Loci and candidate gene identification for resistance to Sclerotinia sclerotiorum in soybean (Glycine max L. Merr.) via association and linkage maps

Soybean white mold (SWM), caused by Sclerotinia sclerotiorum ((Lib.) W. Phillips), is currently considered to be the second most important cause of soybean yield loss due to disease. Research is needed to identify SWM-resistant germplasm and gain a better understanding of the genetic and molecular basis of SWM resistance in soybean. Stem pigmentation after treatment with oxaloacetic acid is an effective indicator of resistance to SWM. A total of 128 recombinant inbred lines (RILs) derived from a cross of Maple Arrow' (partial resistant to SWM) and Hefeng 25' (susceptible) and 330 diverse soybean cultivars were screened for the soluble pigment concentration of their stems, which were treated with oxalic acid. Four quantitative trait loci (QTLs) underlying soluble pigment concentration were detected by linkage mapping of the RILs. Threehundredand thirty soybean cultivars were sequenced using the whole-genome encompassing approach and 25179 single-nucleotide polymorphisms (SNPs) were detected for the fine mapping of SWM resistance genes by genome-wide association studies. Three out of five SNP markers representing a linkage disequilibrium (LD) block and a single locus on chromosome 13 (Gm13) were significantly associated with the soluble pigment content of stems. Three more SNPs that represented three minor QTLs for the soluble pigment content of stems were identified on another three chromosomes by association mapping. A major locus with the largest effect on Gm13 was found both by linkage and association mapping. Four potential candidate genes involved in disease response or the anthocyanin biosynthesis pathway were identified at the locus near the significant SNPs (<60kbp). The beneficial allele and candidate genes should be useful in soybean breeding for improving resistance to SWM. Significance Statement Soybean white mold (SWM) caused by Sclerotinia sclerotiorum ((Lib.) W. Phillips) is a destructive fungal disease of soybean production. The identification of SWM resistant germplasm and better understanding of the genetic and molecular basis of SWM resistance are critical for disease resistance breeding of soybean. The article reported novel quantitative trait loci (QTL) and single nucleotide polymorphisms (SNPs) associated with soybean white mold resistance through linkage and genome wide association (GWA) mappings. The beneficial allele and candidate genes were predicted and should be useful in soybean breeding for improving SWM resistance.