Combining High-Throughput Molecular Approaches and QTL Analysis to Select Genes Showing Differential Response to Sclerotinia Stem Rot in Soybean

Sclerotinia stem rot or white mold (WM) is an important fungal disease affecting soybean production [Glycine max (L.) Merr.]. White mold is prevalent in cool and moist environments and causes significant damage to yield and grain quality particularly in the soybean growing regions of northern United States and Canada. Although sources of complete resistance have not yet been identified, several quantitative trait loci (QTL) have been reported. However, most of these the QTL came from independent and unrelated studies that have not always been validated. Modern DNA technologies such as high-throughput genotyping (via GBS or SNP arrays) have been used to dissect complex disease resistance traits using genome wide association studies (GWAS). The objective of our study was to combine two innovative approaches, a genome-wide gene expression technology using RNA - sequencing (RNA-Seq) with the GWAS and QTL studies to dissect the genetics of resistance to WM as one of the most complex diseases in soybean. Comparing the results from a number of studies and using in-silico sequence analysis, we have identified promising genomic regions that may harbor genes showing differential expression within the QTL regions. Altogether 100 genes were chosen as having any relation with the disease. These genes were used to improve our understanding of genetic basis for WM resistance and identify significant genomic regions for future breeding efforts.