Genome Wide Association Mapping of Resistance in Soybean with a Genotyping-by-Sequencing Approach

摘要

Sclerotinia stem rot (SSR) is one of the most important pests in cool soybean growing regions of the Northeastern United States and Canada. However, the intensity of infestations varies considerably from year to year according to weather conditions, thus making it difficult for breeders to select under uniform disease pressure. Selection for resistance to SSR would be greatly facilitated by the use of molecular markers. In this work, a collection of 130 lines was inoculated using the cotton pad method and was genetically characterized using a genotyping-by-sequencing (GBS) protocol optimized for soybean. Genome-wide association mapping (AM) and linkage disequilibrium (LD) analyses were performed with 7864 single nucleotide polymorphisms (SNPs). Linkage disequilibrium varied considerably over physical distance, reaching a r2 value of 0.2 after 8.5 Mb in the pericentromeric region and 0.5 Mb in the telomeric region. The mixed linear model (MLM) performed very well in accounting for population structure and relatedness, as only 5.5% of the observed p-values were 0.05. The strongest association was found on chromosome Gm15 (p-value = 1.38 × 10–6; q-value [adjusted p-value] = 0.011). Two additional SNP markers in the vicinity had a q-value 0.1. This marker was validated in the progeny of a biparental cross, where F_4:6 lines carrying the susceptibility allele developed lesions 17.6 mm longer than lines carrying the resistance allele. Interestingly, other genes contributing to resistance to pathogens have been reported in this region of Gm15. Three other association peaks having a q-value 0.1 were detected on chromosomes Gm01, Gm19, and Gm20.