Identification of Quantitative Trait Loci for Resistance to White Mold in Soybeans via Genome-Wide Association and Linkage Mapping

Abstract

White mold disease in soybeans is one of the most important causes of yield losses in the northern regions of the United States and Canada. Host resistance continues to be the most viable tactic for managing white mold; however, progress is slow due to laborious phenotyping techniques that are difficult to replicate and the polygenic nature of the white mold resistance trait. Breeding for white mold resistance will be significantly facilitated by improved screening methods and the use of molecular markers. In this work, we developed and validated a phenotyping method using spray mycelium and inoculated sorghum in two field environments. Using this methodology, a collection of 230 F5:12 recombinant inbred lines derived from the Minsoy x Noir1 cross and 280 diverse PIs and cultivars were phenotyped for white mold resistance in two field environments. Additionally, both populations were phenotyped in the greenhouse using the cut stem method. Five breeding lines and one PI with resistance levels similar to the current resistant check S19-90 were identified. This material is adapted to the Upper Midwest and could be used as potential donor germplasm to improve resistance to white mold. Linkage mapping analysis was performed on the Minsoy x Noir1 population using a set of 957 SSR and SNP markers. Four markers showed significant associations with white mold resistance on Chromosomes 6, 7, 8, and 12 (LOD>3), explaining 45% of the variability. Marker Satt567 on chromosome 7 is a new white mold resistance QTL, explaining 17% of the variability. Genome-wide association (GWAS) was performed using 1,536 SNP markers. Five QTLs showed significant associations with white mold resistance (FDR, qvalue≤0.1). The identified QTLs correspond to two regions on chromosome 19 and one region on chromosome 14. Of particular interest is marker BARC-039375-07306 on the short arm of chromosome 19; this marker corresponds with a major QTL associated with canopy architecture in soybeans. A second region on chromosome 19 consists of three markers positioned between 47,988,748 and 48,229,536 bp. Among these three markers, BARC-007569-00135 was the most significant and consistent across environments. Phenotypic variation explained by all significant markers was 13%. The QTLs on chromosome 19 were identified in field experiments, whereas the QTL on chromosome 14 resulted from the greenhouse evaluation.