Genetic loci associated with soybean cyst nematode resistance and methods of use

Abstract

Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with 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 improved resistance to soybean cyst nematode.

1 . A method of identifying a first soybean plant or a first soybean germplasm that displays 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 is between about marker Satt574 and about marker Satt615 on linkage group D2.   
     
     
         2 . The method of  claim 1 , wherein:
 the at least one marker locus comprises S07161-1-Q1 or a marker closely linked thereto.   
     
     
         3 . The method of  claim 1 , wherein at least two marker loci are detected. 
     
     
         4 . The method of  claim 3 , wherein the at least two marker loci comprise a haplotype that is associated with said resistance. 
     
     
         5 . The method of  claim 3 , wherein the at least two marker loci comprise a marker profile that is associated with said resistance. 
     
     
         6 . The method of  claim 1 , wherein the germplasm is a soybean variety. 
     
     
         7 . 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. 
     
     
         8 . The method of  claim 7 , further comprising crossing the selected first soybean plant or first soybean germplasm with a second soybean plant or second soybean germplasm. 
     
     
         9 . The method of  claim 8 , wherein the second soybean plant or second soybean germplasm comprises an exotic soybean strain or an elite soybean strain. 
     
     
         10 . The method of  claim 1 , wherein the detecting comprises amplifying said marker loci and detecting the resulting amplified marker amplicon. 
     
     
         11 . The method of  claim 10 , 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.   
     
     
         12 . The method of  claim 11 , wherein said method comprises:
 amplifying a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 157 or 158.   
     
     
         13 . The method of  claim 11 , wherein said primer or primer pair comprises:
 a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 157, 158, or complements thereof.   
     
     
         14 . The method of  claim 13 , wherein said primer or primer pair comprises:
 a nucleic acid sequence comprising SEQ ID NOs: 82, 83, 84, 85, 86, or variants or fragments thereof.   
     
     
         15 . The method of  claim 14 , wherein said primer pair comprises:
 SEQ ID NO: 82 and SEQ ID NO: 83.   
     
     
         16 . The method of  claim 11 , wherein the method further comprises providing one or more labeled nucleic acid probes suitable for detection of each marker locus being amplified. 
     
     
         17 . The method of  claim 16 , 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: 157, 158, or complements thereof.   
     
     
         18 . The method of  claim 17 , wherein the labeled nucleic acid probe comprises:
 a nucleic acid sequence comprising SEQ ID NOs: 109 or 110.   
     
     
         19 . The method of  claim 1 , wherein the detecting comprises DNA sequencing of said marker loci. 
     
     
         20 . An isolated polynucleotide capable of detecting a marker locus of the soybean genome comprising:
 (a) S04196-1-B, S04938-1-A, S04937-1-Q1, S08344-1-Q1, S08343-1-Q1, S08346-1-Q1, S06786-1, S06787-1, S06803-1, S04197-1, or a marker closely linked thereto;   (b) S07162-1-Q1 or a marker closely linked thereto;   (c) S07161-1-Q1 or a marker closely linked thereto;   (d) S00350-1-A, S02183-1-A, or a marker closely linked thereto;   (e) S01519-1-A, S08177-1-Q1, S00479-1-A, S02136-1-A, S00875-1-A, S12875-1-Q1, S12950-1-Q1, S12947-1-Q1, S12933-1-Q1, S12853-1-Q1, S03246-1-A, S12962-1-Q1 S00144-1-A, S08166-1-Q1, S01081, S02621-1-A, or a marker closely linked thereto;   (f) S02874-1-A, S04785-1-A, or a marker closely linked thereto;   (g) S04348-1-A, S01209-1-A, S01999-1-A, or a marker closely linked thereto;   (h) S04937-2-A, S04937-1-Q1, S04938-1-A, S04938-2-A, S06786-2-Q1, S06786-3-Q1, S06786-1-Q1, S06787-2-Q1, S06787-1-Q1, S06803-1-Q1, S06804-1-Q1, S06788-1-Q1, S06805-1-Q1, S06789-1-Q1, S06790-1-Q1, S06791-2-Q1, S06791-1-Q1, S06792-1-Q1, or a marker closely linked thereto;   (i) S03252-1-A, S02112-1-A, or a marker closely linked thereto; or   (j) S02074-1-A, S03991-1-A, or a marker closely linked thereto.   
     
     
         21 . The isolated polynucleotide of  claim 20 , wherein the polynucleotide comprises:
 (a) a polynucleotide comprising:
 (i) SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 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 or 71; 
 (ii) SEQ ID NOs: 72, 73, 74, 75, 76, 77, 78, 79, 80 or 81; 
 (iii) SEQ ID NOs: 82, 83, 84, 85 or 86; or 
 (iv) SEQ ID NOs: 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 or 248; 
   (b) a polynucleotide comprising:
 (i) SEQ ID NOs: 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105 or 106; 
 (ii) SEQ ID NOs: 107 or 108; 
 (iii) SEQ ID NOs: 109 or 110; or 
   (iv) SEQ ID NOs: 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 or 338;   (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).   
     
     
         22 . A kit for detecting or selecting at least one soybean plant or soybean germplasm with 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, wherein:
 (i) the marker locus is between about marker Sat_123 and about marker Satt453 on linkage group B1; 
 (ii) the marker locus is between about marker Sat_207 and about marker Satt713 on linkage group C1; 
 (iii) the marker locus is between about marker Satt574 and about marker Satt615 on linkage group D2; 
 (iv) the marker locus is flanked by marker locus S00875 and S02621 on linkage group D1b; 
 (v) the marker locus is flanked by marker locus S00479 and S02136 on linkage group D1b; 
 (vi) the marker locus is flanked by marker locus Sat_264 and BARC-020449-04623 on linkage group B2; 
 (vii) the marker locus is flanked by marker locus S02874 and S04785 on linkage group B2; 
 (viii) the marker locus is flanked by marker locus S04348 and S01999 on linkage group B1; 
 (ix) the marker locus is flanked by marker locus S01209 and S01999 on linkage group B1; 
 (x) the marker locus is flanked by marker locus Satt557 and Satt307 on linkage group C2; 
 (xi) the marker locus is flanked by marker locus S03252 and S02112 on linkage group C2; 
 (xii) the marker locus comprises S00350-1-A, S02183-1-A, or a marker closely linked thereto; or 
 (xiii) the marker locus is flanked by marker locus S02074 and S03991 on linkage group L; 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.   
     
     
         23 . The kit of  claim 22 , wherein the primers or probes are capable of detecting a marker locus comprising
 (a) S04196-1-B, S04938-1-A, S04937-1-Q1, S08344-1-Q1, S08343-1-Q1, S08346-1-Q1, S06786-1, S06787-1, S06803-1, S04197-1, or a marker closely linked thereto;   (b) S07162-1-Q1 or a marker closely linked thereto;   (c) S07161-1-Q1 or a marker closely linked thereto;   (d) S01519-1-A, S08177-1-Q1, S00479-1-A, S02136-1-A, S00875-1-A, S12875-1-Q1, S12950-1-Q1, S12947-1-Q1, S12933-1-Q1, S12853-1-Q1, S03246-1-A, S12962-1-Q1 S00144-1-A, S08166-1-Q1, S01081, S02621-1-A, or a marker closely linked thereto;   (e) S02874-1-A, S04785-1-A, or a marker closely linked thereto;   (f) S04348-1-A, S01209-1-A, S01999-1-A, or a marker closely linked thereto;   (g) S04937-2-A, S04937-1-Q1, S04938-1-A, S04938-2-A, S06786-2-Q1, S06786-3-Q1, S06786-1-Q1, S06787-2-Q1, S06787-1-Q1, S06803-1-Q1, S06804-1-Q1, S06788-1-Q1, S06805-1-Q1, S06789-1-Q1, S06790-1-Q1, S06791-2-Q1, S06791-1-Q1, S06792-1-Q1, or a marker closely linked thereto;   (h) S03252-1-A, S02112-1-A, or a marker closely linked thereto; or   (i) S02074-1-A, S03991-1-A, or a marker closely linked thereto.   
     
     
         24 . The method of  claim 1 , further comprising detecting in the genome of said first soybean plant or in the genome of said first soybean germplasm at least one or more marker locus that is associated with the resistance, wherein:
 (a) the at least one marker locus is between about marker Sat_123 and about marker Satt453 on linkage group B1;   (b) the at least one marker locus is between about marker Sat_207 and about marker Satt713 on linkage group C1;   (c) the at least one marker locus is between about marker Satt574 and about marker Satt615 on linkage group D2;   (d) the at least one marker locus is flanked by marker locus S00875 and S02621 on linkage group D1b;   (e) the at least one marker locus is flanked by marker locus S00479 and S02136 on linkage group D1b;   (f) the at least one marker locus is flanked by marker locus Sat_264 and BARC-020449-04623 on linkage group B2;   (g) the at least one marker locus is flanked by marker locus S02874 and S04785 on linkage group B2;   (h) the at least one marker locus is flanked by marker locus S04348 and S01999 on linkage group B1;   the at least one marker locus is flanked by marker locus S01209 and S01999 on linkage group B1;   the at least one marker locus is flanked by marker locus Satt557 and Satt307 on linkage group C2;   (k) the at least one marker locus is flanked by marker locus S03252 and S02112 on linkage group C2;   (1) the at least one marker locus comprises S00350-1-A, S02183-1-A, or a marker closely linked thereto; or   (m) the at least one marker locus is flanked by marker locus S02074 and S03991 on linkage group L.