGATTTTT
      Gm08:828 8288200 [C/T] 98 281 0.883 0.851 TTTAAAAAAATGTTCATAAAATATCAGCAT[C/T] T
      8200 GTCAATTGCATGTTTATGAGGTAAAAAATTGC TT
      TATTTATGAAAATATTTAGGATCCAAAACAAGAG
      TAGGAAAGTAATTTTTAAAAGACATTTTTTTCCA
      GCACTGCAATTGTAGGAACAAGTTTTAAAATACA
      AATGYCTTGAAAATCTTTCTAATACTTAATGGAA
      AATATTAAATAAAAATAAAAATAAAAATA
      TAGGAAAGTAATTTTTAAAAGACATTTTTTTCCA
      GCACTGCAATTGTAGGAACAAGTTTTAAAATACA
      AATGYCTTGAAAATCTTTCTAATACTTAATGGAA
      AATATTAAATAAAAATAAAAATAAAAATAAAAA
      TATTTAATGTTTTAAAAACTTTAAAAACATTCAA
      Gm08:828 8288470 [A/T] 99 282 0.852 0.652 ATACTTTC TTTATTTAATAAGAGGAGGATGA [A/T]
      8470 GGGATTAGAATTATTCAATTTTTTTATATTAAAAT
      ATAACGAATCCATAACAAATTTACAGTAGTACTT
      TGTTTCATAAAAAAATACTGATTGGATGAAGCAG
      AKAGGAGAGAGGAAGATGTCAGTAAGTCATAAA
      TGTGCCATTAATACATTTAATAACTTTTTTTTTTT
      ACAAAAGGGAGAAAGGCTTACATTTAAAT
      TTTTTTTTTTTACAAAAGGGAGAAAGGCTTACAT
      TTAAATTGCTATTACTTTTTTTAAACGAAAAAGG
      GGTGAAAC GC CCAAAATAAATCATCATAAATAA
      GATAATAAGATAAGGAAGGAGAAAATAAATTTA
      AATATTGATCACAAATAAATTTTGYATAAATACA
      Gm08:828 8288831 100 283 0.852 0.612 AATAAAATATAAGATAATAAATATCGATCAAT+C/
      8831 T+CGTGAAACAATTTGCGGAAGAGCAAAATTTGA
      GAAAAAAAATCGAAGAARCAAAATTCGCGATAT
      TATAAAACTTTAGAGATAAAAAAAAATTCATGAT
      AAATAATACAGTATATTATAATTTTAATCTTTAGT
      TTTTAATACAACTGTAAAAAAAATTCATGATAAA
      TAATATATTATAATTATAATCTTTAGTTTTAA
      AACTTTTTGTTAGTAACAGAAAGTGTAAACTGGT
      TTGGAGAAAATGTGAGAGATGGCAGGATACTAT
      GAGTAACTAGTTGGATTGGAAAATGTTGTATCCA
      GCTGTAAATTACCCATTCCATTATTGGAAGGAAA
      TATTCCGCATGAGCCAAACTATGCGAAAATGACA
      Gm08:828 TGGTGAAAATTGATAAAGGTAAAGAAAAAGT+A/
      9392 8289392 [G/A] 101 284 0.929 0.785 G+GAGCTCAGAAAGGTGTTATTCTTCATCAAGAA
      GAGCTATTTCCAAAGCAACTATRTTACTTGTGCA
      ACTCTTTATTTTTTGTACATATACTACTATTATTA
      TTACTTGTGCTACTCTGATAAATAGAAAGTAGAA
      AACAAAGAAGTGGTATTGATTGATGTTACGTAAG
      TTACATAAAAGTTTGATGCGTATTGATTGAT
      ACAAAGCAATGGATCCAGGACTCATATATGATAT
      CACCACTGAGGATTATGTCCAATTCCTATGTTCC
      ATGGATCACAGTAGTGCATCCATTAGCAAAGTGA
      CTAAGACCACCACAAGTTGTAAGAAAGGAAATC
      ACCAAGCACTGAACCTCAACCTTCCTTCCATATC
      Gm08:829 AGTGCCAAACCTGAAGAGGGCTGCAACAGTA+A/
      0740 8290740 [A/T] 102 285 1 0.912 T+TGAGAACAGTGACAAACGTGGGAAATATTACT
      GCAGTCTRCAAAGCTCTAGTGAAAGTTCCACATG
      GCATAAAAGTTAGAGTTGAACCTCAAACTTTGAG
      TTTCAATTCAGRTGTACGAATCCTTAACTTTAKTG
      TCAGTTTTCTGTCAACTMAAAAATTTCATGGAGA
      TTACAAATTTGGGAGCCTAACATGGACAGAT
      TAATATTTTTTCTTTTTAAAATACAGAWGGAAGT
      ACAAGAATAAAAAGTGGTTCAACTTCCATGAATA
      AAAATGGTCTTTACATGATTTGCACTTAATCTAA
      ATAACCAAGCACAAAATATATCAAAYWTGTGTA
      TATTTTCAGTTTAGTATTAATTATTAATGACTAGC
      Gm08:829 8291682 [G/A] 103 286 0.866 0.715 AATAGAATTTAGATTTATAGAGACAATACA[A/G]
      1682 TTAGTAAATTTTATTTTAGAAATTATTTTAAAATA
      TTCTAATAATTAAATTACTCTTTTGTTTTTACATT
      GCAAGTGCAAGCATCTAYGTGCAAAAGGAGGGT
      ACGATACTCAACAATAGATAAATTTGCACAACAT
      CATCAGTCTTTGTTYTTCTTTTTCTTTTTTACTTTA
      GATACGTAAGGCAGTAACAACATACGA
      GACAAAAGATAAGAGAAACAAGCTTACATTACT
      ACAACGTTATAAGAAGCAAATAACCTACGAAGA
      AAATCAAGATAAATAAATAGATGGTACAAATTT
      GCATGTGTTCGGATATCCATCGACATCATTCATTT
      CGATCAAAATTCACGTTTTGGACATAAAAGCAAT
      Gm08:829 TCTTCGTCGCTTCAGATAATGCGTGTCGTGGA+A/
      2207 8292207 [G/A] 104 287 0.912 0.904 G+CAGAGGATGCAAAACCATACATGCAGAAAATT
      ATGCTTGCAGAATGACACWTACGATGGAGCACC
      AAGATATGAGGCAAGTCGTAAAATATCACTAAA
      TATTCCACCAGCGGTGACTTGAGCACCAGCTCCT
      GGCCCACGAACTATCAGAGGCTGATCCTTATACC
      TTCGTGTTGTAAATGCAATAATGTTATCTGACCC
      CTGTTATTGATTGATSAATCACTTATTACTATCTG
      ATGGAAGATGAGTTTTATATAATAGAGTTACCTT
      GTCCTGCAAGCTTACAATAGAAAMTTCAGCTGYC
      TACAGCTATTAAGACTAACTAAACTTCAGTTAAG
      CCAATATTAATTGTGTTTTACTATTTAAGTCCTAG
      Gm08:829 8297064 [C/T] 105 288 0.929 0.857 TTTACAATTTCTCCTATATTTTTATTTC[C/T]ATTA
      7064 CTTGTTTCGAAAGCAATCATCTGAATTTTCTCTAT
      CTTCTTGTATAATGATAAGAACCTTGGGAGATCT
      ACACCACAAAAACTAGTCATTGTAGTTTGGAGAG
      CCAAGGACCTTATACATCCTAAACTTCAAATGTG
      AGACTCAAGTCTCATACCTTGCAATTGGATCCTA
      ACATTCCATCTTGCTTTGCAGCCAC
      AAATGTAGAATGATAAATCTTCAGTCTGATATCA
      CTAAAGAGAGTCAAGTCTTAACAATTGAACAGA
      AACATGCATTTGGTTTTAGAAGAATTGGATTTAG
      CACC TGAGAAAGAC GC CCATTATC CAAAGCTTGA
      CGAAATC TAGATTGCAATGCC TCAGCAACAGC TT
      Gm08:829 8299433 [A/T] 106 289 0.929 0.787 TTACTTCTTTCTCGGGCACAGCAAAGCATAC [A/T]
      9433 GAATGCTCACTACTAGCCTACATAAATACTGTTA
      ATGATTAATGCCATTTCTTATATATCARCGTGGA
      CAACTAGAAAAATTGAAAAAAGTTATAAGTGCA
      CC TGAGATATCATGATAACATTAGCTC CAACATC
      TTTTACTGCACCAAAAATAGCACTGGCAGTACCT
      GGAACACCAGCCATTCCAGTTCTGCAAAAAA
      TTAATGCCATTTCTTATATATCARCGTGGACAACT
      AGAAAAATTGAAAAAAGTTATAAGTGCACCTGA
      GATATCATGATAACATTAGCTCCAACATCTTTTA
      CTGCACCAAAAATAGCACTGGCAGTACCTGGAA
      CACCAGCCATTCCAGTTCTGCAAAAAAGCATCAA
      Gm08:829 8299672 [A/T] 107 290 0.919 0.702 AGAAAAATTTATTGGAATCTACAACTTGGAC +A/T
      9672 +ATTAATATTGGTTAAAGAAAACCTTAAATTAAA
      TAGAAATC CTC GTGCAGCAAAAAATGC CAAC TAT
      TCATCATGTAACACAACTGCAATTCATGACTCAC
      CCCTCGACGTTTACAAGTGCCAAGTTGTCTATGG
      TTGCAAATCCTTTGACAAAATTTTGCAGGTTCTG
      GC TATC TTCATGATCATTAACAGAAGGATGG
      CTTGTGGATAAGGTCATACATCATATCTGTCACC
      TTTGACATTGCAGAAACAACCACCAATTTCCTCT
      CC GAATCATCC TTAAGAATTATGTC YGCAACATT
      TTTTATTCTC TGAGAGGTTCC CACACAGGTTC CAC
      CAAATTTGTGAACAGACCAAGTTTCTCCTTTGGG
      Gm08:830 8301839 +GIN 108 291 0.937 0.721 TAGTTGTTTTTCCTCCAAGGACACATTCG[A/G] TG
      1839 AAACATCTGCTAGCAAATATAGAAAGGACAAAA
      AAACATAAGTTACTGTATTTGTCTATTAGAGTTCT
      AAGGTTGACTTGATGGTAAAAGGAGAAGGGAGA
      GAGGGAAAGGTCGTGGGTGGGTTCAATTTTCTCC
      GC TAACAAAAAAC TAACAATTAACAAC TAATATT
      TGCTGATAATAAAAAAAACTRTATTCGTC
      GAAGGGAGAGAGGGAAAGGTCGTGGGTGGGTTC
      AATTTTCTCCGCTAACAAAAAACTAACAATTAAC
      AACTAATATTTGCTGATAATAAAAAAAACTRTAT
      TCGTCTATTTCAAAACATAACCATAAGAGTAAGT
      CGTAACCTGTAAATGAAGCACGTACAGATGTACT
      Gm08:830 8302134 [C/A] 109 292 0.924 0.758 CGGTGCC TC TCTTC CC CGTGGTAAAGTAAGA [A/C]
      2134 CC TTCC TGAGACAGAAACCATTGTATC GTC GTGA
      ATCAGTATATAGCAAAACACAAAAATCCAATTA
      ATCTCATGGGGAGAATATCATTTAAACTGCCAAA
      ATTCCGAAAACACTCTAATCTCTGCAAAGGATAA
      ATATACAAAAAGGAAAAAAAAAAGTACAGAATA
      TACTGCTTGTAGAACAACCAATCATCTAAGAG
      TTGAGTTGAAATAATGAAATGAAATGGATCATAA
      TCCATCATCATCTTCCATTATGTTTCATTTCAACT
      TTTACAAATCAAACAATCCAACACCTTTTCCTTCC
      AC TCCATCC TTC TTCATTC CATACTC TACAACCAA
      TCAAAACATATTCGAAGGTTTCCATGTATGTAGA
      Gm08:830 8303450 110 293 0.843 0.582 ATTATAAATAGGTTGAACAAAATTTTA[C/T]TGRG
      3450 TAGGTTGAAMAGAATTATTTGGTAYTATTATTCG
      TACGCC CC TAAC CATGTGTTTGGATGAAGAATTT
      AAAAATTTCTAAGAAATTTAAATTCATAACATTT
      TAATTGCCTTGATTTTAATTCCTTTCCTTTTGTAA
      ATATTTTGTTTGGATGAGGTAATTCAAATTCTTGT
      ATTTTAATTTTCTTS TTTGGACAA
      AATGATAACAAATTGTACATATTATAGACTAAAA
      TGACAATAATTTTAATCTAAACAATTTATTTATAT
      TTTTTTAATTTTATGATGTGTTAAATTGTGACAGT
      GC CC TACAATTTTAAAGAAC GTACAAAATAATTA
      TTTATTCAAAATTTTAAACATAACATTACCTTTCC
      Gm08:830 8305237 [A/G] 111 294 0.817 0.722 CTACAAC GTCC CC CCGATAGTGTCATC [A/G] GTAG
      5237 GAC TC TTGC TTCAGAACAAAAC GC GAGTC CATAT
      AAGGCAACTGCAATTTTTTTAATTAGTCTTCCGTT
      TGTTTCGGGGGCTAATGGGGAATTATAGCAAGTG
      TGAKAATTTTCTATGCTTTTAAACTAAAATCTAC
      ATATTTATAAAAATATAAAAGTAAAAAAAAAAT
      GC CAC GGATAGTTCAGTCAAAGATAA
      AATTTTAAAGAACGTACAAAATAATTATTTATTC
      AAAATTTTAAACATAACATTACCTTTCCCTACAA
      CGTCC CC CCGATAGTGTCATCRGTAGGAC TC TTG
      CTTCAGAACAAAACGCGAGTCCATATAAGGCAA
      CTGCAATTTTTTTAATTAGTCTTCCGTTTGTTTCG
      Gm08:830 8305348 [G/T] 112 295 0.919 0.737 GGGGC TAATGGGGAATTATAGCAAGTGTGA [G/T]
      5348 AATTTTCTATGCTTTTAAACTAAAATCTACATATT
      TATAAAAATATAAAAGTAAAAAAAAAATGCCAC
      GGATAGTTCAGTCAAAGATAATTCGAAATCATAG
      TAAATATTAAATGATTGGATTTTACAACATS TATT
      TGAAAGAGTCATCATAAAACTTAATACCACAYTT
      TAACCMAAAACTTTAAAAGTCAACTTTAT
      CCAATCCTATTATGTTACCCAAGATGYCGTWAGT
      TCTCTAGGTGGTTTTTTCRAAACAAAAAAAAWTT
      ATTTGTAATAAAATAAATAATATTACTTCATTCTC
      ATGTCTTTTTATATTTAAGGTTATTATTAAGAAAT
      ATTTGATGAAAATAAACATTGTTCACCCTCGTAG
      Gm08:830 8305905 113 296 1 0.491 CC TCC GTTATGGC GAGAGTGCC TCTCAT [C/T] TGC
      5905 GTTC CRAACAGC CC TAGC TTRCACCATAATGGGT
      TGTGTCACCCTCGTAGCCTTCCYTGCATTCTCATT
      ATCATAAACGAYGCCGCTTTGGGAGACGCCTTCC
      ATGTC TATRCCAC CC TTCAGAGCATAGGC CC CAC
      CATCTTGAGCTTGTGGGYTGTCGGACTAGGGYCG
      CTCTCTAAAGYCACCACCGCTGTAGC
      GAGAGTGCC TCTCATYTGCGTTC CRAACAGCC CT
      AGC TTRCACCATAATGGGTTGTGTCAC CC TCGTA
      GC CTTCC YTGCATTCTCATTATCATAAAC GAYGC
      CGCTTTGGGAGACGCCTTCCATGTCTATRCCACC
      CTTCAGAGCATAGGC CC CACCATCTTGAGCTTGT
      Gm08:830 8306090 114 297 1 0.494 GGGYTGTC GGACTAGGGYC GC TC TCTAAAG[C/T]
      6090 CACCAC CGCTGTAGC GGTGGC GCTC GC CGC GTTT
      GTGGTGGTTCTTTCCTRGCCTCAGAGCACAAATT
      TGATAGCTAAACGCATATCATTGGGTCAGATAGT
      AC CACCATGTTGAAATTRAGAGGAAAGAAGTTTT
      AAAAAC CC TAATTTGAGGAAGAAGAAGCAAGTG
      AAGAAGAAAATATTTGACAACTTTTTAAAAT
      GTTGTGTCAC CC TCGTAGCC TTC C YTGCATTCTCA
      TTATCATAAAC GAYGCC GC TTTGGGAGAC GC CTT
      CCATGTCTATRC CACC CTTCAGAGCATAGGC CC C
      AC CATC TTGAGC TTGTGGGYTGTC GGAC TAGGGY
      CGCTC TCTAAAGYCAC CACC GC TGTAGC GGTGGC
      Gm08:830 8306141 [G/A] 115 298 0.848 0.737 GC TC GC CGC GTTTGTGGTGGTTC TTTC CT [A/G] GC
      6141 CTCAGAGCACAAATTTGATAGCTAAACGCATATC
      ATTGGGTCAGATAGTACCACCATGTTGAAATTRA
      GAGGAAAGAAGTTTTAAAAACCCTAATTTGAGG
      AAGAAGAAGCAAGTGAAGAAGAAAATATTTGAC
      AACTTTTTAAAATTTGCATCAAAGTCCAGCTTAC
      ATGTCATAATCTAGGACAATTTGWCACGTT
      CCATGTCTATRCCACCCTTCAGAGCATAGGCCCC
      ACCATCTTGAGCTTGTGGGYTGTCGGACTAGGGY
      CGCTCTCTAAAGYCACCACCGCTGTAGCGGTGGC
      GCTCGCCGCGTTTGTGGTGGTTCTTTCCTRGCCTC
      AGAGCACAAATTTGATAGCTAAACGCATATCATT
      Gm08:830 8306210 [A/G] 116 299 0.929 0.772 GGGTCAGATAGTACCACCATGTTGAAATT[A/G]A
      6210 GAGGAAAGAAGTTTTAAAAACCCTAATTTGAGG
      AAGAAGAAGCAAGTGAAGAAGAAAATATTTGAC
      AACTTTTTAAAATTTGCATCAAAGTCCAGCTTAC
      ATGTCATAATCTAGGACAATTTGWCACGTTAGAT
      AATCTATGTGACAYTAAAATTATTAAAAATATAT
      CTCATTAATGGYGTTAYTTTTAAATTTAACG
      TGCATCAAAGTCCAGCTTACATGTCATAATCTAG
      GACAATTTGWCACGTTAGATAATCTATGTGACAY
      TAAAATTATTAAAAATATATCTCATTAATGGYGT
      TAYTTTTAAATTTAACGGCAAAKACTATTTTRTA
      AAATTTATGCAAAAATAGAGACTATTTTTTACAT
      Gm08:830 8306492 [A/G] 117 300 0.853 0.614 TTAAAAAAAGATAAAGACTAATTTGCAAAA[A/G]
      6492 GAATCAAAAGTTAGAAATCAAAATACCTATTTAY
      TTAAWAAAAAAAACATCATGCGTTAGTTATAAC
      CTTAACTTCTAATTTTTTGCTAACGCCCAAAAAA
      ACTAAGAATTCGAATCAGAAGTAGGYAGAATAG
      KCAATTTGGTTCTTAAAAGTGTATGGAAGGAAAA
      AWTTTCCTTTGACTTTTTAAATTGGAACACGT
      AAAATTTATGCAAAAATAGAGACTATTTTTTACA
      TTTAAAAAAAGATAAAGACTAATTTGCAAAARG
      AATCAAAAGTTAGAAATCAAAATACCTATTTAYT
      TAAWAAAAAAAACATCATGCGTTAGTTATAACC
      TTAACTTCTAATTTTTTGCTAACGCCCAAAAAAA
      Gm08:830 8306627 [G/T] 118 301 0.811 0.689 CTAAGAATTCGAATCAGAAGTAGGYAGAATAG+G
      6627 /T+CAATTTGGTTCTTAAAAGTGTATGGAAGGAAA
      AAWTTTCCTTTGACTTTTTAAATTGGAACACGTC
      TTGATTTTTTTCCCTTGTTGCCCAAAAGCAGTCTT
      ATTATTCATCCGTTGGGAATTTTTGTTTTAATTTC
      GCTGATMAAAAAATTGAGAATTTTATGTCTGCTT
      TGTGAATTACCATTTTWTCGGAACCTGCAT
      TAGAAGKAATAATTTTGTTTTGGCTTGTTGAATT
      GGAAAATGTTACAGTCCCGGTCATTCTTTTTATTT
      TTATATGTTTATTTATTTTTGTCCAAATAGCAGGG
      TCATATTCAAAACTTGGGTTTTACTTTCAAGCTTT
      GGAACAATGTTAGTGTAATTTGTGACTTTTGATA
      Gm08:830 8307172 119 302 0.854 0.63 AAGCCAAAGAAGTAACTTTCGTTCTTA[C/T]TTTC
      7172 ATGTGACTTGTAACAAGTTACAAGTCAGTAATAT
      AACCTATAACTTWYTCTTCATCRTCTGCTTCTTCT
      TTTGATCATAATATCTGTTAAGTGATCTTTCATAG
      AGAGAGAGAGAGAGAGATGGAGAGGTGTGACA
      AGGTGATGAACCAACGCAACATGCATGATTGTCC
      TAAAACAGGTCCTGGCTATCCTTCAC
      TCTGAAAAGGCCAATTCAGCTTCATTGGAGGAAT
      AGATAGGCATTAGGCAGAGAGATCAAGATAGGT
      TTCTCAAGTTGTTGTTACAAACATTTTATATGACA
      TGATACTGGGAACAAGTGACATGTAGAAATATCT
      ATCTCTTTCTAGTGCTATGCATGAAGACTTGGTG
      Gm08:830 8307665 [G/T] 120 303 0.924 0.772 CAGCTTAAACAATTTCTGTCAAAACGTGTA[G/T]T
      7665 TTGGTGATTTTATATATATATATTGGTGATGAATA
      TTCAATTCAATGCAGGAACAGGAAGGGATAAGC
      CTGACTTTCTGGCCACAGTGGATGTGGATCCAAG
      CTCTCCAACGTATTCAAAAGTTATCCATAGGTTA
      CCTGTACCTTATTTAGGTGATGAACTGCACCATTT
      TGGGTGGAATTCATGCAGCTCTTGCTAT
      GTGATGAACTGCACCATTTTGGGTGGAATTCATG
      CAGCTCTTGCTATGGAGATCCATCAGCAGTTCGG
      CGATATCTGATTCTACCTTCACTGGTGTAAGATA
      CTAAACAGC CAC TTTGGATTTTACTTGCAC GCAT
      ATGCGCATGCAYACACACACATAACAAACACTG
      Gm08:830 8308019 [A/G] 121 304 1 0.837 ACAAGGTTCAAGAACTTCACTGGTGTAAGAC +A/G
      8019
      GATTTACCATATTTCAGATCAGGCCGCATTTATG
      TGGTTGACACAAGATCAAATCCAAGGTCTCCATC
      TTTGCACAAAGTTGTTGAGCCAGAAGACATCATA
      AGTAAGACTGGATTAGCTTATGCACACACATCTC
      ATTGTCTTGCTTCTGGTGACGTCATGATCT
      CTGGTACCAACCACAGCATAAGACTATGATTAGC
      TCATCATGGGGTGCTCCTGCTGCTTTCACCAAAG
      GTTTTAACTTACAGCATGTCTCTGATGGTCTTTAT
      GGGAGGCATCTACATGTATACAGCTGGCCTGGGG
      GTGAACTGAGACAAACATTGGACCTTGGTGAGTC
      Gm08:830 8308891 122 305 0.936 0.801 AGGGGTTC TACC CTTGGAGGTACATTGC T [C/T] AA
      8891 TAAATAATTCTGGAGTTATTTCCWCCAATTATAA
      GCACTTTATGTTAATGTACTTGTGATTTAATCATA
      AATATGTTTGTCCTTTGCTACATTTTTTCTCTCTA
      GC CTGTACTTGTGAAGTAATATGTTAAAGGTGGC
      ATAATTTGTAAGCAACTTGTCCTAAATGCAGGTA
      AGGTTTCTGCATGATCCTTCTAAAGA
      TGATTAGCTCATCATGGGGTGCTCCTGCTGCTTTC
      AC CAAAGGTTTTAACTTACAGCATGTC TCTGATG
      GTCTTTATGGGAGGCATCTACATGTATACAGCTG
      GC CTGGGGGTGAAC TGAGACAAACATTGGAC CTT
      GGTGAGTCAGGGGTTCTAC CC TTGGAGGTACATT
      Gm08:830 8308917 [A/T] 123 306 0.87 0.865 GC TYAATAAATAATTC TGGAGTTATTTCC [A/T] CC
      8917 AATTATAAGCACTTTATGTTAATGTACTTGTGATT
      TAATCATAAATATGTTTGTCCTTTGCTACATTTTT
      TCTCTCTAGCCTGTACTTGTGAAGTAATATGTTAA
      AGGTGGCATAATTTGTAAGCAACTTGTCCTAAAT
      GCAGGTAAGGTTTCTGCATGATCCTTCTAAAGAT
      ACAGGTTTCGTKGGGTGTGCATTGT
      GTCAAGTAACATGGTAC GGTTTTTCAAGAC C GAG
      GATGAATCATGGAGTCATGAGGTACACAAAAAG
      GATATAGTAAAAAATCAATGCCTAAATTTTAGGA
      GAATCATGACATCTCATTAATCAGAAGGTTTACA
      TTCAGCTATTCTATTTTTATTTCATTCCTATAATTT
      Gm08:830 8309316 124 307 0.924 0.912 TGGGATTCC TGGTTC TTGGAATTTCC TTT [A/T] TA
      9316 ATTTTCTTCACCTTTTCTATATATTGTATCTGTGCT
      CATATGAAATAATAGAGATGATATAATTTTCATA
      CTCTACTCTACTCATAGATATCCATACTCATTTTR
      TATTGTCATCTGGTATGCGTTTGTGCAGCTTCAAC
      CAAGGTATAATGATCAATAATAC TTACACAC TAG
      AC TGAC TTTGCAGGTTGCAATATC
      TGACATCTCATTAATCAGAAGGTTTACATTCAGC
      TATTCTATTTTTATTTCATTCCTATAATTTTGGGA
      TTCC TGGTTCTTGGAATTTC CTTTWTAATTTTC TT
      CACCTTTTCTATATATTGTATCTGTGCTCATATGA
      AATAATAGAGATGATATAATTTTCATAC TC TACT
      Gm08:830 8309423 [G/A] 125 308 0.854 0.824 CTAC TCATAGATATC CATAC TCATTTT [A/G] TATT
      9423 GTCATCTGGTATGCGTTTGTGCAGCTTCAACCAA
      GGTATAATGATCAATAATACTTACACACTAGACT
      GACTTTGCAGGTTGCAATATCAGTGAAACCATTG
      AAAGTGCAAAACTGGATTCTTCCAGAAATGCCTG
      GGCTTATAACTGATTTTCTGATATCTCTTGATGAT
      CGGTTTCTGTACTTTGTGAATTGGC
      TAGACAATATAACATTGAGGAC C CTAAAAATC CT
      GTACTGACTGGCCAAGTATGGGTTGGGGGACTAC
      TTCAGAAAGGAAGCCCTATAGTAGCAATAACCG
      AAGATGGTAATACTTGGCAATCTGATGTTCCAGA
      CATCCAGGTTTGTGCAGTTTAACTTTTGAAATTA
      Gm08:830 GTGATTCTAGTGTCATGCTTGTTGATTTCTC [A/C]
      8309837 [A/C] 126 309 0.924 0.824
      9837 CATGTTTGGAGTTGATTGGTTCTTAGATGTACTA
      GATATAATAGACTTGTGCATTACATTGGTGCCTT
      CAAACTTTTTGTCACTTTTGTATTTTATCTTGTGTT
      ATGCTTAAACGTGGTAAATAATTGCACTTTAAAT
      TTTGAC CC TTTAGTGGTTGAAGGTGAAGAGATCA
      AAATTTTTAATTTCAGGGAAATAAGTTG
      AAAATGGTGGTC TGAAAATTAAC CCTAATTTC TT
      TGTTGAC TTTGGAGC TGAGCC TGGGGGTC CC TGC
      CTTGCCCATGAGATGAGATATCCTGGTGGTGACT
      GCACTTCAGATATATGGATTTAATAGC TATGC TA
      CTTGAGGCCAGGCTACAAGCAATATCCATGTGAA
      Gm08:831 TAAAATCCTTAGTCCTAGAATGAATCGAGG[A/T]
      8310383 [A/T] 127 310 0.918 0.677
      0383 GGGCTAATGTTATAAATAAATAATAGTTGCATAT
      GTATGATGGTTGCATTGTAATAAAGTTATATTGT
      CATGTAGTTTTCMGTACTTTCTCATTTACATCATC
      CTAAACAGTGTTCTCTRTGAAATAAATCTTGCTC
      AC CTACAAAATTTGGGTC TTC TGATTGAGTAAAT
      CTCTATTGGAGTAACATTCTAGATTAATG
      TGAGATATCCTGGTGGTGACTGCACTTCAGATAT
      ATGGATTTAATAGCTATGCTACTTGAGGCCAGGC
      TACAAGCAATATCCATGTGAATAAAATCCTTAGT
      CC TAGAATGAATC GAGGWGGGC TAATGTTATAA
      ATAAATAATAGTTGCATATGTATGATGGTTGCAT
      Gm08:831 8310464 [A/C] 128 311 0.924 0.787 TGTAATAAAGTTATATTGTCATGTAGTTTTC [A/C]
      0464 GTACTTTCTCATTTACATCATCCTAAACAGTGTTC
      TCTRTGAAATAAATCTTGCTCACCTACAAAATTT
      GGGTCTTCTGATTGAGTAAATCTCTATTGGAGTA
      ACATTCTAGATTAATGGCCTTACTTGGGATTCTAT
      GATTTTCATTCACATCATGAATGTGCTGCACCTTC
      TACGTTGCTTGTTCCCATTTGAATGYA
      TTTAATAGCTATGCTACTTGAGGCCAGGCTACAA
      GCAATATCCATGTGAATAAAATCC TTAGTCC TAG
      AATGAATCGAGGWGGGCTAATGTTATAAATAAA
      TAATAGTTGCATATGTATGATGGTTGCATTGTAA
      TAAAGTTATATTGTCATGTAGTTTTCMGTACTTTC
      Gm08:831 TCATTTACATCATC CTAAACAGTGTTC TCT [A/G] T
      8310503 [A/G] 129 312 0.933 0.734
      0503 GAAATAAATCTTGCTCACCTACAAAATTTGGGTC
      TTCTGATTGAGTAAATCTCTATTGGAGTAACATT
      CTAGATTAATGGCCTTACTTGGGATTCTATGATTT
      TCATTCACATCATGAATGTGC TGCAC CTTC TAC GT
      TGCTTGTTCCCATTTGAATGYATTTGAAATCACA
      AC CCAAC CAAATCATTTCAATATGATG
      CMGTACTTTCTCATTTACATCATCCTAAACAGTG
      TTCTCTRTGAAATAAATCTTGCTCACCTACAAAA
      TTTGGGTCTTCTGATTGAGTAAATCTCTATTGGAG
      TAACATTCTAGATTAATGGCCTTACTTGGGATTCT
      ATGATTTTCATTCACATCATGAATGTGC TGCAC CT
      Gm08:831 TCTACGTTGCTTGTTCCCATTTGAATG[C/T]ATTTG
      8310663 130 313 1 0.847
      0663 AAATCACAACCCAACCAAATCATTTCAATATGAT
      GTACTTCTTAACAAATCAATGCACAAATAATTTT
      AATCATAAATTCAGAACTTATGCAGTGAATATTC
      TCGTTGTTAAGTTATAAGGGGC GGGGGGAATC TT
      ATATATGTGATTTTTGGTATATGAACGTTTGGTTT
      GTGAATTGTGATTGTCAGATGGTA
      ACAACAGAGGATGCTCCAGGATATGCAAATGCA
      GAAAATGAAGTCTTCAGTTCGTTCAATGGGAAGA
      ATAAGGAAATCATATACCTATTTTTCATCTTTTAT
      ATTTATGCAGTCGTCTATGATGAATTGATGAGTG
      TTTTCCTGGCCATGTGTGTTGTTTTGGCTTCTGCT
      Gm08:831 TTGTAAACACAAGATAATAATACAGGCAC [A/C] A
      8311631 [A/C] 131 314 0.843 0.772
      1631 TAATAAACTGTATAATGACATGAAGATCAATATC
      TTTCTTTGAAGCTAAGAAAAATTGTTATAGCATG
      TAGCTACTTTTGTTGTCCCACAAATGTGTGGCAT
      GGAGCAATTTTTTAATATATTCAAAATATTTATTT
      TGTGGACTCGACAGTCTACATCTATTTTATGAAG
      TGTAGTGAATCCAACATCAAACCCCTTT
      AC TTTTGTTGTC CCACAAATGTGTGGCATGGAGC
      AATTTTTTAATATATTCAAAATATTTATTTTGTGG
      AC TC GACAGTC TACATC TATTTTATGAAGTGTAG
      TGAATC CAACATCAAACC CC TTTGTCC CACTTTA
      CAAAAACCCTCTGATCATTTGAACCTCCTAAATG
      Gm08:831 AATACAAAC TGTGTCCATAAAAAAAAATT [A/G] T
      8311906 [A/G] 132 315 0.824 0.62
      1906 TGTGTCCTACGTGCTT
      CACTAC CC TATTTTGTTTTTATCATGTTAAATATA
      TGAAAATAAATTATTGCCAAGTCCAAATTGTTTG
      CTACTATTGAAGCCTGCATTTGTCTCGATGTAAA
      ATAGTAGTACTTATCCAAACACAGTATCAGGTTG
      AAGCAAACTAGTTCATATTATTGATGAGA
      CCACCACAACTGTATGTTGAGGTCCATTGTCTGA
      TAGAAGACTGAGAGTTTAGGTGGGGCAACTTCG
      AGGAATATGTACCAAATATTTTAGATGTATGATT
      ATATCAACACACACACCTTTGCCTCTGTTCTCTCC
      TTTTTC TTTTGCCATGATAATAC CC TTCC TATAAT
      Gm08:831 8312536 133 316 0.924 0.824 CC TATTCAC CCAAC GC CACATTTGTTTTC [A/T] TG
      2536 TATACTTAAATGTGTGTTAAGGGTAAGGGCTTCA
      AATAAGAAACTTAGCTAAAACAGTTAAGTAACT
      ATTTACTCCCATCATTTTGCACAAATTTTTATGAA
      CTTAGATTTTACCAAAGGAGGGACAAAACTAAG
      AAC CAAAAAAWTATCATCATATTCAGAWGC CAC
      AACCAACCACATGTTTTCTATACATATTTT
      ATTTTGCACAAATTTTTATGAACTTAGATTTTACC
      AAAGGAGGGACAAAACTAAGAACCAAAAAAWT
      ATCATCATATTCAGAWGCCACAACCAACCACAT
      GTTTTCTATACATATTTTTTCAATATGGGGTACTA
      ACAAAAAAGTCTTATTTGGTATGGAATTTTTAAT
      Gm08:831 TACTCTATATTTATAGTATACAATATACTTG[A/G]
      8312819+ G/A+ 134 317 0.87 0.836
      2819 GACATATTAGAATTTTATCTTCCAAGAGCAACCT
      AATCTCAGTTATC TCATACATATGCAATC GC TTAT
      TAGCAGAGTAAATCAGWAGTCTTCACAGAAAAG
      AGAAAAAAAATCATCTGTAGCACATGGAAAATA
      ACATAATTTCCTTGTTGTCCAAAAGGTTTGGTGA
      AGTGC GC TCTATCAGC TTATCAC TAATGCAA
      GC TTC TTAGTGGAGAGTGGAAGRWAGGGTACAT
      CCAATCCAAGACACAGAACAGAAGAATGGCCTC
      AAAATCATCCACCATYARACTTGTTTGTTTCTGCT
      AC TTCATGC TCTTCAGC TCTATGCATTTCAC CAGC
      TGCACCGTGCTCTCATTGAAAAGTCATGCAAGCA
      Gm08:831 CATGCAATGGTTCCATAGCTGAATGCAATC [A/G]
      8313273 [A/G] 135 318 0.854 09
      3273 AGAAGATGAGCTGTTGATGGAGTCTGAAATAAG
      CC GAAGGTTTC TGGAGCAGAAGAGATCATACATT
      TCCAATGGAGCTTTACAGAGAGACAAACCAGTTT
      GTAATGGTGGTGGCTCTGGTGAAGCTTATAGTAA
      AACTGGAGGGTGTCTTCCTCCCCCCTCAAATCCT
      CAAAGTAGAGGCTGCTCTAAGTATTATCGTT
      AGGAAAGATCTATGATTGTATTAATTATCCGTTT
      CTTGTCATCTCCAATCTTTCTTTGTTCCATTATGC
      TRGATGGAATTTGATTTTTTCTTCTTTTTTTTTTGG
      GTGAAATGTTTTKGTAATGCACATAATGCAAC CA
      TAAGGTATAAATC CTC TTACACATTCTAC CTC GA
      Gm08:831 TATACATATTTAAATAATAAAATATAT [A/G] AAA
      8313923 [A/G] 136 319 0.655 0.806
      3923 ATATAGAATTATATAAAATGAGATTTTATTTTAA
      ACATATAAGAGTTCACRTGGGTAAAGTATTCACA
      TTCAC TTTACTATTAYCAAATAAAATTTGTS AGA
      AACATTTTCGGCTCAACATCATGCAATTAAACCA
      GAAACTTATGTCTCAATGTCAYATTCTATYAGAT
      CATTTTATTCYGACATCCTCCAACATA
      TTCTTCTTTTTTTTTTGGGTGAAATGTTTTKGTAA
      TGCACATAATGCAACCATAAGGTATAAATCCTCT
      TACACATTCTACCTCGATATACATATTTAAATAA
      TAAAATATATRAAAATATAGAATTATATAAAATG
      AGATTTTATTTTAAACATATAAGAGTTCACRTGG
      Gm08:831 GTAAAGTATTCACATTCACTTTACTATTA[C/T] CA
      8314010 137 320 0.842 0.823
      4010 AATAAAATTTGTSAGAAACATTTTCGGCTCAACA
      TCATGCAATTAAACCAGAAACTTATGTCTCAATG
      TCAYATTCTATYAGATCATTTTATTCYGACATC CT
      CCAACATAAGATTTCTTAAAGCAATCCATCTAGT
      CATTTGCTTCCACAAACACAAGGTTCGAGATCAT
      CACAAGATCCAAACACAAACAGCAYAC
      TGGGTGAAATGTTTTKGTAATGCACATAATGCAA
      CCATAAGGTATAAATCCTCTTACACATTCTACCT
      CGATATACATATTTAAATAATAAAATATATRAAA
      ATATAGAATTATATAAAATGAGATTTTATTTTAA
      ACATATAAGAGTTCACRTGGGTAAAGTATTCACA
      Gm08:831 8314025 [C/G] 138 321 0.817 0.808 TTCACTTTACTATTAYCAAATAAAATTTGT[C/G]A
      4025 GAAACATTTTCGGCTCAACATCATGCAATTAAAC
      CAGAAACTTATGTCTCAATGTCAYATTCTATYAG
      ATCATTTTATTCYGACATCCTCCAACATAAGATTT
      CTTAAAGCAATCCATCTAGTCATTTGCTTCCACA
      AACACAAGGTTCGAGATCATCACAAGATCCAAA
      CACAAACAGCAYACARGGAATGAGTTATC
      TAYCAAATAAAATTTGTSAGAAACATTTTCGGCT
      CAACATCATGCAATTAAACCAGAAACTTATGTCT
      CAATGTCAYATTCTATYAGATCATTTTATTCYGA
      CATCC TCCAACATAAGATTTC TTAAAGCAATC CA
      TCTAGTCATTTGCTTCCACAAACACAAGGTTCGA
      Gm08:831 GATCATCACAAGATCCAAACACAAACAGCA[C/T]
      8314208 139 322 0.757 0.829
      4208 ACARGGAATGAGTTATCACATTCCCAACTAATAG
      AGAGAAACGAGACAATATGTAGATATACATATT
      ATATAAATGAAATATARCTYACTYAAACATAGCT
      CACATCATTCCATCACTTATCGTGTAACATCACA
      TCTCAACACTACACATCTCACACATTTTCACATTA
      TTTACGTRCTCAAGGATCGAAACACAATAT
      YAGATCATTTTATTCYGACATCCTCCAACATAAG
      ATTTCTTAAAGCAATCCATCTAGTCATTTGCTTCC
      ACAAACACAAGGTTCGAGATCATCACAAGATCC
      AAACACAAACAGCAYACARGGAATGAGTTATCA
      CATTCCCAACTAATAGAGAGAAACGAGACAATA
      Gm08:831 TGTAGATATACATATTATATAAATGAAATATA+A/
      8314292 [A/G] 140 323 1 0.715
      4292 G+ CTYACTYAAACATAGCTCACATCATTCCATCAC
      TTATCGTGTAACATCACATCTCAACACTACACAT
      CTCACACATTTTCACATTATTTACGTRCTCAAGGA
      TCGAAACACAATATCACTCAACCAATCAATATCG
      AYCAATRCACAAGCGTTATGCAACAAATATACTA
      AGACTTAATCCTATATGTAATGTGGTATCA
      ATCATTTTATTCYGACATCCTCCAACATAAGATTT
      CTTAAAGCAATCCATCTAGTCATTTGCTTCCACA
      AACACAAGGTTCGAGATCATCACAAGATCCAAA
      CACAAACAGCAYACARGGAATGAGTTATCACAT
      TCCCAACTAATAGAGAGAAACGAGACAATATGT
      Gm08:831 AGATATACATATTATATAAATGAAATATARCT+C/
      8314295 [C/T] 141 324 1 0.715
      4295 T+ACTYAAACATAGCTCACATCATTCCATCACTTA
      TCGTGTAACATCACATCTCAACACTACACATCTC
      ACACATTTTCACATTATTTACGTRCTCAAGGATC
      GAAACACAATATCAC TCAAC CAATCAATATC GAY
      CAATRCACAAGCGTTATGCAACAAATATACTAAG
      AC TTAATCC TATATGTAATGTGGTATCATGT
      ATCATTCCATCACTTATCGTGTAACATCACATCTC
      AACACTACACATCTCACACATTTTCACATTATTTA
      CGTRCTCAAGGATCGAAACACAATATCACTCAAC
      CAATCAATATCGAYCAATRCACAAGCGTTATGCA
      ACAAATATACTAAGACTTAATCCTATATGTAATG
      Gm08:831 TGGTATCATGTYAGTGAAAAATCTCATC [A/G] GG
      8314513 [A/G] 142 325 1 0.895
      4513 CGCCTAGAAGTATATGACAAGATAAACCACACA
      CTGGTAAGTCAGGTCACTCTCAYTAGATAAAATC
      ATAAGGAGATTAGTTAGGGTCACTCTRTTTTGCG
      AGAACACTTCAATCATACGAAATCAACATAGGTT
      TCAAGGAACATTCAAACC GAGTATATTTAC CC CT
      AAGGCCTACACTCTAAAGAGTCCGTTAGG
      GATAAACCACACACTGGTAAGTCAGGTCACTCTC
      AYTAGATAAAATCATAAGGAGATTAGTTAGGGT
      CACTC TRTTTTGC GAGAACAC TTCAATCATAC GA
      AATCAACATAGGTTTCAAGGAACATTCAAACCGA
      GTATATTTAC CC CTAAGGCC TACAC TCTAAAGAG
      Gm08:831 8314736 143 326 0.871 0.614 TCCGTTAGGACCTCTCCCTCTTGATTCAGGT[C/T]
      4736 CAACCTAGAAAATATTTTAGCACCYAGACTCTAT
      TTATGAACTGTACAAAACACYCGACTCCTCAATT
      GTTC TCAAAATAATTTTATCTCATCGC GC CTCAA
      AGTGATTAAACTCGTCGAGTTYCCACAATGGTTC
      TCATCACAATAC TC GTCGCACATTAAC TCATC GT
      TCTGAAAGGGTCTTATAGTCGTGTGGTGGT
      ATTAGTTAGGGTCACTCTRTTTTGCGAGAACACT
      TCAATCATACGAAATCAACATAGGTTTCAAGGAA
      CATTCAAACC GAGTATATTTAC C CCTAAGGCC TA
      CACTC TAAAGAGTC C GTTAGGACC TCTC CCTC TT
      GATTCAGGTYCAACCTAGAAAATATTTTAGCACC
      Gm08:831 YAGACTCTATTTATGAACTGTACAAAACAC [C/T] C
      8314791 144 327 0.884 0.688
      4791 GACTCCTCAATTGTTCTCAAAATAATTTTATCTCA
      TCGC GC CTCAAAGTGATTAAAC TCGTC GAGTTYC
      CACAATGGTTCTCATCACAATACTCGTCGCACAT
      TAACTCATCGTTCTGAAAGGGTCTTATAGTCGTG
      TGGTGGTAYGGTACATAACTCAAAACTCCATGCA
      CACAATATTTCAATACACATGTATTTTA
      ATTCAAAC C GAGTATATTTAC CC CTAAGGCC TAC
      AC TC TAAAGAGTC CGTTAGGAC CTC TCC CTC TTG
      ATTCAGGTYCAACCTAGAAAATATTTTAGCACCY
      AGACTCTATTTATGAACTGTACAAAACACYCGAC
      TCCTCAATTGTTCTCAAAATAATTTTATCTCATCG
      Gm08:831 CGCCTCAAAGTGATTAAACTCGTCGAGTT[C/T] CC
      8314860 145 328 0.912 0.715
      4860 ACAATGGTTCTCATCACAATACTCGTCGCACATT
      AACTCATCGTTCTGAAAGGGTCTTATAGTCGTGT
      GGTGGTAYGGTACATAACTCAAAACTCCATGCAC
      ACAATATTTCAATACACATGTATTTTAYAATTCA
      ACAYGCAC TCAATTTATCACATAC GC TCAATC TC
      GTTATAATCTCAATATAACAATTTATCA
      GTTTATTCTAACCTCAATTGCGATAAACTCATCTC
      TTACCTCTAAGYAGGCTCACATGTGTAGTCYGAC
      AACGATAGTGACGTTTCTAGCGATTTCCTAAGAT
      TCTTCAAAATTTTCCTAAGATTTTCTAACRTYAGA
      GAAAAAGAGAAAGGATTATAACCTATATTTCACT
      Gm08:831 GTCTCCGTCTCCRTGCGAGGGACATTTC [A/T] CTA
      8315543 [A/T] 146 329 0.825 0.756
      5543 AC TGAAGACATTGTTTCACAAATCC TAAYAGTGG
      GATTGTGAGAAAATGAGTTTYAAACCTGATTTTT
      AAATTTCACAATGATTCAATGGTTAATGARTCCG
      AGATCATAGTTTTAATGGRACAAGTTTGGATGTA
      TGCAGGAAGAGCATCTTGTGAGGGACATTGTTCT
      CACCACAGACATTATTTAAAAATTCCA
      ATTCTTCAAAATTTTCCTAAGATTTTCTAACRTYA
      GAGAAAAAGAGAAAGGATTATAACCTATATTTC
      AC TGTC TCC GTCTC CRTGCGAGGGACATTTCWCT
      AACTGAAGACATTGTTTCACAAATCCTAAYAGTG
      GGATTGTGAGAAAATGAGTTTYAAACCTGATTTT
      Gm08:831 TAAATTTCACAATGATTCAATGGTTAATGA[A/G]T
      8315644 [G/A] 147 330 0.929 0.786
      5644 CC GAGATCATAGTTTTAATGGRACAAGTTTGGAT
      GTATGCAGGAAGAGCATCTTGTGAGGGACATTGT
      TCTCACCACAGACATTATTTAAAAATTCCAAC GA
      TGGGAATGTGAGAAAATGAGTTTGGAACTTGGTG
      TTCAAATTTCATGATAATTCAATGATTAACGAGT
      ATAGGATCGTAGTTTTACCTGATAGGTTT
      TAGAAATATATTATGTGTAAAATCTGATCTAATA
      TRTCTATTTATAGATATS GTACTCTYAATTTATTA
      TTTACTCTAKCTTTTCTTTATTTTATTATTTTATW
      AAAAAAATTCTATTTTTACTCCCTATCAAATGAA
      TAAATAAAATATTCTTTTTTATTTTCCTTCAAAYT
      Gm08:831 8316113 148 331 1 0.85 ATTATTTTAATTAATAAAATTATTTTT[C/T]CTAAT
      6113 TTATTTAATTATAAAAATCTTATTATTTTTCAAAA
      AC TC TATTTATTTTTAAATAAAATGCTTTTWAATT
      TATTTAAAAAAAGACGAGATGTTACAAATGTTTG
      AAGCACACTTTGCAATGTTATAAATGTTGACCTC
      AGACATCAATTGCAATATACACACCATAAAACA
      ACATATGAAGTACACGTATGAGAT
      GC TC GAATATAATGAATC TAAACATATATGAAAA
      ATCAGTAACTGACCTTTTCGACACAGTCACATGA
      ACAAACTCGCAGCAACAACGCATACACTAGTAA
      CAGCAGTCARCGCACTCTCTTGAGAAAATTTGAT
      GTAAATGTATTTATAACTTTGTGACAAATATTTTT
      Gm08:831 TTTC CC TCATTC CACACAGGAATAAAAAGT [A/G] T
      8316689 [G/A] 149 332 0.896 0.63
      6689 CCAAGTGAGTGAAAGAGATGAGGAATAGATAGA
      CWTCTTTCTCCTTATTTTAAAATCCCAAGAAACT
      AATTACCTAGAACATTTGTAACAAAAACTAGTGT
      TAATTTATTTC CATTTATC CC TTTTC TC TCTGC TTT
      ATTTRTGGGAWGCTATAAAGAACGCTCTTCTCTC
      CTGAAAATTGCTMATTTAAGAAATTATT
      GTGAAAGAGATGAGGAATAGATAGACWTCTTTC
      TCC TTATTTTAAAATCC CAAGAAACTAATTAC CT
      AGAACATTTGTAACAAAAACTAGTGTTAATTTAT
      TTCCATTTATC CC TTTTC TCTC TGCTTTATTTRTGG
      GAWGCTATAAAGAACGCTCTTCTCTCCTGAAAAT
      Gm08:831 TGCTMATTTAAGAAATTATTTTCGAAGGA[A/C]C
      8316899 [C/A] 150 333 0.895 0.737
      6899 ACATTTTAATCTGTTAGAAATAGCCMAAAAAAA
      ATAGACAGAAAAATTACTCTAATTTTTTTTTTTTT
      TKGAATGATTGACTAGTCAAATTAACTCCAGTAA
      ACAAACAAGCAGCGGCGGGTTGAACATGAATAA
      CTTTCAATATGCC CC TTTGTTAAGCTAAAAGATT
      AC CC TAACATGGAAGTTTATGC TACATATA
      CATTTTGTCATTATACTTTGCACGAAGTGGGTCAT
      TGTAAGTCCACCTGTATTACAATTCAACAATAAC
      AAGAATGTCGAATAATTTTAGTATTTTACAGCAG
      TTAATATGTAAGTATAAAATGCTACTTGCAGTAG
      AAGAAAC CC TTTTTTCAGGGGAAGGGGAGGTC TG
      Gm08:831 GAC TC TGGAGGTTAGTTGCAC GTTAAGCA[A/G] A
      8317852 [A/G] 151 334 0.924 0.776
      7852 ATGAATC SC TATCATCAATGTGTTAACAAATCCA
      AAATTCTTGGTAAGGGAGAAATATCGGACAGAA
      AAAAAATTAAGATGTCAGAAAGCCAATGCAGAA
      TTTTCTCAGCAAATACATTGAATGCTGCCTTAAC
      ATACTAAAAC CC CATTATTC GAAAGATGATTATC
      AATATTTAATARCATGACTGCAAGCCTATCA
      ATTATACTTTGCACGAAGTGGGTCATTGTAAGTC
      CACCTGTATTACAATTCAACAATAACAAGAATGT
      CGAATAATTTTAGTATTTTACAGCAGTTAATATG
      TAAGTATAAAATGCTACTTGCAGTAGAAGAAACC
      CTTTTTTCAGGGGAAGGGGAGGTCTGGACTCTGG
      Gm08:831 [C/G] 152 335 0.924 0.923 AGGTTAGTTGCACGTTAAGCARAATGAATC [C/G]
      8317861
      7861 CTATCATCAATGTGTTAACAAATCCAAAATTCTT
      GGTAAGGGAGAAATATCGGACAGAAAAAAAATT
      AAGATGTCAGAAAGCCAATGCAGAATTTTCTCAG
      CAAATACATTGAATGCTGCCTTAACATACTAAAA
      CCCCATTATTCGAAAGATGATTATCAATATTTAA
      TARCATGACTGCAAGCCTATCAACCAACAAT
      GTTAGTTGCAC GTTAAGCARAATGAATC SC TATC
      ATCAATGTGTTAACAAATCCAAAATTCTTGGTAA
      GGGAGAAATATCGGACAGAAAAAAAATTAAGAT
      GTCAGAAAGCCAATGCAGAATTTTCTCAGCAAAT
      ACATTGAATGC TGCC TTAACATACTAAAAC CC CA
      Gm08:831 8318033 [A/G] 153 336 0.912 0.809 TTATTC GAAAGATGATTATCAATATTTAATA [A/G]
      8033 CATGACTGCAAGCCTATCAACCAACAATACATGA
      AAAAATTCTGGTGTGATAAAAAAAATTGTGTAGA
      CTCCTTTTAATGTCATAAAATCAGAAGTGTGGCA
      GAATCAGTCTAACATGTTACATCAACATTGAAAA
      CATAAACAGATTCAGGACTCTGTAGATAATAAAT
      GTAGCATTTCAGATATTCTCAGAACAGAGA
      AACCCAAAAGTACTATGAAAACAGATGAGCATA
      AC TCATGAGCATGCACTTTTGTCAAGATCTCAAA
      CCATATCAAGGGCTGCTAATAAACAACTCATTTA
      AATTGTGAGTTGTGACATGCAATATGATCCCTTC
      TTACTGTCCAGCTAAATTCACATAGAAGTCAAGG
      Gm08:831 GAGTCAGGGTAAAGTTGACAAACTAAGAACG+C/
      8319087 [C/T] 154 337 1 0.857
      9087 T+TGTAAACAATAAACTTCAAGCCAAGTACATAT
      TTCTACAAAATGAATGCCAAAAAAATAAAATAA
      GATTTGTGAGATGGCATAATTATGCTTACTCTAA
      ATGAAATATGTCTTTTAACTATATTCCTTCCAATC
      AACTCTCCCTCTTGAACCTCAATCTCACCCACAA
      TCAAATTCCTAAATAAGCAAAATGATAGGTAC
      TTCTCCCAGCCCAAGCCTAATTCCACCCTACCTTG
      TACACAC CC TTCTC GGGCTAATGTTCTC TGTC TTC
      TTACAACAAGCCCACATGCACTCCTCCCATGCTC
      TGCTACAGGGTTGACAGTTGGTTATATCTCTCTCC
      TAAAATTGATCAAGTGAACCTTTTGCCTATCCTT
      Gm08:831 ACATACACCTTATTTTGTGATCTTGGG[C/T]CTTG
      8319642 [C/T] 155 338 0.853 0.531
      9642 RGGCCTCCATCASAAAACCATTCTTCATAAAAAC
      TCTCATTTCACTCTTCTGATGACTAATAGCAGAA
      AATTTTTTAGATAACAAGAGAAAAAGAAATCTTA
      AATGAACATTTCACTATTGRCATGAGCATCTCAA
      TATCATCACATGAATC CGAGATCATTTTGGAC CA
      GTGCCATAGCAGATGAACTTCATAAG
      CCAGCCCAAGCCTAATTCCACCCTACCTTGTACA
      CACCCTTCTCGGGCTAATGTTCTCTGTCTTCTTAC
      AACAAGCCCACATGCACTCCTCCCATGCTCTGCT
      ACAGGGTTGACAGTTGGTTATATCTCTCTCCTAA
      AATTGATCAAGTGAACCTTTTGCCTATCCTTACAT
      Gm08:831 ACACCTTATTTTGTGATCTTGGGYCTTG[A/G]GGC
      8319647 [G/A] 156 339 0.853 0.587
      9647 CTCCATCASAAAACCATTCTTCATAAAAACTCTC
      ATTTCACTCTTCTGATGACTAATAGCAGAAAATT
      TTTTAGATAACAAGAGAAAAAGAAATCTTAAAT
      GAACATTTCACTATTGRCATGAGCATCTCAATAT
      CATCACATGAATCCGAGATCATTTTGGACCAGTG
      CCATAGCAGATGAACTTCATAAGTAAAT
      TTTTTCTCAGGATAAAACAACAAAAAACTAATAC
      CAAAGAATAGAATAAACAATCTACCACTATTCTT
      GAAACCGAAAGATATAGAACATAGGAGAAATTG
      AACTTACGGGTTATTCCAATCAGTAGTATCCTCA
      TTGACAAGATGGGTCCACTTGGTTCTTCCACTAC
      Gm08:832 GACCAAAGTGCTTAACTTGCATAACCTTTGG[C/T]
      8320068 [C/T] 157 340 1 0.837
      0068 AATATTGTCTTGTCCATTTTATCCTCCCCAGTTGG
      GGCAGAGAAATCACGAGCGAAAATACCATCAGA
      TCCAACGGTGGCAGCTCGGTCATCAGATTCATTC
      TGGAAGAAAGCACCTTTGTGATAGTATTTCTGCA
      TAAATCTCCATTTCTGCTTTGGTGGTGGAGCAGG
      TTTGGGATTCCTCCTTTCCCACTCCCTCCT
      TCATCAGCCCATTCAGGAACTTTACCGGGCCAAT
      AACGCTTAACTTTAGTTTGGCCAATTTTACCTCTG
      AGCTTATCCCTAATGGCTATTACAGTATCACTAA
      CACCCGCTGTCACCGACATTGTTCTTCCTCAATTG
      AACGCCAAACCCTATATTGCACAGATGCATAGTA
      Gm08:832 8321253 [C/A] 158 341 0.919 0.773 AATCGGTAAAATGTTTGTTTACACAGCA[A/C]AG
      1253 AAACAGAAGATTCCAGATTAAATAGCAAGAAAA
      TAAATAAATGAATCAAGAAACACAGAAAGATCA
      ATAGTGAATGATAAATTTTGATATGCGAAACATT
      GGAAGGGTTTGTGTTCSAAACACTAACACTTGAA
      TTGTTAGAGAGAATAGAAGAAAAGTTWGAAGGA
      CTTACAATTACAGCGACCGGAAGGAACCCTC
      CCCTCTCTGTCTCTGTCCCGTTCCAGGCAGCGCGT
      CGCCCCACCCCAGCTTGTTCTGTGAACTTTTATTT
      GATTTACTTTCTATAGTATTTATTTTTGTTTTTATG
      AGTATGTAAATGACATCTTTATACGAATATTATG
      TTTTCATTAAATAATAATAATAATAAATTTCTTAA
      Gm08:832 AATTAAATATATATACACTAATGCT[A/C]ATAAA
      8321649 [C/A] 159 342 1 1
      1649 AAAATTGAACGAATATCATATTTATTAAAACTAA
      TTTTTTTATACTAAACTAAAAATAATTTAAAATTT
      ATTATTATTATTATTATAAAGATATTTAAATTTTA
      TATTTTGGAATTGTATATATAAGATAAAATACAT
      TTAAGTTTCCTAAGTTACAACTTTCGCATCGGTTA
      CATTTTAMAGGWTATATATATA
      ATGTCTTTGTCCAAGGCTTGCTAACAAAAAAGGA
      GATTGCAAGATCAATAAAATACCTTACAATAATG
      AGAGACAAAGGGTTTTCAGTAGATGCTGCTACCA
      CAGAAATTACTATCAACTACTTATCTACTAATGA
      AGGAGACACCAGAATTCGAGAATTTTTTTTTCCA
      Gm08:832 AAA AGATAGCAAATGCCAAGAGTTTCACTT[A/G]
      8323937 [G/A] 160 343 1 0.918
      3937 GACATTTATTCAAATCCTGACTCTCAATTCATCCA
      TGTTCCACAATCCTATAGGACCCCATAGAGAGAA
      CTGGCATAGGCTTCAGAACTTACMATTTGTTAAA
      TATATAAAATCATTACCATTCAAGTGCWTCCACC
      TGACAATTTATGTGATTAGGAGAGTTGGTCCTTA
      ACAGGTATCACAACCTTTAAGAAATTATG
      TTGATCCTTGTTGCTTCTCTTCTTCATAATTAACT
      TATATTTGAGCCCAAGGTAAAGTGGGTTTGTGCA
      TTGTCCRCACTTCAAGCTCAAAAAGCTCTGTTTTA
      AGGGGGTCTTAGATATAAATCTTTCTTAGCTCCA
      CCAATCAGCTTAAGCTGTGAATAGAATTGTTC CT
      Gm08:832 TGACATTTTTAGTGGTAAGTATTTTCAC +A/C + TC T
      8324341 [C/A] 161 344 0.929 0.787
      4341 GC TTGCACATTTATTTTGATATAACC TCAAGTTAT
      TAAAATAGCTTAAAAAAATAGACCTATATACAAT
      TTAGAAATTGTGCTGTATCCTTGCATTTTTATGGA
      AC TGAGTAATTTTTTAC TTATGTATATTTGC CTTC
      AAGTAAGTTTAATAATGAAGCAAGTTGCATTAGG
      GATAAGCCAATCAATATTGCTAGT
      TGTTATTTTATATTTTGTTTCCTTTCTTGTGTATTT
      TACTTTTCTGTTTTAGGAGGATTCCTGATCCTTCT
      GCACTGTACTCCTTTTCTCTCCTAGTTCATTGTTT
      GTGATGGGAAWTTTTTTTCCATATTTATTACCTGT
      TAGGAGACGAAAATCTAAGATCTAATTTATGGAT
      Gm08:832 GC TTGC TGTC CTTTC TGCAAAC GTN[A/T] TTTTTTT
      8325127 162 345 0.829 0.706
      5127 TTTTTAC TTTTGACAGTTTTCC CC CCATTTAAAAT
      AACAGTTTGACTTCATGGTTCTTGGTTTGCAGATT
      GAAATCACTYTATGCACTCATTTTGTTATAACTTA
      TGTGCGAGGAAGACCGCAAATAGTTCAGCGATG
      GATCATAGAAGGTTAGTCAAACATTTTTTCTTTG
      CAATATCTGCTCAGCTTGTTT
      CTCTCCTAGTTCATTGTTTGTGATGGGAAWTTTTT
      TTCCATATTTATTACCTGTTAGGAGACGAAAATC
      TAAGATCTAATTTATGGATGCTTGCTGTCCTTTCT
      GCAAACGTNWTTTTTTTTTTTTACTTTTGACAGTT
      TTCC CC CCATTTAAAATAACAGTTTGAC TTCATG
      Gm08:832 8325214 163 346 0.929 0.837 GTTCTTGGTTTGCAGATTGAAATCACT[C/T]TATG
      5214 CACTCATTTTGTTATAACTTATGTGCGAGGAAGA
      CC GCAAATAGTTCAGC GATGGATCATAGAAGGTT
      AGTCAAACATTTTTTCTTTGCAATATCTGCTCAGC
      TTGTTTTTTGTAATTCAAATTTTTTAGCATCATAA
      GTTGTTCGTTTGAAATTTTGAATGAATATTTATCT
      GTTAAGTTATATTTCACTTTTCT
      AATATATTTATCTCAGAATAATGCTTTGACTTTTA
      CAATGTTCC CC TCACAAAATTGATC TCTTTAAAA
      AATAAAAAATAAAAACTTTGGAGTTTGTCCAGCT
      TGGCTCCAATCTTAACCAAAGCAGCATTAAAGCT
      TTGAAGTATAGAGCAAAAGTACACCATATTAGGC
      Gm08:832 TAATCAATGAAAAGGTACAAAGCTC CC GT [C/T]A
      832606 [C/T] 164 347 1 0.768
      6696 GATTTTGAACTAGRCAGATAACTAAGNGAGTGTT
      TAGTTTGGTTGTTTTTTGATTTTATTTTCACTGAA
      AATARAAAACGGTGATGAAAATGTGTTTGGTTTG
      ATTTCTGAAAACATTTTCRGTAAAAATGAAAACA
      GTAAACAACTAGAAAATGAAAACAAAAAATTTT
      CGTTTTCAGWATTTTCAGTTGAGAACAGA
      AAAGGTACAAAGC TC CC GTYAGATTTTGAAC TAG
      RCAGATAACTAAGNGAGTGTTTAGTTTGGTTGTT
      TTTTGATTTTATTTTCACTGAAAATARAAAACGGT
      GATGAAAATGTGTTTGGTTTGATTTCTGAAAACA
      TTTTCRGTAAAAATGAAAACAGTAAACAACTAGA
      Gm08:832 AAATGAAAACAAAAAATTTTC GTTTTCAG[A/T] AT
      8326877 165 348 0.884 0.808
      6877 TTTCAGTTGAGAACAGAAACCTCATTTTGGTTAA
      AATGAAATTGYGGTGACAATAAATGTAGTTTTAA
      RCAAATCTAAAAATACAAAAAGACAATAAGTCA
      ATATATCATAAATTTTCAGTATTTTTATTTCATRA
      AAACAGAAAACAAGAAATCAAACCAAACATRTT
      TTCAGAATTTAAATCTTTTGAAAATAAAA
      TCTCTTCAAAAGCCAAGTCCTTGGTTAGGACAGT
      GGTACTTAACATGGTTAATGCAAATGGTTTGTWG
      CAAATTCATAATAGACCTTTCAACCAGCTTTTGG
      CTCATTTTATTGCATTAGTCTTATTTGTTTTGGAG
      AATTTCTTTTATTTTTTTGGTAACTAGCAGATTTC
      Gm08:832 TTATC CTC CTC CTAGTTGTGC TTCTC TT [A/T] TC TC
      8328633 166 349 0.919 0.651 TTTAATGAATTTCCTCCTATGTAAAAAGCAATAG
      8633 AAAAAGAAAACCAGTTTTAAAAAAATAAAATAA
      AAGAACTAATTTCAGGTACCTTCTTCCATTTTGCA
      ATTAGATTGCGGTCAGCATATCCTTGATCTAAAC
      AGAATTCATACAGTTCTTTAGAAATTTCCTTCCTC
      CGATGGTATAGATCAAATATGTAGC
      TAAGTAAATCTAGAAAATATATAACTTTTGACAA
      AAAAATTATATCACTATTTAAATATATCTTTTTTC
      CTTTGTTTCTTATTTCCTAAATAAATTTTTTTATTA
      AATTTATTAACAAAAATTTCTCATAATTAACGAA
      TGAGGTTAAAAATAATAAAAAAATGAYAAATAT
      AATAAAAACAAATTAAATTTAAAGAC TT [A/G] AA
      Gm08:833
      8330929 [G/A] 167 350 1 0.789 ACATAATTTTTKTGTCWCATGAAAATATTTTTTTT
      0929 ATTCTAAACAAATTGTTTAAAGATAATRAAAATA
      TCATTTTTTTAAATCCTAWAAATATACCARATAA
      CTATAATTATTTAAATTAAATCACTCTAGCATAT
      ATTTTTAATAAATCAAATTAATATATACAAATAT
      TTTAATTTACTTTAAATTTAAAGATAA
      ACATAATTTTTKTGTCWCATGAAAATATTTTTTTT
      ATTCTAAACAAATTGTTTAAAGATAATRAAAATA
      TCATTTTTTTAAATCCTAWAAATATACCARATAA
      CTATAATTATTTAAATTAAATCACTCTAGCATAT
      ATTTTTAATAAATCAAATTAATATATACAAATAT
      Gm08:833 8331132 [C/T] 168 351 1 0.657 TTTAATTTACTTTAAATTTAAAGATAATA[C/T] GA
      1132 TAATATAAATATAGTAAAATTTTATAGAATTTTT
      AAACAATATTTTYCATTTATCTTTTTTTTTTCTTTT
      ATCTCTCTAGTTGCATGGAGCATGAGCCAACTTC
      CTAGTTTATTGTATATTTTCGTGATAATGTTGTGG
      CATTTGTTAGACATTTTAAAATATTAAATCTTATT
      AATTATTTTWAAATCATATTTATA
      GTTTAAAGATAATRAAAATATCATTTTTTTAAAT
      CC TAWAAATATACCARATAAC TATAATTATTTAA
      ATTAAATCACTCTAGCATATATTTTTAATAAATC
      AAATTAATATATACAAATATTTTAATTTACTTTAA
      ATTTAAAGATAATAYGATAATATAAATATAGTAA
      Gm08:833 AATTTTATAGAATTTTTAAACAATATTTT[C/T] CA
      8331181 [C/T] 10 352 0.87 0.612
      1181 TTTATCTTTTTTTTTTCTTTTATCTCTCTAGTTGCA
      TGGAGCATGAGCCAACTTCCTAGTTTATTGTATA
      TTTTCGTGATAATGTTGTGGCATTTGTTAGACATT
      TTAAAATATTAAATCTTATTAATTATTTTWAAAT
      CATATTTATATGAAAAATATGATTTTTTATTTAAT
      CTTTCTAGAAAAATCTTAATGTAT
      TCTCTAGTTGCATGGAGCATGAGCCAACTTCCTA
      GTTTATTGTATATTTTCGTGATAATGTTGTGGCAT
      TTGTTAGACATTTTAAAATATTAAATCTTATTAAT
      TATTTTWAAATCATATTTATATGAAAAATATGAT
      TTTTTATTTAATCTTTCTAGAAAAATCTTAATGTA
      Gm08:833 TCCACTTCCAACTTTTACATTTAAAAT[C/T]CCATT
      8331408 [C/T] 170 353 0.842 0.771
      1408 ATATATTTTTTTTCTAATTAACCTTCTCTAACAAT
      TGTTCAACACTTTCTTCCTAAACCTCTATTTCAGT
      TTC TCTC CC TCTTC GGTC TTCC CATTGAATTC CAG
      GATTTTACATACAAAAAATTTGWTAGTTTTGTTG
      TCTTGACAAGTTTTCGGAGGATTTGTTAAATTC TA
      AAGGACTTATGCACTACGTTG
      CGTGATGTCACTCATCTCATATTATCTATTTTGTG
      AC TAAC TCATGAATTTATGATAGATTGATGATCG
      GTGATTTTGGCCTACTACAATAACAATTTTAACTT
      TTAAGGAATAATC CC GAC CACTTTAAGGTATATT
      AATATATTAATTATTTTTTTCTCCAATCTTAATTT
      Gm08:833 AATTTGTTTGATGGTAATGAATCAGAT +A/C +AAC G
      8331827 [C/A] 171 354 0.838 0.772
      1827 ATTTTGGGACTGTTGTTGTTGTTCCATTTTCAGTT
      TTTTATTTTGTTTATGACTAGTTGAGTTTGYAATC
      GGTTCTTGCTCGGTGATTTTAGAGGTTTTGGACAT
      GATTTTAGAGTATGTTGTATTGTGTAAAACTTTGT
      TGCAATCTCGTGTGGTTAAATGGGTGTTAGGATG
      TGAAAATTTTATGTCTAAAATT
      AATACACTTGTGCATTCAAATATCCATAATAGTT
      AATAACAACAACTTATTCAATATACTATATTATC
      TAGGGTCACTAGATTAAACCCACTTCTAAAAAAA
      TCTTAAAACATCCAAATTTTATTAATACGTTATCT
      TGAACATACTTTCTTCTATAAATGTTAAAATTTAT
      Gm08:833 TTGAAAATTTGAAATCTTAGAAGGTCTC [A/G] TAC
      8332651 [A/G] 172 355 1 0.836
      2651 TTTAATTAATAAATATCTTTTATAATTTTTMATGA
      ATAGTACAATCAAGTGTGTTAAAAAATATTTTCT
      TGAAACTCCTCTAAATTTAATGCTACAAAAATTA
      CTTTTTCTTGCTTTCTCTTCAAACTTAGTGAGCAT
      TTTTGCACTCTTAAATTATGTTTGTCAAAATATTT
      GAATTGATTTTTAGTTTTTTTATT
      AATAACAACAACTTATTCAATATACTATATTATC
      TAGGGTCACTAGATTAAACCCACTTCTAAAAAAA
      TCTTAAAACATCCAAATTTTATTAATACGTTATCT
      TGAACATACTTTCTTCTATAAATGTTAAAATTTAT
      TTGAAAATTTGAAATC TTAGAAGGTCTC RTAC TT
      Gm08:833 8332685 [C/A] 173 356 0.857 0.772 TAATTAATAAATATC TTTTATAATTTTT [A/C] ATG
      2685 AATAGTACAATCAAGTGTGTTAAAAAATATTTTC
      TTGAAACTCCTCTAAATTTAATGCTACAAAAATT
      ACTTTTTCTTGCTTTCTCTTCAAACTTAGTGAGCA
      TTTTTGCACTCTTAAATTATGTTTGTCAAAATATT
      TGAATTGATTTTTAGTTTTTTTATTAACAGAAAAG
      TTTATTTAGTTGTTTGATAAAGAA
      ACTTTTTCTTGCTTTCTCTTCAAACTTAGTGAGCA
      TTTTTGCACTCTTAAATTATGTTTGTCAAAATATT
      TGAATTGATTTTTAGTTTTTTTATTAACAGAAAAG
      TTTATTTAGTTGTTTGATAAAGAAGTTTTTTAAAT
      AATTTTTAACATTTTTTTAAACACTACTTCAAGTA
      Gm08:833 ATATTTTTWAAAATATTATTTATTT[C/T] TTCATAT
      8332957 174 357 0.902 0.787
      2957 ATTCTYTTTTTATTTATTTTTAATATATTTATCAA
      ATTTATTATTTATCCTTTTTAAGCAAATCATTATT
      TTATTATTTTWAAGTTATTTTATATTTTTTAAC TA
      TTTCAAAAACTAATTTTATCACACACTTAATTTTA
      ATAAATTAATTTTTTAACTTCCAACTAATTTATTA
      GTTTTCAGCTAATTTTAT
      TGATTTTTCTGCATCTGAAACAATTTGAAATTTCA
      AAATTTCTCTTTTCTTTACGAGGTCATCAAAGCAC
      AAAGC TAACAAATTC CC TAGAAGAGGGTGCATA
      AAACTCCAACCTGTTTCCTCTGTTTTTTCCCTTGC
      AATTATTACTCTTTTTTATTGRTAGAAATTGAATT
      Gm08:834 RTTGAARTATAAATGTGAAATAAAGTC [C/T] CAC
      8343167 [C/T] 175 358 0.904 0.883
      3167 ATCCAATAAAAATAAAAAAATTTAACATCATATA
      AGTAAAAATAACTAAATCTTAAAGTTTTTAAATT
      GC TATTCTC TTTCATGTAAAGATAAAACACATAA
      ATCTAACTCTTAAAGTCTCTTGATTACTATTTTTC
      ATCTTTCATGATATAAGTGATGATTTAGCCTCTA
      GATTTCATGGTGATTATAGAAGTGTA
      CAAGATAGGACCTTTTTACTTTGTTGGTCTATTAA
      TATCCAAGTTGTTCATGCTTATTTTCACACCTAAC
      ATTAGCTTATTCAAGATTCTTAATAAAATATTAG
      GGAAAATATCATGAAACTTTTATCAAAATTGTTT
      ATTTGTCGTTGACGTTTTTGGAAACATCTCAATA
      Gm08:834 GTGACTTGTTACTCAATCAATCTTTACT[A/G]GCA
      8345187 [A/G] 176 359 0.933 0.799
      5187 CTCTCATACTTGGTTTTCGTTATTCCTGTTTTCAA
      ACCACATACTTTGACTAATGGACTATGAATGAGG
      CTGCGTATAAAAATACAATTGGCGTATTCGAGAT
      GCAAATTGTGTTATTGGCCTCTTGTCCTTTTCCAG
      ATCAGTATTGAGAAGTTCAGGCAAGGCTTGTATT
      GAATCTGACTCTGACAGATACATAA
      ATACGACTTTTWCTTGTTGCCACTCTTTACCAAC
      AGCATTCAAGACGTACGTTAGGATATTCAAATCC
      AATGCGTCACTGAGGAACTTTTGCACTCATTTTTT
      CACGCAAAAACAGAGAATCATCCAGCACAGAGT
      CTTGCAAAAATTGATGTGAAACAAGAATGCTCTG
      Gm08:834 AGCCTAAATTGGATCAATGTGCATGCTAAA[A/G]
      8345720[A/G]177 360 0.871 0.587
      5720 TTTAGACCCATATMKTATKGGGAAGTTTTTATCC
      CTTAGTCGCTTTTGTCTTTTTCCTTTCCTTTTTCTA
      AGCAACAAACCATATTGTTTTATAATTTGGGCGA
      GGTCTAAATTCGTTTTATCATTGTAACAAAAACT
      AAAGAAATTAAAGCAAACGATTTCATAGGCTATT
      TGGGAGCTATGTTTTATGAGGTTAATAA
      AAATTCGTTTTATCATTGTAACAAAAACTAAAGA
      AATTAAAGCAAACGATTTCATAGGCTATTTGGGA
      GCTATGTTTTATGAGGTTAATAACAAAATAGGAA
      TCTCTTGATTTTAAGAATGAACAATTTTTTTTTCA
      CTATGAAAGGAGTCCTGAACATTATAATTGGATT
      Gm08:834 8346030 [C/G] 178 361 0.87 0.721 GGGTGTTAAGGAGAGAAATAGAAAGGAGA[C/G]
      6030 ATTTCACTCGATTGGTTCARAAAGAAATAAGAAC
      GAAATTGACAAATTCTGTGGGTTCATTTGGGAAA
      TTCTTCTCCATTGTTCATGATTGGAAATGATTTTG
      TGTATCTTCTTTTTTTTTCTTAATTTCTTTTTAAAA
      AATCAAATAATTTTTTTWAAAATAATTTCTTTATT
      AAAATACTTTTACTTTAYGATAAATA
      ACAAAAACTAAAGAAATTAAAGCAAACGATTTC
      ATAGGCTATTTGGGAGCTATGTTTTATGAGGTTA
      ATAACAAAATAGGAATCTCTTGATTTTAAGAATG
      AACAATTTTTTTTTCACTATGAAAGGAGTCCTGA
      ACATTATAATTGGATTGGGTGTTAAGGAGAGAAA
      Gm08:834 TAGAAAGGAGASATTTCACTCGATTGGTTCA[A/G]
      8346050 [A/G] 179 362 0.929 0.718
      6050 AAAGAAATAAGAACGAAATTGACAAATTCTGTG
      GGTTCATTTGGGAAATTCTTCTCCATTGTTCATGA
      TTGGAAATGATTTTGTGTATCTTCTTTTTTTTTCTT
      AATTTCTTTTTAAAAAATCAAATAATTTTTTTWA
      AAATAATTTCTTTATTAAAATACTTTTACTTTAYG
      ATAAATACTATGAATTAAAAAGATAAA
      CTTAATTTCTTTTTAAAAAATCAAATAATTTTTTT
      WAAAATAATTTCTTTATTAAAATACTTTTACTTT
      AYGATAAATACTATGAATTAAAAAGATAAATAT
      ATTCTCTTATTTTCTTATTTCTCTTCCAAGGATTGT
      CGAGATGGGAGAAGATTAACGTAAAGAATTTTT
      Gm08:834 ATTTTTTTATTAAAACAGCGAAAATATAG[G/T]GT
      8346352 180 363 0.936 0.841
      6352 ATATATATAAAAGGCACAAATGGGTGCCCCCAAT
      CAATTACAAAGTGGATAAAAGTCCAACAAAGAT
      AGTATACCTCGGTTACACCATATTAACAAAGGAG
      AGTAAATATAGTTTAACCAAGGCCAAAAACATC
      ACTCCTAGCCACACTCCAGTAAATATAGTTTAAC
      GTGAAGAATTTGATTCAACTTGTGAGAGCT
      AAGAATTTGATTCAACTTGTGAGAGCTTCACCCC
      TTAAGTTAATTCACCATATAGCTCAAATCGGATT
      AGTTGGAGAACTTAATTACCCTGATTGCCCTTTCT
      TAAAAATATTGCAGAAGCACCAAATAATACCAC
      AATGTGTCGATGTGTTTCCGAAACTAGATGATAG
      Gm08:834 ATGGGTAGGAATTTTTTTATTTTCTTTGAT[A/G]T
      8346726 [G/A] 181 364 0.87 0.8
      6726 ATTGAAAAGGCAGAAAGAAACACAAATTTTAGT
      ATTTAATAAAGCAAAATGCACACATCCCCCAAAC
      AAAACAAGCCTTATTCAACCCAAATTGGTTTCAT
      ATCACAGAAACCAACAGGATGCCGCCTTCCTCCT
      TACTGGTCCCACCCACTCGAACAAAAGTTSTACA
      GAAATAAAAATGGCTACAATTCTTCTACCA
      AGAGCCTGAAGGGCACAGATGGGATCAATCTCG
      GTCACGATGACACGAGCACCAGCCTGCTTCATTG
      CAGCAGCACAACCCTTGCCAACATCACCATATCC
      AGCCACAACAGCCACCTTTCCAGCAATCATAACA
      TCGGTAGCCCTCATGAGACCATCAGGGAGAGAG
      Gm08:834 TGACGGCACCCATACAAGTTGTCAAACTGTTA+A/
      8347799 [C/A] 182 365 0.919 0.757
      7799 C+AAAACCACAGATTAAAAGGTTAAACAAACAAA
      ACACAAGCAACAAAGCAAAATCCAATTATAATC
      AACTAGATCCATGACCAGCTAGTATAATGTCCTC
      AAAATCCAATCACCCACTTCTTACTTTCAATACC
      CTAATCAATAAACAACCCGTCACAAAAGACTCG
      GTTTGGATCAATGTTTGCAAAACCAATTTTGAAT
      AACAAACAAAACACAAGCAACAAAGCAAAATCC
      AATTATAATCAACTAGATCCATGACCAGCTAGTA
      TAATGTCCTCAAAATCCAATCACCCACTTCTTACT
      TTCAATACCCTAATCAATAAACAACCCGTCACAA
      AAGACTCGGTTTGGATCAATGTTTGCAAAACCAA
      Gm08:834 8348022183 366 0.854 0.848 TTTTGAATGAAAACGATTTCGAGTTAAAAT[A/T]G
      8022 ATTTYGAAACAACATGATTTATGTTTGAACATTT
      TTTTATTTTAAAACCAAAAACAGTAGTAAAATTC
      AGTATAATTTATTTTATCCTATCCAAAAGTAGCTT
      CAAATCAAAATGTGCACTCAGAATCAATTCCTTA
      TTTGTGTAATAAAACATGTGACCATTTACCTAAA
      GTCACGTTAGCAAGCAACTTACTAATGT
      CAAAACACAAGCAACAAAGCAAAATCCAATTAT
      AATCAACTAGATCCATGACCAGCTAGTATAATGT
      CCTCAAAATCCAATCACCCACTTCTTACTTTCAAT
      ACCCTAATCAATAAACAACCCGTCACAAAAGACT
      CGGTTTGGATCAATGTTTGCAAAACCAATTTTGA
      Gm08:834 ATGAAAACGATTTCGAGTTAAAATWGATTT[C/T]
      8348028 184 367 0.844 0.787
      8028 GAAACAACATGATTTATGTTTGAACATTTTTTTAT
      TTTAAAACCAAAAACAGTAGTAAAATTCAGTATA
      ATTTATTTTATCCTATCCAAAAGTAGCTTCAAATC
      AAAATGTGCACTCAGAATCAATTCCTTATTTGTG
      TAATAAAACATGTGACCATTTACCTAAAGTCACG
      TTAGCAAGCAACTTACTAATGTTCTGAC
      AMTATGAAAAATTATACTTCAAACAAGTCTCTCA
      TAAGAATGTTTATGGTCTCATACAGATGAATATT
      TTCACTTCGAATACACGTAAAACTAATATGAATT
      CACACAAGTGATTAAAGATCTAAAACTAACTTTT
      GTCTTCTTTTTTTTATAGATGTGGGTTTCATTCTCT
      Gm08:834 ATCATGCCACTAAAACTATCATCTAATA[G/T]ATT
      8349925 [G/T] 185 368 0.929 0.717
      9925 CTTTGACATCTAAGGACTAATTGAATAAATACAA
      TTAAGTAAAATTGTCTATGATTTAGGCCTGTGGA
      ATAATCCTTGAGTAAGCCTTTATTGACATCGCTA
      ACAAGTAGCATGTCATTAAGGTTTCATTCGATGG
      TATTGATCAGGCCTCTATAAAATTTTGTACATTTT
      AATATGCATCAAATGAGCATACKGGT
      ATAKATTCTTTGACATCTAAGGACTAATTGAATA
      AATACAATTAAGTAAAATTGTCTATGATTTAGGC
      CTGTGGAATAATCCTTGAGTAAGCCTTTATTGAC
      ATCGCTAACAAGTAGCATGTCATTAAGGTTTCAT
      TCGATGGTATTGATCAGGCCTCTATAAAATTTTG
      Gm08:835 TACATTTTAATATGCATCAAATGAGCATAC[G/T]G
      8350122 186 369 0.929 0.649
      0122 GTAAAGATTTCGGTGCTCAAGTTAATAGTTGGTA
      AAGTAAAAGCATTATATGTAAGATTTTCATGTAC
      TTGKTAAAGCTAAGGGACTATCGGAGATTGTTGA
      TAAGCATTTAAAAAACTCTCAACAATCTTCTATC
      TGCCTATAAAGTTTTCTYAAAAAGCATTTAAAAA
      ATTTATAGGTTAATTAGAGATTTGTTAGG
      CTCTATAAAATTTTGTACATTTTAATATGCATCAA
      ATGAGCATACKGGTAAAGATTTCGGTGCTCAAGT
      TAATAGTTGGTAAAGTAAAAGCATTATATGTAAG
      ATTTTCATGTACTTGKTAAAGCTAAGGGACTATC
      GGAGATTGTTGATAAGCATTTAAAAAACTCTCAA
      Gm08:835 CAATCTTCTATCTGCCTATAAAGTTTTCT[C/T]AA
      8350277 [C/T] 187 370 0.929 09 .0
      0277 AAAGCATTTAAAAAATTTATAGGTTAATTAGAGA
      TTTGTTAGGTAGGTTAACATACATGTAAAGATTT
      TTCTTTTTTTGGAAAATACATGTAAAGAGTTTTGT
      AAAAGTAGAACTTGTGAATACGTGATTTATAAGA
      CAATTCATATTCCTCCCAATCAGGTAATTTTGTGC
      AAAAAGTCTTATTAAGTTGGTGTGTA
      ATATTGTAAAACACAAAATATTTATATTCCAATC
      TTMAATGTTTTTATTTGACATTATAAATATTTAAA
      GGATAGAATCAATGTTAATCAAGTTAACATAAAA
      AATAAAAAATTACATAGCATTCAACATGTAGGTA
      TCAAATCTATGTTATAAAATGTTTATTAGATAGA
      Gm08:835 8351061 [G/A] 188 371 1 0.823 GAAAAATATTTGCTAAAATTTWGATAATT[A/G]T
      1061 GCTATGTTTATATGTTGAATGATGGGTAAAATAA
      AATGACGCATAATTAAGTAACATAAGTAAAATA
      AAAATTAAGTTTAATTTTTATGAATTATCAATAT
      AAAAAAATAAAATATATTCCTAACATTTCTCTTT
      CCTCTATTTTACATTCATTTTATTTTCTTAATTTTT
      TTCATTTTGATATCCTTTAATATAATAA
      CCCGGTCAAAATATAGGTTTAACAATTAGTCAAT
      TACTATATAAATAGGTTTTGTATTTGAATATGTTA
      GTAAAAAGTAGTTTTAATATATCTTATTCCAGTA
      AAATTATCAATTACTTTTAATAATAAAGTCATAC
      AAATTTGTATAAAACTATTTTCCCCCTACGATAA
      Gm08:835 AAGTTGTTTCGAAAAAAAAGTAAGTTGGA[A/G]A
      8351503 [A/G] 189 372 0.869 0.718
      1503 AATTTATTGAAGTGATGAAAACTATTTTTATGGT
      TATTTTTTATCACACAAATTAATTTTGGAATCTTA
      TAATTAGAAATGGTTGAATTTATATATTGGTTAA
      CTTTATTTTCTTATTTCGTCCACAGTAATGAATTG
      TTTCAAACAAAAAAAAAATCAATTAATATATATT
      TTATAATTTTACTATTGAAAAATACCT
      AGCATAATCACAATTATTGAGAAGATATTTTTAT
      TTTATTTTTACCGAATCGTCGCACGACTCGGCGT
      GTTGCAACCGCATTAAATCTTTGTGTTGGTCTCAC
      CCTGTCTTTTTGTGGATGATCGATCCTCTTGGATT
      GGTTTTTATAAAACTCAACTTCCCATCGGTGTTCT
      Gm08:835 TTAGTAATTGGAGTATCTTTGGATGTT[C/T]GTTA
      8352313 [C/T] 190 373 1 0.743
      2313 CATTTTATGATAAATTTAAATGATCCACAATCAC
      TAACTCAATTTTGCAAAGCAGGATTCTGAATGTT
      TTTGTAAATCTCGTTTTGTCCTAAAAGTTCGTCTA
      TAACAATAAAACAAACATGCACTTGGTTGTTTTT
      AAAATTGTCTCAAAACTCTGTTATAAAGAAATAA
      GACCTAAAGATATTTTTTACAAATT
      ATATCCTTAGATTAATTTATTTTSTTGATAAAAAA
      AAWKGATAAAAATTTCCATGCTTTAAATTTGTCA
      TTGGTC CATC TGATC GACTC TATACATCAAAC TT
      GAGTGTTATTTGCATACAAAAGGAAAACATCAG
      AGACATGACAGAGTAGGTTGCATTGGTGTTTAGT
      Gm08:835 TGACCTGATTAAGAAGTTACACACAAAGTG[C/T]
      8352743 [C/T] 191 374 0.843 0.72
      2743 TCC TCTATC TC CTC TTCAAGGTC CTC CTACC TATA
      GTCTTCTTGTACCTCTTATTATATGGATTAATTAG
      TGTAGAATTATTTCAACTTAATTAATAATTTTGAA
      TTTAAGTCATGAGAATGAGTATCAAAAYTTTTTC
      AC CTATAAAAATC GAATRTGCTTCAAATAAGATT
      GTCTCTAATAAATAATATGTGTTTAAT
      AAACCTATGTCGGTTGGTTCCTCTTTAAAGAAAA
      GAGAATAAAAATAACAAAGAAAAAAAAGTCGCC
      TTCCATTTCATTCGCATTCATAGTAAAAGAGTGA
      GC GATC CC GGGAAATGAATTAATATACGAC TAA
      AAAGATTTGAGAATTATAATAATTAATAATTAAT
      Gm08:835 AATTCTTTTTCAAAAGTAAAGTACAGTACTGC +A/
      8353341 [A/T] 192 375 0.812 0.774
      3341 T+GGAAACATGAGCATGTTCATAGATTAAAATTT
      AAAAGAATATTATCAGTAACAAAAAAATAAAAA
      TTAACCCATGCATCCAAGAAAGAAATACYCATGT
      GC TTCAGTTGTCC GC TGTC TGAGATGTGGTGACC
      TTTTTTCAAATGATCATAATAGTTACTTCATAATG
      AC GACATGCATCAAAC TATTTTTTC TTCAAAA
      TATCCCCCATGTTAATGAAGCAAGGTGTGGGGGA
      AGGAAAGAGTCAGCATCAGTGAAGTAGAGAGGG
      GGGTTGGTGATTTTGGTGGGAATAAATTGGCTAT
      ATTGC CC CCACCAACC TC GTTGC TAC CAAATAC C
      AACAACACTGACTCACTGAGAATTGGGAAAGAA
      Gm08:835 8355175 [C/T] 193 376 0.867 0.787 AC TTAAAAC CAAGTCTTGCAGTGAC GTACATG+C/
      5175 T+AGTGTGTGCATCACACATTCAGGTTTCCAGTCA
      AATTGTAGAACAAATGAATTTC TTGC TTTAAC TT
      AAGTTGAAGTTTAAGAAGTGAAGCTGATGCTTGT
      TTTTGAATGAAAAGCCTTTGATAGTTTGATGTAA
      GCATTTTCCAAATTTAACTCTTCCCATGCTTGACA
      GAGCCAATTAAGCTAACTGGTTTGATAACA
      CACCCCTCATTAGAGGCTTAGGATTTTTTTGAGTC
      CTAGAACACACATCTTATCTCAATAATGATTTCT
      ATCATTGCCAGAATTACAATTAAAAACTAAAATA
      TAATCAATTAGATTGAATTGAACTTCTACAGACC
      CCAAAGGCACTCGATGCATTTTCACTGTATGTGG
      Gm08:836 TTTGTCTTTC TGTAC TATAC TGCAC GCTT [A/G] GC
      8360133
      0133 [A/G] 194 377 1 0.773 AAAATAATCAGTAACACATGTTAAGAGAGCTTGC
      AC TTTATTTTTATC TTGTTGAC GGGTTTGTTGTCA
      TTGAAAACACATTATATTCAGAGGAATTTGACTC
      AACATGTTCAACCCACCAATTATCACATTTAAAC
      AAATYTAAATCAATCGCAAATCATATATATTCAG
      AATTTTACATATTAAATATTTCATATC
      AATAACATGGTTATGTTGAAAACAAAAGAAAAA
      AATATCAAATTTAATTCATGAATCTTTCAACTAA
      TTAAAAAATGACCAATCCTAACTAGTTGCAGAAG
      CTATTAATTAAATTTTTAAAAAAGTATATCTTTCT
      CTC TTATGAC TCACATAATTTATAKTC CC TATACT
      Gm08:836 CAAAGTCTCACATAATTTATACTACAAAA[A/T]CT
      8363193
      3193 195 378 1 0.703 TAGGTTTAATTTC GTACC TATTGTTAATGTTTC CT
      AATCGAAATTAGAATTTCACCCCGATAATTAAAA
      GTTTACATTAAAAAATTAYATAAATTACCGAAAT
      AAAACTCAAAATTTAGTCAAACAATAATGTAAGC
      AC TAAGCAGCAAC TAAGAAGC TATAAACAAAGT
      TTTGATAAATAGTTAAATTTATC CTC CA
      AAGTGGGGAACTGTCGATCCATGGTGCTGGCAGC
      AACCGTAACATGCCAGGGTGCGAGATTTTCCGCA
      GTGGCTTCC GC GGGCCCACTGTTGCCAGCAGAGC
      AAACCACCACAAC GCCAC GC TTGGCCGCATGGA
      AGGATCC GATGGCAACACTATCCTTGAAAAAC GT
      Gm08:836 GGAGGAAGAGCCACCGAGCGAGACGGAGAGG+A/
      3888 8363888 [A/G] 196 379 0.825 0.809 G+ CATCGACGCCGTCGTGGATGGCGAGGTCGAAG
      GCCGCCAAGATATCAGCGTCGAAGCACTCCTCGC
      CTCCGACGGGGGGCCAGCAGACCTTGTAGGCTGC
      CACACGTGCCATTGGTGAGCCACCCTTGGCTGTT
      CCC TGGCCC TGGCC GAAGAC GC TGACAC GTGC GA
      CCATGTTCCCGCCAGCTGTGGATAGGGTGTGG
      TGCCATTGGTGAGCCACCCTTGGCTGTTCCCTGG
      CCCTGGCCGAAGACGCTGACACGTGCGACCATGT
      TCCCGCCAGCTGTGGATAGGGTGTGGGTCCCGTG
      GCCCTCGTTGTCACGTGGCGAGTCAAAGGAGGA
      GTTCAGTGGGCCCGCCACTGAGGCGTAGCCCTTG
      Gm08:836 TTGAAGTACCTTGCCCCTATTAGCTTCCTGC [A/G]
      8364195 [A/G] 197 380 0.919 0.788
      4195 TTCAACATCTCCACTTAACGTTTCTTTAATTTWTC
      AAAACAAAATCATTGAAAGATTGGTCTGGTTGGT
      GTGAAAACACTAGTACTATAAAAGAATAAGATA
      AC GAAAGAAACATGTC TGC GTTCAAAGGAGTGC
      TTAACCCTTTCATTGTAGTATTCACCTAATAAAG
      AGTGCCAATTTAAAGGCATATGACTACAGAA
      R = Resistan;
      S = Susceptible
      *Liu et al. (2012). A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature 492: 256-260.
    • [0000]
      TABLE 4 
      Non-limiting Examples of Amplicons Comprising the Various Marker Loci
      Provided Herein.
      Resistant
      Linkage (R) or
      Marker Group Susceptible SEQ Amplicon
      Name (ch) Primer 1 Primer 2 (S) Allele ID NO Amplicon Sequence Size (bp)
      S07160-1 A2 136868 136869 R 11 TGTGTTGTGTTTGACTG 118
      (Gm08) CCATAACATGATGTTTG
      GATTAAATATAAACAA
      TAATATC C TATGCAGTT
      AGTGAGGCTGTGATTT
      GGAAGACACTGTCTTA
      TCAAGAGGCTTGGGAA
      ATG
      S07160-1 A2 136868 136869 S 12 TGTGTTGTGTTTGACTG 118
      (Gm08) CCATAACATGATGTTTG
      GATTAAATATAAACAA
      TAATATC A TATGCAGTT
      AGTGAGGCTGTGATTT
      GGAAGACACTGTCTTA
      TCAAGAGGCTTGGGAA
      ATG
    • [0081]
      In another embodiment, the method of detecting comprises DNA sequencing of at least one of the marker loci provided herein. As used herein, “sequencing” refers to sequencing methods for determining the order of nucleotides in a molecule of DNA. Any DNA sequencing method known in the art can be used in the methods provided herein. Non-limiting examples of DNA sequencing methods useful in the methods provided herein include Next Generation Sequencing (NGS) technologies, for example, as described in Egan, A. N, et al. (2012) American Journal of Botany 99(2):175-185; genotyping by sequencing (GBS) methods, for example, as described in Elshire, R. J., et al. (2011) PLoS ONE 6(5):e19379; Molecular Inversion Probe (MIP) genotyping, as described, for example, in Hardenbol, P., et al. (2003) Nature Biotechnology 21(6):673-678; or high throughput genotyping by whole-genome resequencing, as described, for example in Huang, X et al., (2009) Genome Research 19:1068-1076. Each of the above references is incorporated by reference in their entirety herein.
    • [0082]
      An active variant of any one of SEQ ID NOS: 1-380 can comprise a polynucleotide having at least 75%, 80% 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to SEQ ID NOS: 1-380 as long as it is capable of amplifying and/or detecting the marker locus of interest. By “fragment” is intended a portion of the polynucleotide. A fragment or portion can comprise at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, 75, 100, 150, 200, 250, 300, 350, 400 contiguous nucleotides of SEQ ID NOS: 1-380 as long as it is capable of amplifying and/or detecting the marker locus of interest.
    • [0083]
      Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using GAP Version 10 using the following parameters: % identity and % similarity for a nucleotide sequence using GAP Weight of 50 and Length Weight of 3, and the nwsgapdna.cmp scoring matrix; or any equivalent program thereof. By “equivalent program” is intended any sequence comparison program that, for any two sequences in question, generates an alignment having identical nucleotide residue matches and an identical percent sequence identity when compared to the corresponding alignment generated by GAP Version 10.
    • [0084]
      Traits or markers are considered to be linked if they co-segregate. A 1/100 probability of recombination per generation is defined as a map distance of 1.0 centiMorgan (1.0 cM). Genetic elements or genes located on a single chromosome segment are physically linked. Two loci can be located in close proximity such that recombination between homologous chromosome pairs does not occur between the two loci during meiosis with high frequency, e.g., such that linked loci co-segregate at least about 90% of the time, e.g., 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, 99.75%, or more of the time. Genetic elements located within a chromosome segment are also genetically linked, typically within a genetic recombination distance of less than or equal to 50 centimorgans (cM), e.g., about 49, 40, 30, 20, 10, 5, 4, 3, 2, 1, 0.75, 0.5, or 0.25 cM or less. That is, two genetic elements within a single chromosome segment undergo recombination during meiosis with each other at a frequency of less than or equal to about 50%, e.g., about 49%, 40%, 30%, 20%, 10%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, or 0.25% or less. Closely linked markers display a cross over frequency with a given marker of about 10% or less (the given marker is within about 10 cM of a closely linked marker). In specific embodiments, a closely linked marker is within 10 cM, 9 cM, 8 cM, 7 cM, 6 cM, 5 cM, 4 cM, 3 cM, 2 cM or 1 cM of any given marker disclosed herein. In further embodiments, a marker associated with one of the markers disclosed herein can be within 75 Kb, 60 Kb, 50 Kb, 40 Kb, 30 Kb, 20 K, 10 Kb, 5 Kb or less of the disclosed marker.
    • [0085]
      Put another way, closely linked loci co-segregate at least about 90% of the time. Genetic linkage as evaluated by recombination frequency is impacted by the chromatin structure of the region comprising the loci. Typically, the region is assumed to have a euchromatin structure during initial evaluations. However, some regions, such are regions closer to centrosomes, have a heterochromatin structure. Without further information, the predicted physical distance between genetic map positions is based on the assumption that the region is euchromatic, however if the region comprises heterochromatin the markers may be physically closer together. With regard to physical position on a chromosome, closely linked markers can be separated, for example, by about 1 megabase (Mb; 1 million nucleotides), about 500 kilobases (Kb; 1000 nucleotides), about 400 Kb, about 300 Kb, about 200 Kb, about 100 Kb, about 50 Kb, about 25 Kb, about 10 Kb, about 5 Kb, about 2 Kb, about 1 Kb, about 500 nucleotides, about 250 nucleotides, or less.
    • [0086]
      When referring to the relationship between two genetic elements, such as a genetic element contributing to resistance and a proximal marker, “coupling” phase linkage indicates the state where the “favorable” allele at the resistance locus is physically associated on the same chromosome strand as the “favorable” allele of the respective linked marker locus. In coupling phase, both favorable alleles are inherited together by progeny that inherit that chromosome strand. In “repulsion” phase linkage, the “favorable” allele at the locus of interest (e.g., a QTL for resistance) is physically linked with an “unfavorable” allele at the proximal marker locus, and the two “favorable” alleles are not inherited together (i.e., the two loci are “out of phase” with each other).
    • [0087]
      Markers are used to define a specific locus on the soybean genome. Each marker is therefore an indicator of a specific segment of DNA, having a unique nucleotide sequence. Map positions provide a measure of the relative positions of particular markers with respect to one another. When a trait is stated to be linked to a given marker it will be understood that the actual DNA segment whose sequence affects the trait generally co-segregates with the marker. More precise and definite localization of a trait can be obtained if markers are identified on both sides of the trait. By measuring the appearance of the marker(s) in progeny of crosses, the existence of the trait can be detected by relatively simple molecular tests without actually evaluating the appearance of the trait itself, which can be difficult and time-consuming because the actual evaluation of the trait requires growing plants to a stage and/or under environmental conditions where the trait can be expressed. Molecular markers have been widely used to determine genetic composition in soybeans.
    • [0088]
      Favorable genotypes associated with at least trait of interest may be identified by one or more methodologies. In some examples one or more markers are used, including but not limited to AFLPs, RFLPs, ASH, SSRs, SNPs, indels, padlock probes, molecular inversion probes, microarrays, sequencing, and the like. In some methods, a target nucleic acid is amplified prior to hybridization with a probe. In other cases, the target nucleic acid is not amplified prior to hybridization, such as methods using molecular inversion probes (see, for example Hardenbol et al. (2003) Nat Biotech 21:673-678). In some examples, the genotype related to a specific trait is monitored, while in other examples, a genome-wide evaluation including but not limited to one or more of marker panels, library screens, association studies, microarrays, gene chips, expression studies, or sequencing such as whole-genome resequencing and genotyping-by-sequencing (GBS) may be used. In some examples, no target-specific probe is needed, for example by using sequencing technologies, including but not limited to next-generation sequencing methods (see, for example, Metzker (2010) Nat Rev Genet 11:31-46; and, Egan et al. (2012) Am J Bot 99:175-185) such as sequencing by synthesis (e.g., Roche 454 pyrosequencing, Illumina Genome Analyzer, and Ion Torrent PGM or Proton systems), sequencing by ligation (e.g., SOLiD from Applied Biosystems, and Polnator system from Azco Biotech), and single molecule sequencing (SMS or third-generation sequencing) which eliminate template amplification (e.g., Helicos system, and PacBio RS system from Pacific BioSciences). Further technologies include optical sequencing systems (e.g., Starlight from Life Technologies), and nanopore sequencing (e.g., GridION from Oxford Nanopore Technologies). Each of these may be coupled with one or more enrichment strategies for organellar or nuclear genomes in order to reduce the complexity of the genome under investigation via PCR, hybridization, restriction enzyme (see, e.g., Elshire et al. (2011) PLoS ONE 6:e19379), and expression methods. In some examples, no reference genome sequence is needed in order to complete the analysis.
    • [0089]
      The use of marker assisted selection (MAS) to select a soybean plant or germplasm which has a certain marker locus, haplotype or marker profile is provided. For instance, in certain examples a soybean plant or germplasm possessing a certain predetermined favorable marker locus or haplotype will be selected via MAS. In certain other examples, a soybean plant or germplasm possessing a certain predetermined favorable marker profile will be selected via MAS.
    • [0090]
      Using MAS, soybean plants or germplasm can be selected for markers or marker alleles that positively correlate with soybean cyst nematode resistance, without actually raising soybean and measuring for resistance (or, contrawise, soybean plants can be selected against if they possess markers that negatively correlate with resistance). MAS is a powerful tool to select for desired phenotypes and for introgressing desired traits into cultivars of soybean (e.g., introgressing desired traits into elite lines). MAS is easily adapted to high throughput molecular analysis methods that can quickly screen large numbers of plant or germplasm genetic material for the markers of interest and is much more cost effective than raising and observing plants for visible traits.
    • [0091]
      In some embodiments, the molecular markers or marker loci are detected using a suitable amplification-based detection method. In these types of methods, nucleic acid primers are typically hybridized to the conserved regions flanking the polymorphic marker region. In certain methods, nucleic acid probes that bind to the amplified region are also employed. In general, synthetic methods for making oligonucleotides, including primers and probes, are well known in the art. For example, oligonucleotides can be synthesized chemically according to the solid phase phosphoramidite triester method described by Beaucage and Caruthers (1981) Tetrahedron Letts 22:1859-1862, e.g., using a commercially available automated synthesizer, e.g., as described in Needham-VanDevanter, et al. (1984) Nucleic Acids Res. 12:6159-6168. Oligonucleotides, including modified oligonucleotides, can also be ordered from a variety of commercial sources known to persons of skill in the art.
    • [0092]
      It will be appreciated that suitable primers and probes to be used can be designed using any suitable method. It is not intended that the invention be limited to any particular primer, primer pair or probe. For example, primers can be designed using any suitable software program, such as LASERGENE® or Primer3.
    • [0093]
      It is not intended that the primers be limited to generating an amplicon of any particular size. For example, the primers used to amplify the marker loci and alleles herein are not limited to amplifying the entire region of the relevant locus. In some embodiments, marker amplification produces an amplicon at least 20 nucleotides in length, or alternatively, at least 50 nucleotides in length, or alternatively, at least 100 nucleotides in length, or alternatively, at least 200 nucleotides in length.
    • [0094]
      Non-limiting examples of polynucleotide primers useful for detecting the marker loci provided herein are provided in Table 1 and include, for example, SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8 or variants or fragments thereof.
    • [0095]
      PCR, RT-PCR, and LCR are in particularly broad use as amplification and amplification-detection methods for amplifying nucleic acids of interest (e.g., those comprising marker loci), facilitating detection of the markers. Details regarding the use of these and other amplification methods are well known in the art and can be found in any of a variety of standard texts. Details for these techniques can also be found in numerous journal and patent references, such as Mullis, et al. (1987) U.S. Pat. No. 4,683,202; Arnheim & Levinson (Oct. 1, 1990) C&EN 36-47; Kwoh, et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173; Guatelli, et al., (1990) Proc. Natl. Acad. Sci. USA 87:1874; Lomell, et al., (1989) J. Clin. Chem. 35:1826; Landegren, et al., (1988) Science 241:1077-1080; Van Brunt, (1990) Biotechnology 8:291-294; Wu and Wallace, (1989) Gene 4:560; Barringer, et al., (1990) Gene 89:117, and Sooknanan and Malek, (1995) Biotechnology 13:563-564.
    • [0096]
      Such nucleic acid amplification techniques can be applied to amplify and/or detect nucleic acids of interest, such as nucleic acids comprising marker loci. Amplification primers for amplifying useful marker loci and suitable probes to detect useful marker loci or to genotype SNP alleles are provided. For example, exemplary primers and probes are provided in SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and in Tables 1 and 2, and the genomic loci comprising the various marker loci provided herein are provided in SEQ ID NOS: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380 and in Tables 3A and 3B. Non-limiting examples of amplicon sequences comprising the marker loci provided herein are provided SEQ ID NOS: 11, 12 and in Table 4.
    • [0097]
      However, one of skill will immediately recognize that other primer and probe sequences could also be used. For instance primers to either side of the given primers can be used in place of the given primers, so long as the primers can amplify a region that includes the allele to be detected, as can primers and probes directed to other SNP marker loci. Further, it will be appreciated that the precise probe to be used for detection can vary, e.g., any probe that can identify the region of a marker amplicon to be detected can be substituted for those examples provided herein. Further, the configuration of the amplification primers and detection probes can, of course, vary. Thus, the compositions and methods are not limited to the primers and probes specifically recited herein.
    • [0098]
      In certain examples, probes will possess a detectable label. Any suitable label can be used with a probe. Detectable labels suitable for use with nucleic acid probes include, for example, any composition detectable by spectroscopic, radioisotopic, photochemical, biochemical, immunochemical, electrical, optical, or chemical means. Useful labels include biotin for staining with labeled streptavidin conjugate, magnetic beads, fluorescent dyes, radiolabels, enzymes, and colorimetric labels. Other labels include ligands, which bind to antibodies labeled with fluorophores, chemiluminescent agents, and enzymes. A probe can also constitute radiolabelled PCR primers that are used to generate a radiolabelled amplicon. Labeling strategies for labeling nucleic acids and corresponding detection strategies can be found, e.g., in Haugland (1996) Handbook of Fluorescent Probes and Research Chemicals Sixth Edition by Molecular Probes, Inc. (Eugene O R); or Haugland (2001) Handbook of Fluorescent Probes and Research Chemicals Eighth Edition by Molecular Probes, Inc. (Eugene O R).
    • [0099]
      Detectable labels may also include reporter-quencher pairs, such as are employed in Molecular Beacon and TaqMan™ probes. The reporter may be a fluorescent organic dye modified with a suitable linking group for attachment to the oligonucleotide, such as to the terminal 3′ carbon or terminal 5′ carbon. The quencher may also be an organic dye, which may or may not be fluorescent, depending on the embodiment. Generally, whether the quencher is fluorescent or simply releases the transferred energy from the reporter by non-radiative decay, the absorption band of the quencher should at least substantially overlap the fluorescent emission band of the reporter to optimize the quenching. Non-fluorescent quenchers or dark quenchers typically function by absorbing energy from excited reporters, but do not release the energy radiatively.
    • [0100]
      Selection of appropriate reporter-quencher pairs for particular probes may be undertaken in accordance with known techniques. Fluorescent and dark quenchers and their relevant optical properties from which exemplary reporter-quencher pairs may be selected are listed and described, for example, in Berlman, Handbook of Fluorescence Spectra of Aromatic Molecules, 2nd ed., Academic Press, New York, 1971, the content of which is incorporated herein by reference. Examples of modifying reporters and quenchers for covalent attachment via common reactive groups that can be added to an oligonucleotide in the present invention may be found, for example, in Haugland, Handbook of Fluorescent Probes and Research Chemicals, Molecular Probes of Eugene, Oreg., 1992, the content of which is incorporated herein by reference.
    • [0101]
      In certain examples, reporter-quencher pairs are selected from xanthene dyes including fluoresceins and rhodamine dyes. Many suitable forms of these compounds are available commercially with substituents on the phenyl groups, which can be used as the site for bonding or as the bonding functionality for attachment to an oligonucleotide. Another useful group of fluorescent compounds for use as reporters are the naphthylamines, having an amino group in the alpha or beta position. Included among such naphthylamino compounds are 1-dimethylaminonaphthyl-5 sulfonate, 1-anilino-8-naphthalene sulfonate and 2-p-touidinyl-6-naphthalene sulfonate. Other dyes include 3-phenyl-7-isocyanatocoumarin; acridines such as 9-isothiocyanatoacridine; N-(p-(2-benzoxazolyl)phenyl)maleimide; benzoxadiazoles; stilbenes; pyrenes and the like. In certain other examples, the reporters and quenchers are selected from fluorescein and rhodamine dyes. These dyes and appropriate linking methodologies for attachment to oligonucleotides are well known in the art.
    • [0102]
      Suitable examples of reporters may be selected from dyes such as SYBR green, 5-carboxyfluorescein (5-FAM™ available from Applied Biosystems of Foster City, Calif.), 6-carboxyfluorescein (6-FAM), tetrachloro-6-carboxyfluorescein (TET), 2,7-dimethoxy-4,5-dichloro-6-carboxyfluorescein, hexachloro-6-carboxyfluorescein (HEX), 6-carboxy-2′,4,7,7′-tetrachlorofluorescein (6-TET™ available from Applied Biosystems), carboxy-X-rhodamine (ROX), 6-carboxy-4′,5′-dichloro-2′,7′-dimethoxyfluorescein (6-JOE™ available from Applied Biosystems), VIC™ dye products available from Molecular Probes, Inc., NED™ dye products available from Applied Biosystems, and the like. Suitable examples of quenchers may be selected from 6-carboxy-tetramethyl-rhodamine, 4-(4-dimethylaminophenylazo) benzoic acid (DABYL), tetramethylrhodamine (TAMRA), BHQ-0™, BHQ-1™, BHQ-2™, and BHQ-3™, each of which are available from Biosearch Technologies, Inc. of Novato, Calif., QSY-7™, QSY-9™, QSY-21™ and QSY-35™, each of which are available from Molecular Probes, Inc., and the like.
    • [0103]
      In one aspect, real time PCR or LCR is performed on the amplification mixtures described herein, e.g., using molecular beacons or TaqMan™ probes. A molecular beacon (MB) is an oligonucleotide which, under appropriate hybridization conditions, self-hybridizes to form a stem and loop structure. The MB has a label and a quencher at the termini of the oligonucleotide; thus, under conditions that permit intra-molecular hybridization, the label is typically quenched (or at least altered in its fluorescence) by the quencher. Under conditions where the MB does not display intra-molecular hybridization (e.g., when bound to a target nucleic acid, such as to a region of an amplicon during amplification), the MB label is unquenched. Details regarding standard methods of making and using MBs are well established in the literature and MBs are available from a number of commercial reagent sources. See also, e.g., Leone, et al., (1995) Molecular beacon probes combined with amplification by NASBA enable homogenous real-time detection of RNA, Nucleic Acids Res. 26:2150-2155; Tyagi and Kramer, (1996) Molecular beacons: probes that fluoresce upon hybridization, Nature Biotechnology 14:303-308; Blok and Kramer, (1997) Amplifiable hybridization probes containing a molecular switch, Mol Cell Probes 11:187-194; Hsuih. et al., (1997) Novel, ligation-dependent PCR assay for detection of hepatitis C in serum, J Clin Microbiol 34:501-507; Kostrikis, et al., (1998) Molecular beacons: spectral genotyping of human alleles, Science 279:1228-1229; Sokol, et al., (1998) Real time detection of DNA:RNA hybridization in living cells, Proc. Natl. Acad. Sci. U.S.A. 95:11538-11543; Tyagi, et al., (1998) Multicolor molecular beacons for allele discrimination, Nature Biotechnology 16:49-53; Bonnet, et al., (1999) Thermodynamic basis of the chemical specificity of structured DNA probes, Proc. Natl. Acad. Sci. U.S.A. 96:6171-6176; Fang, et al. (1999) Designing a novel molecular beacon for surface-immobilized DNA hybridization studies, J. Am. Chem. Soc. 121:2921-2922; Marras, et al., (1999) Multiplex detection of single-nucleotide variation using molecular beacons, Genet. Anal. Biomol. Eng. 14:151-156; and Vet, et al., (1999) Multiplex detection of four pathogenic retroviruses using molecular beacons, Proc. Natl. Acad. Sci. U.S.A. 96:6394-6399. Additional details regarding MB construction and use is found in the patent literature, e.g., U.S. Pat. Nos. 5,925,517; 6,150,097; and 6,037,130.
    • [0104]
      Another real-time detection method is the 5′-exonuclease detection method, also called the TaqMan™ assay, as set forth in U.S. Pat. Nos. 5,804,375; 5,538,848; 5,487,972; and 5,210,015, each of which is hereby incorporated by reference in its entirety. In the TaqMan™ assay, a modified probe, typically 10-25 nucleic acids in length, is employed during PCR which binds intermediate to or between the two members of the amplification primer pair. The modified probe possesses a reporter and a quencher and is designed to generate a detectable signal to indicate that it has hybridized with the target nucleic acid sequence during PCR. As long as both the reporter and the quencher are on the probe, the quencher stops the reporter from emitting a detectable signal. However, as the polymerase extends the primer during amplification, the intrinsic 5′ to 3′ nuclease activity of the polymerase degrades the probe, separating the reporter from the quencher, and enabling the detectable signal to be emitted. Generally, the amount of detectable signal generated during the amplification cycle is proportional to the amount of product generated in each cycle.
    • [0105]
      It is well known that the efficiency of quenching is a strong function of the proximity of the reporter and the quencher, i.e., as the two molecules get closer, the quenching efficiency increases. As quenching is strongly dependent on the physical proximity of the reporter and quencher, the reporter and the quencher are preferably attached to the probe within a few nucleotides of one another, usually within 30 nucleotides of one another, more preferably with a separation of from about 6 to 16 nucleotides. Typically, this separation is achieved by attaching one member of a reporter-quencher pair to the 5′ end of the probe and the other member to a nucleotide about 6 to 16 nucleotides away, in some cases at the 3′ end of the probe.
    • [0106]
      Separate detection probes can also be omitted in amplification/detection methods, e.g., by performing a real time amplification reaction that detects product formation by modification of the relevant amplification primer upon incorporation into a product, incorporation of labeled nucleotides into an amplicon, or by monitoring changes in molecular rotation properties of amplicons as compared to unamplified precursors (e.g., by fluorescence polarization).
    • [0107]
      Further, it will be appreciated that amplification is not a requirement for marker detection—for example, one can directly detect unamplified genomic DNA simply by performing a Southern blot on a sample of genomic DNA. Procedures for performing Southern blotting, amplification e.g., (PCR, LCR, or the like), and many other nucleic acid detection methods are well established and are taught, e.g., in Sambrook, et al., Molecular Cloning—A Laboratory Manual (3d ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 2000 (“Sambrook”); Current Protocols in Molecular Biology, F. M. Ausubel, et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (supplemented through 2002) (“Ausubel”)) and PCR Protocols A Guide to Methods and Applications (Innis, et al., eds) Academic Press Inc. San Diego, Calif. (1990) (Innis). Additional details regarding detection of nucleic acids in plants can also be found, e.g., in Plant Molecular Biology (1993) Croy (ed.) BIOS Scientific Publishers, Inc.
    • [0108]
      Other techniques for detecting SNPs can also be employed, such as allele specific hybridization (ASH). ASH technology is based on the stable annealing of a short, single-stranded, oligonucleotide probe to a completely complementary single-stranded target nucleic acid. Detection is via an isotopic or non-isotopic label attached to the probe. For each polymorphism, two or more different ASH probes are designed to have identical DNA sequences except at the polymorphic nucleotides. Each probe will have exact homology with one allele sequence so that the range of probes can distinguish all the known alternative allele sequences. Each probe is hybridized to the target DNA. With appropriate probe design and hybridization conditions, a single-base mismatch between the probe and target DNA will prevent hybridization.
    • [0109]
      Real-time amplification assays, including MB or TaqMan™ based assays, are especially useful for detecting SNP alleles. In such cases, probes are typically designed to bind to the amplicon region that includes the SNP locus, with one allele-specific probe being designed for each possible SNP allele. For instance, if there are two known SNP alleles for a particular SNP locus, “A” or “C,” then one probe is designed with an “A” at the SNP position, while a separate probe is designed with a “C” at the SNP position. While the probes are typically identical to one another other than at the SNP position, they need not be. For instance, the two allele-specific probes could be shifted upstream or downstream relative to one another by one or more bases. However, if the probes are not otherwise identical, they should be designed such that they bind with approximately equal efficiencies, which can be accomplished by designing under a strict set of parameters that restrict the chemical properties of the probes. Further, a different detectable label, for instance a different reporter-quencher pair, is typically employed on each different allele-specific probe to permit differential detection of each probe. In certain examples, each allele-specific probe for a certain SNP locus is 11-20 nucleotides in length, dual-labeled with a florescence quencher at the 3′ end and either the 6-FAM (6-carboxyfluorescein) or VIC (4,7,2′-trichloro-7′-phenyl-6-carboxyfluorescein) fluorophore at the 5′ end.
    • [0110]
      To effectuate SNP allele detection, a real-time PCR reaction can be performed using primers that amplify the region including the SNP locus, for instance the sequences listed in Tables 3A and 3B, the reaction being performed in the presence of all allele-specific probes for the given SNP locus. By then detecting signal for each detectable label employed and determining which detectable label(s) demonstrated an increased signal, a determination can be made of which allele-specific probe(s) bound to the amplicon and, thus, which SNP allele(s) the amplicon possessed. For instance, when 6-FAM- and VIC-labeled probes are employed, the distinct emission wavelengths of 6-FAM (518 nm) and VIC (554 nm) can be captured. A sample that is homozygous for one allele will have fluorescence from only the respective 6-FAM or VIC fluorophore, while a sample that is heterozygous at the analyzed locus will have both 6-FAM and VIC fluorescence.
    • [0111]
      The KASPar® and Illumina® Detection Systems are additional examples of commercially-available marker detection systems. KASPar® is a homogeneous fluorescent genotyping system which utilizes allele specific hybridization and a unique form of allele specific PCR (primer extension) in order to identify genetic markers (e.g. a particular SNP locus associated with soybean cyst nematode resistance). Illumina® detection systems utilize similar technology in a fixed platform format. The fixed platform utilizes a physical plate that can be created with up to 384 markers. The Illumina® system is created with a single set of markers that cannot be changed and utilizes dyes to indicate marker detection.
    • [0112]
      These systems and methods represent a wide variety of available detection methods which can be utilized to detect markers associated with resistance or improved resistance to soybean cyst nematode, but any other suitable method could also be used.
    • [0113]
      Introgression of soybean cyst nematode resistance into non-resistant or less-resistant soybean germplasm is provided. Any method for introgressing one or more marker loci into soybean plants known to one of skill in the art can be used. Typically, a first soybean germplasm that contains soybean cyst nematode resistance derived from a particular marker locus, haplotype or marker profile and a second soybean germplasm that lacks such resistance derived from the marker locus, haplotype or marker profile are provided. The first soybean germplasm may be crossed with the second soybean germplasm to provide progeny soybean germplasm. These progeny germplasm are screened to determine the presence of soybean cyst nematode resistance derived from the marker locus, haplotype or marker profile, and progeny that tests positive for the presence of resistance derived from the marker locus, haplotype or marker profile are selected as being soybean germplasm into which the marker locus, haplotype or marker profile has been introgressed. Methods for performing such screening are well known in the art and any suitable method can be used.
    • [0114]
      One application of MAS is to use the resistance markers, haplotypes or marker profiles to increase the efficiency of an introgression or backcrossing effort aimed at introducing a resistance trait into a desired (typically high yielding) background. In marker assisted backcrossing of specific markers from a donor source, e.g., to an elite genetic background, one selects among backcross progeny for the donor trait and then uses repeated backcrossing to the elite line to reconstitute as much of the elite background's genome as possible.
    • [0115]
      Thus, the markers and methods can be utilized to guide marker assisted selection or breeding of soybean varieties with the desired complement (set) of allelic forms of chromosome segments associated with superior agronomic performance (resistance, along with any other available markers for yield, disease tolerance, etc.). Any of the disclosed marker loci, marker alleles, haplotypes, or marker profiles can be introduced into a soybean line via introgression, by traditional breeding (or introduced via transformation, or both) to yield a soybean plant with superior agronomic performance. The number of alleles associated with resistance that can be introduced or be present in a soybean plant ranges from 1 to the number of alleles disclosed herein, each integer of which is incorporated herein as if explicitly recited.
    • [0116]
      The markers and methods provided herein can also be utilized to guide marker assisted selection or breeding of soybean varieties comprising other soybean cyst nematode resistance markers or alleles to create a molecular stack for soybean cyst nematode resistance. For example, any of the marker loci provided herein can be introduced into a soybean line having one or more of the soybean cyst nematode resistance loci rhg1, rhg2, rhg3 or rhg5. In one embodiment, any one or more of the marker loci provided herein can be stacked with the rhg1 locus. In another embodiment, any one or more of the marker loci provided herein can be stacked with the rhg2 locus. In a further embodiment, any one or more of the marker loci provided herein can be stacked with the rhg1 and rhg2 loci.
    • [0117]
      This also provides a method of making a progeny soybean plant and these progeny soybean plants, per se. The method comprises crossing a first parent soybean plant with a second soybean plant and growing the female soybean plant under plant growth conditions to yield soybean plant progeny. Methods of crossing and growing soybean plants are well within the ability of those of ordinary skill in the art. Such soybean plant progeny can be assayed for alleles associated with resistance and, thereby, the desired progeny selected. Such progeny plants or seed can be sold commercially for soybean production, used for food, processed to obtain a desired constituent of the soybean, or further utilized in subsequent rounds of breeding. At least one of the first or second soybean plants is a soybean plant in that it comprises at least one of the marker loci or marker profiles, such that the progeny are capable of inheriting the marker locus or marker profile.
    • [0118]
      Often, a method is applied to at least one related soybean plant such as from progenitor or descendant lines in the subject soybean plants pedigree such that inheritance of the desired resistance can be traced. The number of generations separating the soybean plants being subject to the methods provided herein will generally be from 1 to 20, commonly 1 to 5, and typically 1, 2, or 3 generations of separation, and quite often a direct descendant or parent of the soybean plant will be subject to the method (i.e., 1 generation of separation).
    • [0119]
      Genetic diversity is important for long term genetic gain in any breeding program. With limited diversity, genetic gain will eventually plateau when all of the favorable alleles have been fixed within the elite population. One objective is to incorporate diversity into an elite pool without losing the genetic gain that has already been made and with the minimum possible investment. MAS provides an indication of which genomic regions and which favorable alleles from the original ancestors have been selected for and conserved over time, facilitating efforts to incorporate favorable variation from exotic germplasm sources (parents that are unrelated to the elite gene pool) in the hopes of finding favorable alleles that do not currently exist in the elite gene pool.
    • [0120]
      For example, the markers, haplotypes, primers, probes, and marker profiles can be used for MAS in crosses involving elite x exotic soybean lines by subjecting the segregating progeny to MAS to maintain major yield alleles, along with the resistance marker alleles herein.
    • [0121]
      As an alternative to standard breeding methods of introducing traits of interest into soybean (e.g., introgression), transgenic approaches can also be used to create transgenic plants with the desired traits. In these methods, exogenous nucleic acids that encode a desired marker loci, marker profile or haplotype are introduced into target plants or germplasm. For example, a nucleic acid that codes for a resistance trait is cloned, e.g., via positional cloning, and introduced into a target plant or germplasm.
    • [0122]
      Experienced plant breeders can recognize resistant soybean plants in the field, and can select the resistant individuals or populations for breeding purposes or for propagation. In this context, the plant breeder recognizes “resistant” and “non-resistant” or “susceptible” soybean plants. However, plant resistance is a phenotypic spectrum consisting of extremes in resistance and susceptibility, as well as a continuum of intermediate resistance phenotypes. Evaluation of these intermediate phenotypes using reproducible assays are of value to scientists who seek to identify genetic loci that impart resistance, to conduct marker assisted selection for resistant populations, and to use introgression techniques to breed a resistance trait into an elite soybean line, for example.
    • [0123]
      By “improved resistance” is intended that the plants show a decrease in the disease symptoms that are the outcome of plant exposure to soybean cyst nematode. That is, the damage caused by soybean cyst nematode is prevented, or alternatively, the disease symptoms caused by soybean cyst nematode is minimized or lessened. Thus, improved resistance to soybean cyst nematode can result in reduction of the disease symptoms by at least about 2% to at least about 6%, at least about 5% to about 50%, at least about 10% to about 60%, at least about 30% to about 70%, at least about 40% to about 80%, or at least about 50% to about 90% or greater. Hence, the methods provided herein can be utilized to protect plants from soybean cyst nematode.
    • [0124]
      Screening and selection of soybean cyst nematode resistant soybean plants may be performed, for example, by exposing plants to soybean cyst nematode and selecting those plants showing resistance to soybean cyst nematode. Various assays can be used to measure resistance or improved resistance to soybean cyst nematode. For example, soybean cyst nematode resistance can be determined by visual observations after plant exposure to a particular race of soybean cyst nematode, such as race 1, 2, 3, 5 or 14. Scores range from 1 to 9 and indicate visual observations of resistance as compared to other genotypes in the test. A score of 1 indicates soybean cyst nematode are able to infect the plant and cause yield loss, while a score of 9 indicates soybean cyst nematode resistance. Preliminary scores are reported as double digits, for example, ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.
    • [0125]
      Non-limiting examples of soybean cyst nematode resistance phenotypic screening are described in detail below.
    • [0126]
      Multiple populations of Heterodera glycines are maintained and increased on host plants. These populations are used to identify, purify, and characterize elite soybean varieties for resistance to soybean cyst nematode. The following races of soybean cyst nematode are maintained: Race 1 (Type HG 2.5), Race 2 (Type HG 1.2.5.7), Race 3 (Type HG 0 or Type HG 7), Race 5 (Type HG 2.5.7), and Race 14 (Type HG 1.3.6.7).
    • [0127]
      Eggs or second stage juveniles (J2) are used to inoculate host plants to increase their population. Soybean cyst nematode infestation requires a minimum 35 days before the cysts reach maturity and can be used to inoculate soybean experiments. Cyst eggs/J2 inoculant is harvested through a series of washings, grindings, and screenings. Screens are used progressing from larger to smaller sizes, ending with a #500 (25 μm) screen.
    • [0128]
      Soybean plants are grown in cones. Cones are long containers approximately 12 inches long and 1.5 inches in diameter at the top (e.g., Ray Leach Cone-tainers™). The cone is designed to easily remove the root mass. Three to seven days after planting, an inoculum channel is made in the cone containing the experimental line by poking a 4 inch hole with a 10 ml pipette tip. One ml of inoculum is dispensed into the channel. The plants are watered manually for the duration of the test, with watering being moderately light during the first 3-5 days until J2 infects the roots.
    • [0129]
      Plants are scored approximately 28-35 days following inoculation when cyst reproduction on susceptible checks is sufficiently high. Plants are removed from their cones and the soil is removed from the roots by gently dipping the roots into a bucket of water. The plants are screened to identify native resistance to one or more of the five races of soybean cyst nematode inoculated using a combination of three methods (1) visual 9-6-1 score; (2) visual full count; and/or (3) microscope count score depending on the stage of the line when screened. In general, lines earlier in the development cycle (R1-R2) are screened by the visual 9-6-1 method, and lines that have progressed to later development phases (R3-R5) are screened by the visual full count and/or microscope count method(s).
    • [0130]
      One typical phenotyping method is a visual evaluation of the roots. Susceptible checks are first evaluated for the development of cysts on the root system. These counts are recorded and averaged across the experiment to determine the susceptible (SUS) check average. Roots from the test plants are then scored based on a comparison with the average of the susceptible checks as follows:
    • [0131]
      9=0-15% of the susceptible checks average
    • [0132]
      6=16-40% of the susceptible checks average
    • [0133]
      1=≧41% of the susceptible checks average
    • [0000]
      Visual counts: In this method, known checks are counted and reported in full. Observed cysts on the test plants are counted for comparison to the susceptible check plant scores. Cyst counts are converted to 1-9 scores based on the female index (FI). The female index (FI) is the percentage of the number of females cysts produced on each experimental line divided by the number produced on a standard susceptible soybean check, then the result is multiplied by 100. A low FI (<10) means that the soybean cyst nematode population is not able to reproduce well on the test line, a high FI means that the soybean cyst nematode population is able to reproduce well on the test line.
      Microscope counts: Cysts counts for soybean cyst nematode assays for checks and experimental line are determined by washing cysts from roots and counting the number of cysts under the microscope.
    • [0134]
      At about 28-35 days after inoculation, roots from the susceptible check controls are examined for yellow cysts to assess whether to begin the process of evaluating the test. Experimental lines are compared with known standard checks. Once adequate levels of cysts are detected on the check varieties, plants from the test lines are removed from cones one at a time. Soil is removed from roots by gently dipping the roots into a bucket of water. The root tissue is placed on a 850 micron (#20) pore sieve stacked over a 250 micron (#60) pore sieve and sprayed with a jet of water to dislodge cysts from the roots. Collected cysts are rinsed from the #60 sieve into a clean labeled cup using no more than 30 mls of additional water.
    • [0135]
      Once all the samples are collected, each sample is counted using a gridded counting dish under a stereo microscope. The number of cysts counted are recorded for each sample. Cyst counts on the test plants are converted to the 1-9 scoring scale based on the female index (FI) described above.
    • [0136]
      The following exemplary soybean cyst nematode checks, provided in Table 5, can be planted and used to monitor cyst development:
    • [0000]
      TABLE 5
      Exemplary soybean cyst nematode checks.
      Race 1 Race 2 Race 3 Race 5 Race 14
      92B12 RES 95M60 RES 9182 RES 92B12 RES 9182 RES
      9281 SUS 9281 SUS 9281 SUS 9281 SUS 9281 SUS
      9234 RES PI437654 RES 9234 RES 9234 RES 9234 SUS
      9392 SUS 9392 SUS 9392 SUS 9392 SUS 9392 SUS
      91M12 MR 9234 MR 93B15 MR 91M12 SUS 93B15 MR
      RES = Resistant; SUS = Susceptible; and, MR = Moderately Resistant
    • [0137]
      In some examples, a kit or an automated system for detecting marker loci, haplotypes, and marker profiles, and/or correlating the marker loci, haplotypes, and marker profiles with a desired phenotype (e.g., soybean cyst nematode resistance) are provided. As used herein, “kit” refers to a set of reagents for the purpose of performing the various methods of detecting or identifying herein, more particularly, the identification and/or the detection of a soybean plant or germplasm having improved resistance to soybean cyst nematode.
    • [0138]
      In one embodiment, a kit for detecting or selecting at least one soybean plant or soybean germplasm with resistance or improved resistance to soybean cyst nematode is provided. Such a kit comprises (a) primers or probes for detecting one or more marker loci associated with resistance to soybean cyst nematode, wherein at least one of the primers and probes in the kit are capable of detecting a marker locus, wherein the marker locus is associated with the rhg4 locus on linkage group A2; and (b) instructions for using the primers or probes for detecting the one or more marker loci and correlating the detected marker loci with predicted resistance to soybean cyst nematode.
    • [0139]
      In a specific embodiment, the primers and probes of the kit are capable of detecting a marker locus comprising: (a) S07160-1 or a marker closely linked thereto on linkage group A2; or (ii) a marker locus comprising Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linked thereto.
    • [0140]
      Thus, a typical kit or system can include a set of marker probes or primers configured to detect at least one favorable allele of one or more marker loci associated with resistance to soybean cyst nematode, for instance a favorable marker locus, haplotype or marker profile. These probes or primers can be configured, for example, to detect the marker loci noted in the tables and examples herein, e.g., using any available allele detection format, such as solid or liquid phase array based detection, microfluidic-based sample detection, etc. The systems and kits can further include packaging materials for packaging the probes, primers, or instructions, controls such as control amplification reactions that include probes, primers or template nucleic acids for amplifications, molecular size markers, or the like.
    • [0141]
      A typical system can also include a detector that is configured to detect one or more signal outputs from the set of marker probes or primers, or amplicon thereof, thereby identifying the presence or absence of the allele. A wide variety of signal detection apparatus are available, including photo multiplier tubes, spectrophotometers, CCD arrays, scanning detectors, phototubes and photodiodes, microscope stations, galvo-scans, microfluidic nucleic acid amplification detection appliances and the like. The precise configuration of the detector will depend, in part, on the type of label used to detect the marker allele, as well as the instrumentation that is most conveniently obtained for the user. Detectors that detect fluorescence, phosphorescence, radioactivity, pH, charge, absorbance, luminescence, temperature, magnetism or the like can be used. Typical detector examples include light (e.g., fluorescence) detectors or radioactivity detectors. For example, detection of a light emission (e.g., a fluorescence emission) or other probe label is indicative of the presence or absence of a marker allele. Fluorescent detection is generally used for detection of amplified nucleic acids (however, upstream and/or downstream operations can also be performed on amplicons, which can involve other detection methods). In general, the detector detects one or more label (e.g., light) emission from a probe label, which is indicative of the presence or absence of a marker allele. The detector(s) optionally monitors one or a plurality of signals from an amplification reaction. For example, the detector can monitor optical signals which correspond to “real time” amplification assay results.
    • [0142]
      System or kit instructions that describe how to use the system or kit or that correlate the presence or absence of the favorable allele with the predicted resistance are also provided. For example, the instructions can include at least one look-up table that includes a correlation between the presence or absence of the favorable alleles, haplotypes, or marker profiles and the predicted resistance. The precise form of the instructions can vary depending on the components of the system, e.g., they can be present as system software in one or more integrated unit of the system (e.g., a microprocessor, computer or computer readable medium), or can be present in one or more units (e.g., computers or computer readable media) operably coupled to the detector. As noted, in one typical example, the system instructions include at least one look-up table that includes a correlation between the presence or absence of the favorable alleles and predicted resistance. The instructions also typically include instructions providing a user interface with the system, e.g., to permit a user to view results of a sample analysis and to input parameters into the system.
    • [0143]
      Isolated polynucleotides comprising the nucleic acid sequences of the primers and probes provided herein are also encompassed herein. In one embodiment, the isolated polynucleotide comprises a polynucleotide capable of detecting a marker locus of the soybean genome comprising: (a) S07160-1, or a marker closely linked thereto on linkage group A2; or (b) Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linked thereto.
    • [0144]
      In specific embodiments, the isolated polynucleotide comprises: (a) a polynucleotide comprising SEQ ID NOS: 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10; (c) a polynucleotide having at least 90% sequence identity to SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10; or (d) a polynucleotide comprising at least 10 contiguous nucleotides of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10.
    • [0145]
      In certain embodiments, the isolated nucleic acids are capable of hybridizing under stringent conditions to nucleic acids of a soybean cultivar resistant to soybean cyst nematode, for instance to particular SNPs that comprise a marker locus, haplotype or marker profile.
    • [0146]
      As used herein, a substantially identical or complementary sequence is a polynucleotide that will specifically hybridize to the complement of the nucleic acid molecule to which it is being compared under high stringency conditions. A polynucleotide is said to be the “complement” of another polynucleotide if they exhibit complementarity. As used herein, molecules are said to exhibit “complete complementarity” when every nucleotide of one of the polynucleotide molecules is complementary to a nucleotide of the other. Two molecules are said to be “minimally complementary” if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under at least conventional “low-stringency” conditions. Similarly, the molecules are said to be “complementary” if they can hybridize to one another with sufficient stability to permit them to remain annealed to one another under conventional “high-stringency” conditions.
    • [0147]
      Appropriate stringency conditions which promote DNA hybridization, for example, 6× sodium chloride/sodium citrate (SSC) at about 45° C., followed by a wash of 2×SSC at 50° C., are known to those skilled in the art or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. Typically, stringent conditions for hybridization and detection will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1.0 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C. Optionally, wash buffers may comprise about 0.1% to about 1% SDS. Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours. The duration of the wash time will be at least a length of time sufficient to reach equilibrium.
    • [0148]
      Non-limiting examples of methods and compositions disclosed herein are as follows:
    • [0000]
      1. A method of identifying a first soybean plant or a first soybean germplasm that displays resistance or improved resistance to soybean cyst nematode, the method comprising detecting in the genome of said first soybean plant or in the genome of said first soybean germplasm at least one marker locus that is associated with the resistance, wherein the at least one marker locus comprises (a) S07160-1 or a marker closely linked thereto on linkage group A2; or (b) Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linked thereto.
      2. The method of embodiment 1, wherein at least two marker loci are detected.
      3. The method of embodiment 2, wherein the at least two marker loci comprise a haplotype that is associated with said resistance.
      4. The method of embodiment 1, wherein the germplasm is a soybean variety.
      5. The method of embodiment 1, wherein the method further comprises selecting the first soybean plant or first soybean germplasm or a progeny thereof having the at least one marker locus.
      6. The method of embodiment 5, further comprising crossing the selected first soybean plant or first soybean germplasm with a second soybean plant or second soybean germplasm.
      7. The method of embodiment 6, wherein the second soybean plant or second soybean germplasm comprises an exotic soybean strain or an elite soybean strain.
      8. The method of embodiment 1, wherein the detecting comprises DNA sequencing of at least one of said marker loci.
      9. The method of embodiment 1, wherein the detecting comprises amplifying at least one of said marker loci and detecting the resulting amplified marker amplicon.
      10. The method of embodiment 9, wherein the amplifying comprises:
      (a) admixing an amplification primer or amplification primer pair for each marker locus being amplified with a nucleic acid isolated from the first soybean plant or the first soybean germplasm, wherein the primer or primer pair is complementary or partially complementary to a variant or fragment of the genomic locus comprising the marker locus, and is capable of initiating DNA polymerization by a DNA polymerase using the soybean nucleic acid as a template; and (b) extending the primer or primer pair in a DNA polymerization reaction comprising a DNA polymerase and a template nucleic acid to generate at least one amplicon.
      11. The method of embodiment 10, wherein said method comprises amplifying a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379 or 380.
      12. The method of embodiment 10, wherein said primer or primer pair comprises a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380 or complements thereof.
      13. The method of embodiment 12, wherein said primer or primer pair comprises a nucleic acid sequence comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8 or variants or fragments thereof.
      14. The method of embodiment 13, wherein said primer pair comprises SEQ ID NO: 1 and SEQ ID NO: 2.
      15. The method of embodiment 10, wherein the method further comprises providing one or more labeled nucleic acid probes suitable for detection of each marker locus being amplified.
      16. The method of embodiment 15, wherein said labeled nucleic acid probe comprises a nucleic acid sequence comprising a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380 or complements thereof.
      17. The method of embodiment 16, wherein the labeled nucleic acid probe comprises a nucleic acid sequence comprising SEQ ID NOs: 9 or 10.
      18. An isolated polynucleotide capable of detecting a marker locus of the soybean genome comprising (a) S07160-1 or a marker closely linked thereto on linkage group A2; or (b) Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linked thereto.
      19. The isolated polynucleotide of embodiment 18, wherein the polynucleotide comprises: (a) a polynucleotide comprising SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, or 8; (b) a polynucleotide comprising SEQ ID NOs: 9 or 10; (c) a polynucleotide having at least 90% sequence identity to the polynucleotides set forth in parts (a) or (b); or (d) a polynucleotide comprising at least 10 contiguous nucleotides of the polynucleotides set forth in parts (a) or (b).
      20. A kit for detecting or selecting at least one soybean plant or soybean germplasm with resistance or improved resistance to soybean cyst nematode, the kit comprising:
      a) primers or probes for detecting one or more marker loci associated with resistance to soybean cyst nematode, wherein the primers or probes are capable of detecting a marker locus comprising (i) S07160-1 or a marker closely linked thereto; or (ii) Gm08:8300131, Gm08:8257778, Gm08:8257785, Gm08:8258163, Gm08:8258688, Gm08:8258742, Gm08:8259928, Gm08:8260451, Gm08:8260590, Gm08:8261480, Gm08:8261684, Gm08:8262165, Gm08:8263213, Gm08:8263250, Gm08:8263611, Gm08:8264149, Gm08:8265227, Gm08:8265364, Gm08:8265614, Gm08:8266183, Gm08:8266185, Gm08:8266263, Gm08:8266350, Gm08:8266386, Gm08:8266473, Gm08:8266888, Gm08:8267085, Gm08:8267166, Gm08:8267721, Gm08:8267826, Gm08:8268336, Gm08:8268861, Gm08:8269148, Gm08:8269785, Gm08:8270037, Gm08:8270562, Gm08:8270652, Gm08:8271540, Gm08:8271591, Gm08:8271649, Gm08:8271672, Gm08:8271955, Gm08:8273257, Gm08:8273355, Gm08:8273979, Gm08:8275766, Gm08:8275780, Gm08:8275959, Gm08:8276701, Gm08:8276849, Gm08:8276913, Gm08:8277162, Gm08:8277227, Gm08:8277248, Gm08:8277381, Gm08:8277383, Gm08:8277542, Gm08:8277625, Gm08:8277643, Gm08:8277876, Gm08:8277880, Gm08:8277969, Gm08:8278001, Gm08:8278167, Gm08:8278274, Gm08:8278434, Gm08:8279165, Gm08:8279230, Gm08:8279854, Gm08:8280901, Gm08:8280937, Gm08:8281564, Gm08:8282902, Gm08:8284027, Gm08:8286864, Gm08:8287265, Gm08:8287278, Gm08:8287453, Gm08:8287459, Gm08:8288039, Gm08:8288141, Gm08:8288200, Gm08:8288470, Gm08:8288831, Gm08:8289392, Gm08:8290740, Gm08:8291682, Gm08:8292207, Gm08:8297064, Gm08:8299433, Gm08:8299672, Gm08:8301839, Gm08:8302134, Gm08:8303450, Gm08:8305237, Gm08:8305348, Gm08:8305905, Gm08:8306090, Gm08:8306141, Gm08:8306210, Gm08:8306492, Gm08:8306627, Gm08:8307172, Gm08:8307665, Gm08:8308019, Gm08:8308891, Gm08:8308917, Gm08:8309316, Gm08:8309423, Gm08:8309837, Gm08:8310383, Gm08:8310464, Gm08:8310503, Gm08:8310663, Gm08:8311631, Gm08:8311906, Gm08:8312536, Gm08:8312819, Gm08:8313273, Gm08:8313923, Gm08:8314010, Gm08:8314025, Gm08:8314208, Gm08:8314292, Gm08:8314295, Gm08:8314513, Gm08:8314736, Gm08:8314791, Gm08:8314860, Gm08:8315543, Gm08:8315644, Gm08:8316113, Gm08:8316689, Gm08:8316899, Gm08:8317852, Gm08:8317861, Gm08:8318033, Gm08:8319087, Gm08:8319642, Gm08:8319647, Gm08:8320068, Gm08:8321253, Gm08:8321649, Gm08:8323937, Gm08:8324341, Gm08:8325127, Gm08:8325214, Gm08:8326696, Gm08:8326877, Gm08:8328633, Gm08:8330929, Gm08:8331132, Gm08:8331181, Gm08:8331408, Gm08:8331827, Gm08:8332651, Gm08:8332685, Gm08:8332957, Gm08:8343167, Gm08:8345187, Gm08:8345720, Gm08:8346030, Gm08:8346050, Gm08:8346352, Gm08:8346726, Gm08:8347799, Gm08:8348022, Gm08:8348028, Gm08:8349925, Gm08:8350122, Gm08:8350277, Gm08:8351061, Gm08:8351503, Gm08:8352313, Gm08:8352743, Gm08:8353341, Gm08:8355175, Gm08:8360133, Gm08:8363193, Gm08:8363888, Gm08:8364195 or a marker closely linked thereto; and b) instructions for using the primers or probes for detecting the one or more marker loci and correlating the detected marker loci with predicted resistance to soybean cyst nematode.
    • EXPERIMENTAL
    • [0149]
      The following examples are offered to illustrate, but not to limit the claimed invention. It is understood that the examples and embodiments described herein are for illustrative purposes only, and persons skilled in the art will recognize various reagents or parameters that can be altered without departing from the spirit of the invention or the scope of the appended claims.
    • Example 1 Marker Loci Associated with Soybean Cyst Nematode Resistance on Linkage Group A2
    • [0150]
      A SNP marker for the Rhg4 locus (Soybean Cyst Nematode Resistance) on Linkage Group A2 was developed for use in high throughput genotype screening, this marker, as well as markers genetically associated to this marker, are provided. Markers from this region are relevant to elite breeding populations and facilitate selection of soybean plants with resistance to SCN at the Rhg4 locus tracing back to PI437654 and Peking as well as stacks with other marker assisted traits, including yield genes.
    • [0151]
      S07160-1-Q1 was developed and optimized for high throughput PCR-based methods, such as Taqman™ assays. Optimization involved evaluation of amplification, Res, Sus, and heterozygous clustering, primer length, primer composition and the like. The marker distinguishes between the resistant allele from P1437654 or Peking (C) and a susceptible allele from BSR101 (A). Primers and probes useful for detecting the polymorphism are summarized below in Tables 6 and 7, respectively.
    • [0000]
      TABLE 6 
      Primers
      Oligo Product
      Primers: ID Sequence Size
      Primer 1 136868 TGTGTTGTGTTTGACTGCCATA
      (SEQ ID NO: 1)
      Primer 2 136869 CATTTCCCAAGCCTCTTGAT 117 bp
      (SEQ ID NO: 2)
    • [0000]
      TABLE 7 
      Probes
      Probes: Sequence
      102389 6FAM-ACTAACTGCATAaGATAT (SEQ ID NO: 9)
      102390 VIC-CTAACTGCATAcGATATT (SEQ ID NO: 10)
    • [0152]
      The marker was validated against a panel of 31 public or proprietary soybean lines comprising 2 resistant check lines, 27 susceptible lines, and 2 other lines. A summary of the rhg4 marker is provided below in Table 8.
    • [0000]
      Exemplary Amplification Mix
      H20 4.28 ul
      Hot Tub buffer 0.5 ul
      Rox Dye (50X) 0.075 ul
      DNTPs(24 mM each) 0.039 ul
      Primer(100 uM) 0.0375 ul
      Primer(100 uM) 0.0375 ul
      FAM Probe(100 uM 0.005 ul
      VIC Probe(100 uM 0.005 ul
      Hot Tub enzyme 0.025 ul
      Total volume 5.005 ul
    • [0000]
      TABLE 8
      Summary of rhg4 marker.
      Genetic
      Position Physical Pos_PHI
      Gene/ (genetic map); Map Allele Public Consensus
      locus Markers LG GmConsensus 4.0 Position (R/S) Source Name Map v1.1
      rhg4 S07160-1 A2 46.68 8300131 C/A Peking, pBLT65 51.42
      PI437654
      R = Resistant; S = Susceptible
    • Example 2 Identification of SNPs in Linkage Disequilibrium with Known Mutations at the Rhg4 Locus SUMMARY
    • [0153]
      The Rhg4 locus, which conditions resistance to soybean cyst nematode, has been cloned and found to encode a serine hydroxymethyltransferase (Liu et al. (2012). A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature 492, 256-260). Two non-synonymous base substitutions that tightly correlate with SCN resistance were identified in the Rhg4 allele from the resistant source Forrest (Liu et al. Nature, 2012). Using SNP genotype data obtained from re-sequencing 385 Pioneer proprietary elite lines, 181 SNPs were identified that are in high linkage disequilibrium with the described mutations. These SNPs can be used for a variety of plant breeding efforts, including marker assisted selection of the Rhg4 locus.
    • Methods:
    • [0154]
      Linkage Disequilibrium was calculated using Haploview 4.2. 7810 SNP loci were evaluated across 385 elite lines. An interval of ˜1.2 mb or 6.5 cM (Gm08:7800225-8999989 bp; 48.26-54.80 cM) spanning the Rhg4 mutations was interrogated for SNP selection. An r2 above or equal to 0.8 is considered high for this analysis. Haploview settings were set as follows: Ignore Pairwise comparisons: >100 kb; HW p-value cutoff: 0.000; Min genotype %: 50; Max # mendel errors: 1; Min Minor Allele Frequency=0.01.
    • Results
    • [0155]
      The 181 Rhg4 SNPs in Linkage Disequilibrium with the described mutations (Liu et al. Nature, 2012) are summarized in Table 3B.
    • [0000]
      TABLE 9
      Summary of SEQ ID NOs.
      SEQ ID
      NO Description
      1 Primer 136868
      2 Primer 136869
      3 Primer 100532
      4 Primer 80588
      5 Primer 136870
      6 Primer 136871
      7 Primer 136872
      8 Primer 136873
      9 Probe 102389
      10 Probe 102390
      11 Amplicon comprising resistance allele
      12 Amplicon comprising susceptible allele
      13 Reference Sequence comprising S07160-1 resistance allele
      14 Reference Sequence comprising S07160-1 susceptible allele
      15-380 Consensus Reference Sequences comprising the various
      marker loci provided herein (see Table 3B)
    • [0156]
      All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.
    • [0157]
      Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims.
    Patent Citations
    Cited PatentFiling datePublication dateApplicantTitle
    US20030005491 *5 Jan 20012 Jan 2003Monsanto CompanyNucleic acid molecules and other molecules associated with soybean cyst nematode resistance
    US20090241214 *30 Oct 200824 Sep 2009Michigan State UniversityMarkers For Aphid Resistant Germplasm In Soybean Plants
    US20100275286 *29 May 200828 Oct 2010Monsanto Technology LlcSoybean Polymorphisms And Methods Of Genotyping
    US20110083234 *2 Oct 20107 Apr 2011Nguyen Henry TQuantitative Trait Loci Associated With Soybean Cyst Nematode Resistance And Methods Of Their Use
    Non-Patent Citations
    Reference
    1 *Batley and Edwards, 2007, In; Association Mapping in Plants, pp 95-102.
    2 *Hyten et al., 2010, Crop Science 50: 960-968.
    3 *Thomas, 1985, J. Opt. Soc. Am. 2: 1457-1467.
    4 *Yue et al., 2000, Euphytica 116: 181-186.
    Classifications
    U.S. Classification435/6.11, 536/24.3
    International ClassificationC12Q1/68
    Cooperative ClassificationC12Q2600/158, C12Q2600/13, C12Q1/6895, C12Q2600/156, C12Q2600/172
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