Genome-wide association mapping of host-plant resistance to soybean aphid

Authors: HANSON, ANTHONY - University Of Minnesota; LORENZ, AARON - University Of Minnesota; Hesler, Louis; BHUSAL, SIDDHI - University Of Minnesota; BANSAL, RAMAN - The Ohio State University; MICHEL, ANDREW - The Ohio State University; JIANG, GUO-LIANG - Virginia State University; KOCH, ROBERT - University Of Minnesota

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/23/2018
Publication Date: 8/9/2018
Citation: Hanson, A., Lorenz, A., Hesler, L.S., Bhusal, S., Bansal, R., Michel, A., Jiang, G., Koch, R. 2018. Genome-wide association mapping of host-plant resistance to soybean aphid. The Plant Genome. 11:180011. https://doi.org/doi:10.3835/plantgenome2018.02.0011.
DOI: https://doi.org/10.3835/plantgenome2018.02.0011

Interpretive Summary: Soybean aphid is the most damaging insect pest of soybean in the Upper Midwest of the United States and is primarily controlled by insecticides. Resistance to soybean aphid has been found in some soybean lines. However, commercial soybean varieties with aphid resistance have had low adoption rates because the resistance has not been strong enough, and additional resistance sources are needed. Genome-wide association mapping is a sophisticated technique that can aid in identifying additional sources by correlating resistance with point mutations known as SNPs within soybean lines. Aphid population measures from 2,366 soybean lines were collected from published studies screening cultivated soybean and wild soybean with a variety of soybean aphid variants, also known as biotypes. SNP data previously used to genotype the USDA Soybean Germplasm Collection was matched with aphid ratings for each soybean line, and the matches were tested for correlation. SNPs that significantly correlated with soybean aphid resistance were found on 18 of the 20 soybean chromosomes. Significant SNPS were found on chromosomes 7, 8, 13, and 16 with known aphid resistance genes, and these SNPs can be used to determine accessions likely to have aphid resistance traits of value for breeding programs. SNPs were also significant on chromosomes 1, 2, 4 – 6, 9 – 12, 14, and 17 – 20, where aphid resistance genes have not yet been mapped. It is likely that new aphid resistance genes will be identified on this latter set of chromosomes, and these findings can be used as a basis to guide future research.

Technical Abstract: Soybean aphid is the most damaging insect pest of soybean in the Upper Midwest of the United States and is primarily controlled by insecticides. Soybean aphid resistance (i.e., Rag genes) has been documented in some soybean accessions, but more sources of resistance are needed. Incorporation of the resistance into marketed varieties has also been slow. Genome-wide association mapping can aid in identifying resistant accessions by correlating phenotypic data with single nucleotide polymorphisms (SNPs) across a genome. Aphid population measures from 2,366 soybean accessions were collected from published studies screening cultivated soybean (Glycine max) and wild soybean (Glycine soja) with aphids exhibiting biotype 1, 2, or 3 characteristics. Genotypic data were obtained from the SoySNP50K high-density genotyping array previously used to genotype the USDA Soybean Germplasm Collection. Nucleotides measured at SNPs and aphid ratings for each soybean accession were tested for correlation. SNPs significantly correlated with soybean aphid resistance were found on 18 of the 20 soybean chromosomes. Significant SNPS were found on chromosomes 7, 8, 13, and 16 with known Rag genes. SNPs were also significant on chromosomes 1, 2, 4 – 6, 9 – 12, 14, and 17 – 20 where Rag genes have not yet been mapped. These SNPs can be used to determine accessions likely to have aphid resistance traits of value for breeding programs. Discovery of new Rag genes can also be aided by future experiments on accessions with polymorphisms at chromosomes that do not contain known Rag genes.