Rag-based selection methods for improving aphid resistance in soybeans

Abstract

This invention relates to methods of improving resistance to aphids in soybean plants, as well as methods for identifying and/or selecting soybean plants or germplasm that display improved resistance to one or more biotypes of soybean aphid. In certain examples, the method comprises selecting a first and second soybean plant or germplasm, each of which has a different favorable Rag1, Rag2, or Rag3, allele, haplotype, or marker profile, and crossing those first and second soybean plants to produce a progeny plant with improved soybean aphid resistance. This invention further relates to markers, primers, probes, kits, systems, etc., useful for carrying out the methods described herein.

What is claimed is: 
     
         1 . A method of improving resistance to one or more soybean aphid biotypes in a soybean plant, line, or strain, the improved resistance comprising one or more of improved antibiosis resistance and improved antixenosis resistance; the method comprising:
 a) selecting a first soybean plant or germplasm, or a progeny thereof, wherein said first soybean plant, germplasm, or progeny comprises a favorable allele of at least one of Rag1, Rag2, and Rag3;   b) selecting a second soybean plant or germplasm, or a progeny thereof, wherein said second soybean plant, germplasm, or progeny comprises a favorable allele of at least one of Rag1, Rag2, and Rag3 different than that of said first soybean plant, germplasm, or progeny; and   c) crossing said first soybean plant, germplasm, or progeny with said second soybean plant, germplasm, or progeny.   
     
     
         2 . The method of  claim 1 , wherein said first soybean plant, germplasm, or progeny and said second soybean plant, germplasm, or progeny collectively comprise a favorable allele of all three of Rag1, Rag2, and Rag3. 
     
     
         3 . The method of  claim 1 , wherein the improved soybean aphid resistance comprises both improved antibiosis resistance and improved antixenosis resistance. 
     
     
         4 . The method of  claim 1 , wherein the improved soybean aphid resistance comprises improved resistance to at least two soybean aphid biotypes. 
     
     
         5 . The method of  claim 1 , wherein the improved soybean aphid resistance comprises improved resistance to at least three of soybean aphid biotypes 1, 2, 3, X, and Y. 
     
     
         6 . The method of  claim 1 , wherein the selection further comprises detecting said favorable allele, said detecting step comprising amplifying a marker nucleic acid or a portion of the marker nucleic acid and detecting the resulting amplified marker nucleic acid. 
     
     
         7 . The method of  claim 6 , wherein the amplifying comprises performing a polymerase chain reaction (PCR) using one or more nucleic acid from the plant as a template in the PCR. 
     
     
         8 . The method of  claim 1 , wherein said favorable alleles are selected from the group consisting of Rag1-b, Rag1-c, Rag2-d, Rag3-b, and Rag3-d. 
     
     
         9 . The method of  claim 1 , wherein said favorable allele in said first soybean plant comprises Rag1-a, and wherein said favorable allele in said second soybean plant comprises Rag2-b. 
     
     
         10 . The method of  claim 6 , wherein said amplifying comprises amplification of one or more portions of the soybean genome selected from the group consisting of SEQ ID NOs: 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 84, 89, 94, 103, 114, 121, 126, 131, and 136. 
     
     
         11 . The method of  claim 10 , wherein said amplification comprises providing one or more nucleic acid primers, wherein said primers comprise a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1, 2, 6, 7, 11, 12, 16, 17, 21, 22, 26, 27, 31, 32, 36, 37, 41, 42, 46, 47, 51, 52, 56, 57, 61, 62, 66, 67, 71, 72, 76, 77, 80, 81, 85, 86, 90, 91, 95, 96, 99, 100, 104, 105, 108, 109, 110, 111, 115, 116, 119, 120, 122, 123, 127, 128, 132, and 133. 
     
     
         12 . The method of  claim 1 , wherein said detecting comprises hybridization with one or more nucleic acid probes, wherein said probes comprise a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 3, 4, 8, 9, 13, 14, 18, 19, 23, 24, 28, 29, 33, 34, 38, 39, 43, 44, 48, 49, 53, 54, 58, 59, 63, 64, 68, 69, 73, 74, 78, 79, 82, 83, 87, 88, 92, 93, 97, 98, 101, 102, 106, 107, 112, 113, 117, 118, 124, 125, 129, 130, 134, 135, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 84, 89, 94, 103, 114, 121, 126, 131, and 136. 
     
     
         13 . A plant produced by the method of  claim 1 . 
     
     
         14 . A method of selecting a soybean plant or germplasm that displays improved resistance to one or more soybean aphid biotypes, the improved resistance comprising one or more of improved antibiosis resistance and improved antixenosis resistance, the method comprising:
 detecting in a first soybean plant or germplasm, or a part thereof, a favorable allele of at least two of Rag1, Rag2, and Rag3; and   selecting the first soybean plant or germplasm, or selecting a progeny of the first soybean plant or germplasm.   
     
     
         15 . The method of  claim 14 , wherein the detecting involves detection of a favorable allele of all three of Rag1, Rag2, and Rag3. 
     
     
         16 . The method of  claim 14 , wherein the improved soybean aphid resistance comprises both improved antibiosis resistance and improved antixenosis resistance. 
     
     
         17 . The method of  claim 14 , wherein the improved soybean aphid resistance comprises improved resistance to at least two soybean aphid biotypes. 
     
     
         18 . The method of  claim 14 , wherein the improved soybean aphid resistance comprises improved resistance to at least three of soybean aphid biotypes 1, 2, 3, X, and Y. 
     
     
         19 . The method of  claim 14 , wherein said favorable alleles are selected from the group consisting of Rag1-b, Rag1-c, Rag2-d, Rag3-b, and Rag3-d. 
     
     
         20 . The method of  claim 14 , wherein said favorable alleles comprise Rag1-a and Rag2-b. 
     
     
         21 . The method of  claim 14 , wherein the detecting comprises amplifying a marker nucleic acid or a portion of the marker nucleic acid and detecting the resulting amplified marker nucleic acid. 
     
     
         22 . The method of  claim 21 , wherein the amplifying comprises performing a polymerase chain reaction (PCR) using one or more nucleic acid from the plant as a template in the PCR. 
     
     
         23 . The method of  claim 22 , wherein said amplifying comprises amplification of one or more portions of the soybean genome selected from the group consisting of SEQ ID NOs: 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 84, 89, 94, 103, 114, 121, 126, 131, and 136. 
     
     
         24 . The method of  claim 13 , wherein said amplification comprises providing one or more nucleic acid primers, wherein said primers comprise a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 1, 2, 6, 7, 11, 12, 16, 17, 21, 22, 26, 27, 31, 32, 36, 37, 41, 42, 46, 47, 51, 52, 56, 57, 61, 62, 66, 67, 71, 72, 76, 77, 80, 81, 85, 86, 90, 91, 95, 96, 99, 100, 104, 105, 108, 109, 110, 111, 115, 116, 119, 120, 122, 123, 127, 128, 132, and 133. 
     
     
         25 . The method of  claim 14 , wherein said detecting comprises hybridization with one or more nucleic acid probes, wherein said probes comprise a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 3, 4, 8, 9, 13, 14, 18, 19, 23, 24, 28, 29, 33, 34, 38, 39, 43, 44, 48, 49, 53, 54, 58, 59, 63, 64, 68, 69, 73, 74, 78, 79, 82, 83, 87, 88, 92, 93, 97, 98, 101, 102, 106, 107, 112, 113, 117, 118, 124, 125, 129, 130, 134, 135, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 84, 89, 94, 103, 114, 121, 126, 131, and 136. 
     
     
         26 . The method of  claim 14 , further comprising crossing the selected first soybean plant or germplasm with a second soybean plant or germplasm. 
     
     
         27 . The method of  claim 21 , wherein the second soybean plant or germplasm comprises an exotic soybean strain or an elite soybean strain. 
     
     
         28 . A plant selected by the method of  claim 14 . 
     
     
         29 . A plant produced by the method of  claim 21 . 
     
     
         30 . A kit for selecting a soybean plant or germplasm that displays improved resistance to one or more soybean aphid biotypes; the kit comprising:
 a) primers or probes for detecting a favorable allele of at least two of Rag1, Rag2, and Rag3; and   b) instructions for using the primers or probes for detecting the one or more favorable alleles and correlating the detected alleles with predicted improved resistance to aphids.   
     
     
         31 . The kit of  claim 30 , wherein the kit comprises primers or probes for detecting a favorable allele of all three of Rag1, Rag2, and Rag3. 
     
     
         32 . The plant of any one of  claims 13 ,  28 ,  29 , wherein said plant comprises stacked Rag haplotypes selected from the group consisting of a) Rag1-a/Rag2-b; b) Rag1-b/Rag3-b; and c) Rag1-c/Rag3-d. 
     
     
         33 . An isolated polynucleotide capable of detecting: a) a marker locus selected from the group consisting of S15354-001-Q001, S14181-1-Q1, S13871-1-Q1, S14161-1-Q10, S09515-1-Q1, S14151-1-Q1, S14151-2-Q4, S07164-1-Q12, S14182-1-Q1, S00812-1-A, S02780-1-A, S01190-1-A, S14761-001-Q001, S14771-001-Q001, S07165-1-Q3, S14778-001-Q001, S01164-1-Q1 S13662-1-Q3/Q6, S13663-1-Q1, S11411-1-Q1, S13664-1-Q1/Q002, S13672-1-Q1/Q2/Q3, S13674-1-Q1/Q007, S13675-2-Q1; or b) a SNP loci located at a physical position selected from the group consisting of 5453161, 5516385, 5516818, 5598980, 5602544, 5605203, 5605275, 5608106, 5630404, 6754454, and 6671535 on LG-M of the soybean genome, 28187733, 28829625, 28837383, 29097652, 29678319, and 29825175 on LG-F of the soybean genome; and 5140274, 5919650, 5960726, 6066531, 6231641, 6524877, and 6542422 on LG-J of the soybean genome. 
     
     
         34 . The isolated polynucleotide of  claim 33 , wherein the polynucleotide comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-136. 
     
     
         35 . A kit for detecting or selecting at least one soybean plant with stacked Rag haplotypes, the kit comprising:
 a) primers or probes for detecting two or more marker loci associated with one or more quantitative trait loci associated with improved aphid resistance, wherein the primers or probes comprise an isolated nucleic acid of  claim 24 ; and   b) instructions for using the primers or probes for detecting the two or more marker loci and correlating the detected marker loci with predicted improved resistance to aphid infestation.