Skip to main content
ARS Home » Midwest Area » Urbana, Illinois » Soybean/maize Germplasm, Pathology, and Genetics Research » Research » Publications at this Location » Publication #323670
Title: Genome-wide association and genomic prediction identifies associated loci and predicts the sensitivity of Tobacco ringspot virus in soybean plant introduction

Author
item CHANG, HAO-XUN - University Of Illinois
item BROWN, PATRICK - University Of Illinois
item LIPKA, ALEXANDER - University Of Illinois
item Domier, Leslie
item Hartman, Glen

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/10/2016
Publication Date: 5/21/2016
Citation: Chang, H., Brown, P.J., Lipka, A.E., Domier, L.L., Hartman, G.L. 2016. Genome-wide association and genomic prediction identifies associated loci and predicts the sensitivity of Tobacco ringspot virus in soybean plant introduction. Biomed Central (BMC) Genomics. 17:153. doi:10.1186/s12864-12016-12487-12867.

Interpretive Summary: Tobacco ringspot virus (TRSV) is one of the most destructive viral pathogens of soybean. Yet, resistance to TRSV has not been described for commercial soybean cultivars. The goal of this study was to identify soybean accessions from the USDA Soybean Germplasm Collection with reduced sensitivity to TRSV and use genome-wide association to define the regions of soybean chromosomes responsible. In addition to identifying chromosomal locations of genes for desirable traits, genome-wide association studies can be used to predict traits or responses of plant accessions without actually measuring that trait or response. Based on genome-wide association, a single region on soybean chromosome 2 was strongly associated with sensitivity to TRSV infection. The chromosomal region contained two genes that are similar to genes that confer sensitivity to viral and bacterial pathogens in other plant species. The analysis also allowed us to predict with a high degree of confidence the TRSV sensitivities of 18,955 accessions in the USDA soybean germplasm collection without actually experimentally evaluating the lines. This research is important to scientists interested in host resistance genes for managing soybean diseases.

Technical Abstract: The genome-wide association study (GWAS) is a useful tool for detecting and characterizing traits of interest including those associated with disease resistance in soybean. The availability of 50,000 single nucleotide polymorphism (SNP) markers (SoySNP50K iSelect BeadChip; www.soybase.org) on 19,652 soybean and wild soybean plant introductions (PIs) in the USDA Soybean Germplasm Collection allows for fast and robust identification of loci associated with a desired phenotype. By using a genome-wide marker set to predict phenotypic values, genomic prediction for phenotype-unknown but genotype-determined PIs has become possible. The goal of this study was to describe the genetic architecture associated with sensitivity to Tobacco ringspot virus (TRSV) infection in the USDA Soybean Germplasm Collection. TRSV-induced disease sensitivities of 697 soybean PIs were rated on a 1 to 5 scale with plants rated as 1 exhibiting mild symptoms and plants rated as 5 displaying terminal bud necrosis (i.e., bud blight). The GWAS identified a single locus on soybean chromosome 2 strongly associated with TRSV sensitivity. Cross-validation showed a correlation of 0.55 (P < 0.01) without including the most significant SNP marker from the GWAS as a covariate, and provided a better estimation than using mean separation by significant SNPs. The genomic estimated breeding values for the remaining 18,955 unscreened soybean PIs in the USDA Soybean Germplasm Collection were obtained using the GAPIT R package. To evaluate the prediction accuracy, an additional 55 soybean accessions were evaluated for sensitivity to TRSV, which resulted in a correlation of 0.67 (P < 0.01) between actual and predicted severities. A single locus responsible for TRSV sensitivity in soybean was identified on chromosome 2. Two leucine-rich repeat receptor-like kinase genes were located near the locus and may control sensitivity of soybean to TRSV infection. Furthermore, a comprehensive genomic prediction for TRSV sensitivity for all accessions in the USDA Soybean Germplasm Collection was completed.