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Single nucleotide polymorphism markers for rapid detection of the Rsv4 locus for soybean mosaic virus resistance in diverse germplasm

Klepadlo, Mariola, Chen, Pengyin, Shi, Ainong, Mason, Richard E., Korth, Ken L., Srivastava, Vibha
Molecular breeding 2017 v.37 no.1 pp. 10
Glycine max, Soybean mosaic virus, breeding, chromosome mapping, crop yield, crops, genes, genetic markers, genetic resistance, genotype, germplasm, loci, phenotype, rapid methods, screening, seed quality, single nucleotide polymorphism, soybeans, viruses
Soybean mosaic virus (SMV) causes a substantial decrease in soybean yield and reduction of seed quality. The most effective management strategy to control the virus is the deployment of host resistance. Seven SMV strains and three independent multi-allelic loci for SMV resistance have been identified previously. The goal of this research was to detect single nucleotide polymorphisms (SNPs) associated with SMV resistance at the Rsv4 locus. Ten soybean accessions, with confirmed resistance genes, were used for sequencing the candidate gene Glyma.02g121400. Alignment of these sequences revealed three SNPs displaying 100% consistency for genotypes carrying the Rsv4 gene. These SNPs were applied for a rapid screen of diverse soybean germplasm using the Sequenom iPLEX Gold platform, phenotyped with SMV-G1 and G7 strains to determine phenotype and classified into several groups carrying the proposed R-gene. The population of V94-5152 (Rsv4) × Lee 68 (rsv) was screened using novel SNPs to create a genetic map with improved resolution to determine the location of the Rsv4. To observe the recombination frequencies within the population, three additional SNPs on both sides of the Glyma.02g121400 gene were added. A linkage map revealed a distance of 3.6 cM between the Rsv4 locus and the closest SNP, thus shifting the putative Rsv4 region downstream on chromosome 2. With this region, five candidate genes have been proposed. The genomic position of the discovered SNPs, linked to the Rsv4, could increase screening precision and accelerate breeding efforts to develop multi-strain-resistant crops.