Identification of a major QTL related to resistance to soybean mosaic virus in diverse soybean genetic populations

Soybean mosaic virus (SMV) is a member of genus Potyvirus, which causes worldwide soybean [Glycine max (L.) Merr.] yield loss and seed quality deterioration. It is of great significance to find new resistance loci and genes for cultivation of soybean variety. In the present study, a recombinant inbred line (RIL) population and a genome-wide association study (GWAS) panel, which contained 193 lines and 379 germplasms, respectively, were used for QTL mapping of resistance to SMV. Linkage mapping identified a major QTL, qSMV13, on chromosome 13, conferring resistance to SMV SC3 and SC7 strains, explaining phenotypic variations 71.21 and 76.59 %, respectively. The QTL qSMV13 was located close to the known SMV resistance loci Rsv1-h. GWAS analysis revealed five single nucleotide polymorphisms (SNPs) significantly associated with resistance to SC3 on chromosomes 2, 11, 13, 14 and 16. One of the SNP markers, ss715614844, was the right flanking marker of qSMV13. Combining linkage mapping and GWAS analysis enabled us to delimit qSMV13 in a 97.2-kb genomic region containing seven genes. A LRR-RLK protein was proposed as the candidate gene of qSMV13. These results provided selection markers and candidate genes for SMV resistance in soybean molecular breeding programs.