Unraveling the Genetic Architecture of Sclerotinia Basal Stalk Rot Resistance in Cultivated Sunflower Through Genome-Wide Association Mapping

Sclerotinia basal stalk rot (BSR), caused by the necrotrophic fungal pathogen Sclerotinia sclerotiorum , is an economically important disease of cultivated sunflower ( Helianthus annuus L.). Resistance to BSR is quantitative and genetically complex, and although biparental mapping studies have identified genomic regions associated with resistance, knowledge of the broader genetic architecture of BSR resistance in diverse cultivated sunflower germplasm remains limited. In this study, genome-wide association studies were conducted to understand the genetic architecture of BSR resistance using two independent panels. The Sunflower Association Mapping (SAM) panel was evaluated under greenhouse conditions with two S. sclerotiorum isolates differing in aggressiveness, BN166 or NEB-274, using two disease traits: mean days to death and area under the mortality curve. An open-pollinated variety (OPV) panel was evaluated across four field environments after inoculation with isolate NEB-274 and scored for disease incidence. Genotyping datasets comprised 3.2 and 3.5 million single nucleotide polymorphisms for the SAM and OPV panels, respectively. The study identified 20 significant associations in the SAM panel and 7 in the OPV panel. No overlapping associations were detected between panels or isolates, indicating isolate- and environment-specific genetic architecture despite moderate positive correlations between isolates (r ≈ 0.74). Eight loci co-localized with previously reported BSR quantitative trait locus intervals. Candidate genes included a protein kinase at the strongest association, a receptor-like kinase, a glutathione S-transferase, and members of the WD40 repeat protein family detected in both panels. These findings provide genomic resources for marker-assisted selection and resistance breeding.