Genome‐Wide Association Mapping of Host‐Plant Resistance to Soybean Aphid

Abstract

Core Ideas Soybean aphid host‐plant resistance is needed to reduce damage from soybean aphid. Genome‐wide association mapping is effective for finding insect resistance loci. We found single nucleotide polymorphisms associated with soybean aphid resistance for multiple aphid biotypes. Soybean aphid [Aphis glycines Matsumura (Hemiptera: Aphididae)] is the most damaging insect pest of soybean [Glycine max (L.) Merr.] 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 2366 soybean accessions were collected from published studies screening cultivated soybean (G. max) and wild soybean (Glycine soja Siebold & Zucc.) 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. Significant associations between SNPs and soybean aphid counts 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 to 6, 9 to 12, 14, and 17 to 20 where Rag genes have not yet been mapped, suggesting that many Rag genes remain to be discovered. These SNPs can be used to determine accessions that are likely to have novel aphid resistance traits of value for breeding programs.

The Resistant Soybean-Aphis glycines Interaction: Current Knowledge and Prospects

“…Chromosome 13, on which the Rag2, Rag4, rag4, and Rag5 genes have been reported, had the highest number of SNPs (N=9) ( Table 2). Hanson et al (2018) and Natukunda et al (2019) detected the same two significant SNPs (ss715608208 and ss715605620) associated with aphid resistance (Table 2), confirming the usefulness of genome-wide markers for detecting candidate genes. Due to the low number of aphidresistant soybean genotypes included in the Chang and Hartman (2017) GWAS study, only one significant SNP (ss715596142) was detected.…”

“…Identification of additional sources of aphid resistance was followed by studies that aimed to explain the genetic basis of aphid resistance and discover new Rag genes. Three candidate gene identification studies conducted genome-wide association studies (GWAS) (Chang and Hartman, 2017;Hanson et al, 2018;Natukunda et al, 2019). Table 1 lists 69 aphid-resistant soybean plant introductions (PIs) included in GWAS studies, carrying resistance to biotypes 1, 2, and 3 that are prospective sources of new Rag genes.…”

“… Letters next to aphid biotypes denote reference articles that reported soybean accessions. A Hanson et al. (2018) ; B Natukunda et al.…”

“…Chromosome 13, on which the Rag2 , Rag4 , rag4 , and Rag5 genes have been reported, had the highest number of SNPs (N=9) ( Table 2 ). Hanson et al. (2018) and Natukunda et al.…”

Applications of Biotechnology for Characterization of Plants and Pests as the Key Components of Plant Protection and Production Strategies: A Review

“…Strain identification of fruit fly (Sim et al, 2017) Sunflower resistance to orobanche (Louarn et al, 2016) Genome-wide association Study (GWAS) mapping link genotypic and phenotypic variations (Brachi et al, 2011;Xiao et al, 2017) plant-pathogen interactions (Bartoli and Roux, 2017;Genissel et al, 2017); Wheat resistance to rust (Liu et al, 2017b); Rice resistance to fungus (Mgonja et al, 2016) cork borer resistance in maize (Samayoa et al, 2015); Earworm resistance in maize (Warburton et al, 2017); soybean resistance to insects (Chang and Hartman, 2017;Hanson et al, 2018) cowpea tolerance to striga (Burridge et al, 2016); plant-plant interaction (Subrahmaniam et al, 2018) Fig .2. The interrelationships of omics sciences (Source: Van Emon, 2016).…”