Genome-wide association study of the seed transmission rate of soybean mosaic virus and associated traits using two diverse population panels

Authors: LIU, QIONG - University Of Illinois; HOBBS, HOUSTON - University Of Illinois; Domier, Leslie

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/23/2019
Publication Date: 12/1/2019
Citation: Liu, Q., Hobbs, H.A., Domier, L.L. 2019. Genome-wide association study of the seed transmission rate of soybean mosaic virus and associated traits using two diverse population panels. Theoretical and Applied Genetics. 132(12):3413-3424. https://doi.org/10.1007/s00122-019-03434-w.
DOI: https://doi.org/10.1007/s00122-019-03434-w

Interpretive Summary: Soybean mosaic virus (SMV) causes significant reductions in soybean yield and seed quality. Because seedborne infections can serve as primary sources of inoculum for SMV infections, resistance to SMV seed transmission provides a means to limit the impacts of SMV. In this study, two diverse sets of soybean lines from the USDA Soybean Germplasm Collection were evaluated for SMV seed transmission rate, seed coat mottling, and seed yield from SMV-infected plants. When the trait data were analyzed along with molecular marker data, genes controlling the three traits were found clustered in narrow regions on soybean chromosomes 3 and 9. The results suggest that a common set of genes may control the three traits. The results of this study provide additional insight into the genetic architecture of these three important traits and suggest candidate genes for downstream functional validation. This work will be of interest to researchers working to limit the impacts of SMV infection on soybean or studying the mechanisms of transmission of plant viruses through seed.

Technical Abstract: Soybean mosaic virus (SMV) causes significant reductions in soybean yield and seed quality. Because seedborne infections can serve as primary sources of inoculum for SMV infections, resistance to SMV seed transmission provides a means to limit the impacts of SMV. In this study, two diverse population panels (Pop1 and Pop2) composed of 409 and 199 soybean plant introductions, respectively, were evaluated for SMV seed transmission rate, seed coat mottling, and seed yield from SMV-infected plants. The phenotypic data and genotypic data from the SoySNP50K dataset were analyzed using GAPIT and rrBLUP. Markers associated with the three traits were clustered in regions on chromosomes 3 and 9. For SMV seed transmission rate, a single locus was identified on chromosome 9 in Pop1. For SMV-induced seed coat mottling, loci were identified on chromosomes 3 and 9 in Pop1 and on chromosome 3 in Pop2. For seed yield from SMV-infected plants, a single locus was identified on chromosome 3 in Pop2 that was within the map interval of a previously described quantitative trait locus for seed number. The high linkage disequilibrium regions surrounding the markers on chromosomes 3 and 9 contained a predicted nonsense-mediated RNA decay gene, multiple pectin methylesterase inhibitor genes (involved in restricting virus movement), two chalcone synthase genes and a homolog of the yeast Rtf1 gene, (involved in RNA-mediated transcriptional gene silencing). The results of this study provide additional insight into the genetic architecture of these three important traits and suggest candidate genes for downstream functional validation.