GWAS-Guided Development of KASP Markers Associated with Soybean Seedling Resistance to Fusarium solani

Fusarium root rot, primarily caused by Fusarium solani, is a damaging soil-borne disease that restricts soybean growth and reduces yield. In the present study, a panel of 330 soybean germplasm accessions was inoculated with F. solani. Disease responses were evaluated using the disease severity index (DSI). The soybean accessions displayed substantial variation in their susceptibility to F. solani. Based on DSI, 39 accessions were classified as highly resistant, 94 as resistant, 125 as susceptible, and 72 as highly susceptible, accounting for 11.82%, 28.48%, 37.88%, and 21.82% of the panel, respectively. The genome-wide association study (GWAS) was performed using a genotyping dataset of 627,436 high-quality single nucleotide polymorphisms (SNPs) and two models, Fixed and random model Circulating Probability Unification (FarmCPU) and mixed linear model (MLM). Both GWAS models detected putative SNP associations across seven chromosomes. Based on SNP allelic-effect analysis and gene function annotation, eight genes were prioritized and subsequently evaluated by quantitative reverse transcription PCR (qRT-PCR) for their responses to F. solani infection. Two Kompetitive allele-specific PCR (KASP) markers, KASP-S13_37431242 and KASP-S13_37529208, were developed from resistance-associated SNPs on chromosome 13 and evaluated across the diverse soybean association panel used in this study. Accessions carrying the favorable genotypes of these markers were enriched for resistant germplasm, with positive predictive values of 65.52% and 66.67%, respectively, indicating their potential value for preliminary favorable-allele tracking and germplasm prioritization. Collectively, these results improve our understanding of the genomic components underlying soybean responses to F. solani. The identified loci, candidate genes, and KASP assays provide a basis for further functional validation and the development of multi-locus strategies for improving soybean resistance to Fusarium root rot.