Genome-Wide Association Mapping of Sudden Death Syndrome Resistance in Germplasm from the USDA Soybean Collection

Abstract

Sudden Death Syndrome (SDS), caused by Fusarium virguliforme, can significantly impact soybean yields. To advance the understanding of SDS resistance in plant introductions, we conducted genome-wide association studies (GWAS) on a set of 351 accessions from the USDA Soybean Germplasm Collection. The analysis revealed seven single nucleotide polymorphisms (SNPs) significantly associated with foliar SDS resistance; three significant QTL (on chromosomes 3, 9 and 11) were detected with Fixed and Random Model Circulating Probability Unification (FarmCPU) and four (on chromosomes 5, 6 and two on chromosome 7) with Bayesian-information and Linkage disequilibrium Iterative Nested Keyway (BLINK). Localized linkage disequilibrium blocks were estimated for these regions. Notably, all of them overlapped with regions where QTL associated with SDS resistance had been previously reported and where within, or close to, sequences annotated as implicated in plant defense mechanisms, such as toxin transporters and transcription factors. The architecture of SDS resistance appears quantitative and polygenic, with most loci explaining modest phenotypic variance. Six plant introductions in this study--PI 175188, PI 307889A, PI 323559, PI 578307C, PI 445683, and PI 323558--harbor favorable alleles at all seven loci, providing high-value resources for resistance introgression. This study underscores the value of leveraging the USDA Soybean Germplasm Collection for the discovery of resistance loci and provides a foundation for marker-assisted breeding to enhance SDS resistance in elite soybean lines.