Genome-wide association study on resistance of soybean to Rhizoctonia solani root rot in Northeast China

Root rot caused by Rhizoctonia solani poses a severe threat to global soybean production. This study employed an integrated genome-wide association study (GWAS) and transcriptomic approach to identify resistance loci across. This study investigated a natural population of northern Chinese spring soybean, comprising 191 and 301 accessions harvested in 2021 and 2022,respectively. Three elite resistant genotypes were identified through stringent disease index(DI)thresholds. GWAS analysis revealed 48 significant SNPs distributed across 14 chromosomes, with ss715599943 (Chr08, PVE = 9.85%)andss715583097 (Chr02, PVE = 5.69 %) demonstrating the highest phenotypic variance contributions. Notably, chromosomes 2 and 18 exhibited clustered resistance loci spanning 1.34–1.58 Mb regions. Linkage disequilibrium (LD) decay analysis identified 135 candidate genes, including Glyma.02g252200 (encoding subtilisin-like protease) and Glyma.18g179800 (pectin acetylesterase), within 20 kb flanking regions of lead SNPs. Temporal expression profiling via qPCR demonstrated contrasting regulatory patterns: Glyma.02g252200 showed significant upregulation (3.2-fold, P < 0.01) at 72 h post-inoculation, whereas Glyma.18g179800 exhibited sustained downregulation (0.4-fold, P < 0.05), suggesting divergent defense mechanisms. Functional annotation prioritized two pathogenesis-related candidates: Glyma.04g017200 (leucine-rich repeat receptor kinase,LRR-RK) and Glyma.18g182500 (PR-1 family protein). These results provide: 1)novel molecular markers for marker-assisted selection, 2)mechanistic insights into soybean-R.solani interactions through candidate gene validation.