# US 2013/0160155 A1 · Methods to Identify Soybean Aphid Resistant Quantitative Trait Loci in Soybean and Compositions Thereof > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2013/0160155 A1 - Document ID: US20130160155A1 - Status: Published application - Kind: A1 - Application number: 13/781,143 - Filed: 2013-02-28 - Published: 2013-06-20 - Earliest claimed: 2007-08-08 - Assignees: University of Georgia Research Foundation, Inc.; Monsanto Technology LLC - Inventors: VERGEL CONCIBIDO; JAMES NARVEL; JENNIFER YATES; HENRY ROGER BOERMA - Web page: https://patentgrep.com/patent/US20130160155A1 ## CPC - A01H 1/00: Processes for modifying genotypes {; Plants characterised by associated natural traits} (A01H4/00 takes precedence) - A01H 1/045: {using molecular markers} - A01H 5/10: Seeds - A01H 6/542: {Glycine max [soybean]} - C07K 14/415: from plants - C07K 16/16: against material from plants - C12N 15/8247: {involving modified lipid metabolism, e.g. seed oil composition} - C12N 15/8274: {for herbicide resistance} - C12N 15/8275: {Glyphosate} - C12N 15/8278: {Sulfonylurea} - C12N 15/8279: {for biotic stress resistance, pathogen resistance, disease resistance} - C12N 15/8286: {for insect resistance} - C12Q 1/6895: for plants, fungi or algae - C12Q 2600/13: Plant traits - C12Q 2600/156: Polymorphic or mutational markers - C12Q 2600/172: Haplotypes - Y02A 40/146: Genetically Modified [GMO] plants, e.g. transgenic plants - Y10T 436/143333: Saccharide [e.g., DNA, etc.] - A01H: NEW PLANTS OR {NON-TRANSGENIC} PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES - C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00) - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES - Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE - Y10T: TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION ## Abstract The present invention is in the field of plant breeding and aphid resistance. More specifically, the invention includes a method for breeding soybean plants containing quantitative trait loci that are associated with resistance to aphids, Aphis glycines. The invention further includes method for monitoring the introgression quantitative trait loci (QTL) conferring aphid resistance into elite germplasm in a breeding program. ## Claims ### Claim 1 A method of introgressing an allele into a soybean plant comprising: A) Providing a population of soybean plants, B) Genotyping at least one soybean plant in the population with respect to a soybean genomic nucleic acid marker selected from the group comprising SEQ ID NO: 85 through SEQ ID NO: 120, C) Selecting from the population at least one soybean plant comprising at least one allele associated with aphid resistance. ### Claim 2 (depends on 1) The method according to claim 1, wherein said selected soybean plants exhibit at least partial resistance to aphids. ### Claim 3 (depends on 1) The method according to claim 1, wherein said selected soybean plants exhibit at least substantial resistance to aphids. ### Claim 4 (depends on 1) The method of claim 1, wherein the genotype is determined by an assay which is selected from the group consisting of single base extension (SBE), allele-specific primer extension sequencing (ASPE), DNA sequencing, RNA sequencing, micro-array based analyses, universal PCR, allele specific extension, hybridization, mass spectrometry, ligation, extension-ligation, and Flap-Endonuclease-mediated assays. ### Claim 5 (depends on 1) The method of claim 1 wherein the soybean genomic nucleic acid marker selected from the group consisting of SEQ ID NO: 85 and SEQ ID NO: 86. ### Claim 6 (depends on 1) An elite soybean plant obtained by the process of claim 1. ### Claim 7 A method of introgressing an allele into a soybean plant comprising: C) crossing at least one aphid resistant soybean plant with at least one aphid sensitive soybean plant in order to form a segregating population, B) screening said segregating population with one or more nucleic acid markers to determine if one or more soybean plants from said segregating population contains a aphid resistant allele, wherein said aphid resistant allele is an allele selected from the group consisting of 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, and 28 aphid resistant loci where one or more alleles at one or more of their loci are selected from the group consisting of aphid resistance allele 1, aphid resistance allele 2, aphid resistance allele 3, aphid resistance allele 4, aphid resistance allele 5, aphid resistance allele 6, aphid resistance allele 7, aphid resistance allele 8, aphid resistance allele 9, aphid resistance allele 10, aphid resistance allele 11, aphid resistance allele 12, aphid resistance allele 13, aphid resistance allele 14, aphid resistance allele 15, aphid resistance allele 16, aphid resistance allele 17, aphid resistance allele 18, aphid resistance allele 19, aphid resistance allele 20, aphid resistance allele 21, aphid resistance allele 22, aphid resistance allele 23, aphid resistance allele 24, aphid resistance allele 25, aphid resistance allele 26, aphid resistance allele 27, aphid resistance allele 28, aphid resistance allele 29, aphid resistance allele 30, aphid resistance allele 31, aphid resistance allele 32, aphid resistance allele 33, aphid resistance allele 34, aphid resistance allele 35, and aphid resistance allele 36. ### Claim 8 (depends on 7) A method according to claim 7, wherein at least one of said one or more markers is located within 30 cM of said resistant allele. ### Claim 9 (depends on 7) A method according to claim 7, wherein at least one of said one or more markers is located within 20 cM of said resistant allele. ### Claim 10 (depends on 7) A method according to claim 7, wherein at least one of said one or more markers is located within 2 cM of said resistant allele. ### Claim 11 (depends on 7) A method according to claim 7, wherein at least one of said one or more markers is located within 1 cM of said resistant allele. ### Claim 12 (depends on 9) An elite soybean plant obtained by the method of claim 9. ### Claim 13 (depends on 12) The elite soybean plant according to claim 12, wherein said elite soybean plant exhibits a transgenic trait. ### Claim 14 (depends on 12) The elite soybean plant according to claim 12, wherein said transgenic trait is selected from the group consisting of herbicide tolerance, pest resistance, oil composition, and others. ### Claim 15 (depends on 12) The elite soybean plant according to claim 12, wherein said herbicide tolerance is selected from the group consisting of glyphosate, dicamba, glufosinate, sulfonylurea, bromoxynil and norflurazon herbicides. ### Claim 16 (depends on 12) The elite soybean plant according to claim 12, wherein said nucleic acid sequence is present as a single copy in said elite soybean plant. ### Claim 17 (depends on 12) The elite soybean plant according to claim 12, wherein said nucleic acid sequence is present in two copies in said elite soybean plant. ### Claim 18 (depends on 12) The elite soybean plant of claim 12, wherein said elite soybean plant exhibits at least partial resistance to aphid. ### Claim 19 (depends on 16) The elite soybean plant of claim 16, wherein said elite soybean plant exhibits at least substantial resistance to aphids. ### Claim 20 A substantially purified nucleic acid molecule for the detection of loci related to aphid resistance comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 175 and complements thereof. ### Claim 21 (depends on 20) A vector comprising the nucleic acid fragment of claim 20. ### Claim 22 (depends on 21) An expression product of the vector of claim 21 expressed in a host compatible with said vector. ### Claim 23 (depends on 22) An antibody to the expression product of claim 22. ### Claim 24 A method of identifying an aphid resistance allele in a soybean plant comprising detecting a locus associated with a SNP marker selected from the group consisting of SEQ ID NO: 85 through SEQ ID NO: 120. ### Claim 25 A set of oligonucleotides comprising: A) a pair of oligonucleotide primers wherein each of said primers comprises at least 12 contiguous nucleotides and wherein said pair of primers permit PCR amplification of a DNA segment comprising a soybean genomic DNA polymorphism associated with aphid resistance loci identified in Table 6 and 7; and B) at least one detector oligonucleotide that permits detection of a polymorphism in said amplified segment, wherein the sequence of said detector oligonucleotide is at least 95 percent identical to a sequence of the same number of consecutive nucleotides in either strand of a segment of maize DNA that include or are immediately adjacent to said polymorphism of step (a).