Genome Wide Analysis of Loci Associated with Seed Transmission and Seed Coat Mottling Caused By Soybean Mosaic Virus

Soybean mosaic virus (SMV), an aphid- and seed-transmitted member of the Potyviridae, causes significant reductions in soybean yield and seed quality worldwide. In North America, seedborne infections serve as the primary sources of inoculum for SMV infections. Therefore, host-plant resistance to seed transmission of SMV provides a means to limit the impacts of SMV on soybean production. In this study, two diverse population panels composed of 199 and 409 plant introductions respectively from the United States Department of Agriculture Soybean Germplasm Collection were evaluated for seed transmission rate and seed coat mottling caused by SMV using two different SMV strains. To identify loci associated with traits of interest, the phenotypic data and single nucleotide polymorphism (SNP) information derived from SoySNP50K dataset were combined and analyzed using R package rrBLUP. The genome-wide scan revealed a single SNP (ss715605423), which accounts for 23.97% of the phenotypic variation, significantly associated with seed transmission rate in one population panel. Marker assisted selection and genomic prediction were subsequently compared for prediction accuracy of SMV seed transmission rate. Meanwhile, SNPs significantly associated with seed coat mottling caused by SMV were detected in both population panels. Identified loci and putative candidate genes were compared to previously published results of linkage mapping studies. This study provides the most comprehensive analysis of loci associated with seed transmission of an economically important plant virus.