Genetic loci associated with phytophthora tolerance in soybean and methods of use

Abstract

Various methods and compositions are provided for identifying and/or selecting soybean plants or soybean germplasm with tolerance or improved tolerance to Phytophthora infection. In certain embodiments, the method comprises detecting at least one marker locus that is associated with tolerance to Phytophthora infection. In other embodiments, the method further comprises detecting at least one marker profile or haplotype associated with tolerance to Phytophthora infection. 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 tolerance or improved tolerance to Phytophthora infection.

That which is claimed: 
     
         1 . A method of identifying a first soybean plant or a first soybean germplasm that displays tolerance or improved tolerance to  Phytophthora  infection, 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 tolerance, wherein:
 (a) the at least one marker locus comprises S08291-1, S07292-1, S08242-1, S16592-001 or a marker closely linked thereto on linkage group N;   (b) the at least one marker locus comprises S07963-2, S07372-1, S00009-01, S08013-1, any of the Rps1k marker loci in Table 1B or a marker closely linked thereto on linkage group N;   (c) the at least one marker locus comprises S06862-1, S06863-1, S06864-1, S06865-1, S11652-1, S11682-1 or a marker closely linked thereto on linkage group J;   (d) the at least one marker locus comprises S09018-1, S08342-1, S07163-1 or a marker closely linked thereto on linkage group F; or   (e) the at least one marker locus comprises S08442-1, S08341-1 or a marker closely linked thereto on linkage group G.   
     
     
         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 or a marker profile that is associated with said tolerance. 
     
     
         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
 (a) amplifying a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 191-1302, 1343, 1345, 1346, 1347, 1348, 1349, 1350, 1351, 1352, 1353, 1354, 1355, 1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366, 1367, 1368, 1369, 1370, 1371, 1372, 1373, 1374, 1375, 1376, 1377, 1378, 1379, 1380, 1381, 1382, 1383, 1384, 1385, 1386, 1387, 1388, 1389, 1390, 1391, 1392, 1393 or 1394;   (b) amplifying a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 173, 174, 175, 176, 177, 178, 179 or 180;   (c) amplifying a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 181, 182, 183, 184, 185 or 186; or   (d) amplifying a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 187, 188, 189 or 190.   
     
     
         12 . The method of  claim 10 , wherein said primer or primer pair comprises
 (a) a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 191-1302, 1343, 1345, 1346, 1347, 1348, 1349, 1350, 1351, 1352, 1353, 1354, 1355, 1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366, 1367, 1368, 1369, 1370, 1371, 1372, 1373, 1374, 1375, 1376, 1377, 1378, 1379, 1380, 1381, 1382, 1383, 1384, 1385, 1386, 1387, 1388, 1389, 1390, 1391, 1392, 1393, 1394 or complements thereof;   (b) a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 173, 174, 175, 176, 177, 178, 179, 180 or complements thereof;   (c) a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 181, 182, 183, 184, 185, 186 or complements thereof; or   (d) a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 187, 188, 189, 190 or complements thereof.   
     
     
         13 . The method of  claim 12 , wherein said primer or primer pair comprises a nucleic acid sequence comprising
 (a) a nucleic acid sequence comprising 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, 1339, 1340 or variants or fragments thereof;   (b) a nucleic acid sequence comprising SEQ ID NOs: 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 or variants or fragments thereof;   (c) a nucleic acid sequence comprising SEQ ID NOs: 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92 or variants or fragments thereof; or   (d) a nucleic acid sequence comprising SEQ ID NOs: 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104 or variants or fragments thereof.   
     
     
         14 . The method of  claim 13 , wherein said primer pair comprises:
 a) SEQ ID NO: 1 and SEQ ID NO:2, SEQ ID NO: 9 and SEQ ID NO:10, SEQ ID NO: 20 and SEQ ID NO:21, SEQ ID NO: 22 and SEQ ID NO: 23, SEQ ID NO: 24 and SEQ ID NO: 25, SEQ ID NO: 36 and SEQ ID NO: 37, SEQ ID NO: 38 and SEQ ID NO: 39 or SEQ ID NO: 1339 and SEQ ID NO: 1340;   (b) SEQ ID NO: 40 and SEQ ID NO: 41, SEQ ID NO: 46 and SEQ ID NO: 47, SEQ ID NO: 52 and SEQ ID NO: 53, SEQ ID NO: 58 and SEQ ID NO: 59, SEQ ID NO: 64 and SEQ ID NO: 65 or SEQ ID NO: 75 and SEQ ID NO: 76;   (c) SEQ ID NO: 81 and SEQ ID NO: 82, SEQ ID NO: 89 and SEQ ID NO: 90 or SEQ ID NO: 91 and SEQ ID NO: 92; or   (d) SEQ ID NO: 95 and SEQ ID NO: 96 or SEQ ID NO: 101 and SEQ ID NO: 102.   
     
     
         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) a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 191-1302, 1343, 1345, 1346, 1347, 1348, 1349, 1350, 1351, 1352, 1353, 1354, 1355, 1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366, 1367, 1368, 1369, 1370, 1371, 1372, 1373, 1374, 1375, 1376, 1377, 1378, 1379, 1380, 1381, 1382, 1383, 1384, 1385, 1386, 1387, 1388, 1389, 1390, 1391, 1392, 1393, 1394 or complements thereof;   (b) a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 173, 174, 175, 176, 177, 178, 179, 180 or complements thereof;   (c) a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 181, 182, 183, 184, 185, 186 or complements thereof; or   (d) a variant or fragment of one or more polynucleotides comprising SEQ ID NOs: 187, 188, 189, 190 or complements thereof.   
     
     
         17 . The method of  claim 16 , wherein the labeled nucleic acid probe comprises:
 (a) a nucleic acid sequence comprising SEQ ID NOs: 105, 106, 107, 108, 109, 110, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 1341 or 1342;   (b) a nucleic acid sequence comprising SEQ ID NOs: 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138 or 139;   (c) a nucleic acid sequence comprising SEQ ID NOs: 140, 141, 142, 143, 144, 145, 146, 147, 148 or 149; or   (d) a nucleic acid sequence comprising SEQ ID NOs: 150, 151, 152, 153 or 154.   
     
     
         18 . An isolated polynucleotide capable of detecting a marker locus of the soybean genome comprising:
 (a) S08291-1, S07292-1, S08242-1, S16592-001, S07963-2, S07372-1, S00009-01, S08013-1, any of the Rps1k marker loci in Table 1B or a marker closely linked thereto on linkage group N;   (b) S06862-1, S06863-1, S06864-1, S06865-1, S11652-1, S11682-1 or a marker closely linked thereto on linkage group J;   (c) S09018-1, S08342-1, S07163-1 or a marker closely linked thereto on linkage group F; or   (d) S08442-1, S08341-1 or a marker closely linked thereto on linkage group G.   
     
     
         19 . The isolated polynucleotide of  claim 18 , 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, 1339 or 1340; 
 (ii) SEQ ID NOs: 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 or 78; 
 (iii) SEQ ID NOs: 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 or 92; or 
 (iv) SEQ ID NOs: 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103 or 104; 
   (b) a polynucleotide comprising:
 (i) SEQ ID NOs: 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 1341 or 1342; 
 (ii) SEQ ID NOs: 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138 or 139; 
 (iii) SEQ ID NOs: 140, 141, 142, 143, 144, 145, 146, 147, 148 or 149; or 
 (iv) SEQ ID NOs: 150, 151, 152, 153 or 154; 
   (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 tolerance or improved tolerance to  Phytophthora  infection, the kit comprising:
 (a) primers or probes for detecting one or more marker loci associated with tolerance to  Phytophthora  infection, wherein the primers or probes are capable of detecting a marker locus, wherein:
 (i) the at least one marker locus comprises S08291-1, S07292-1, S08242-1, S16592-001 or a marker closely linked thereto on linkage group N; 
 (ii) the at least one marker locus comprises S07963-2, S07372-1, S00009-01, S08013-1, any of the Rps1k marker loci in Table 1B or a marker closely linked thereto on linkage group N; 
 (iii) the at least one marker locus comprises S06862-1, S06863-1, S06864-1, S06865-1, S11652-1, S11682-1 or a marker closely linked thereto on linkage group J; 
 (iv) the at least one marker locus comprises S09018-1, S08342-1, S07163-1 or a marker closely linked thereto on linkage group F; or 
 (v) the at least one marker locus comprises S08442-1, S08341-1 or a marker closely linked thereto on linkage group G; 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 tolerance to  Phytophthora  infection.