Genome-wide association study reveals candidate genes for gummy stem blight resistance in cucumber

Gummy stem blight (GSB), caused by Didymella bryoniae, is a serious fungal disease that leads to decline in cucumber yield and quality. The molecular mechanism of GSB resistance in cucumber remains unclear. Here, we investigated the GSB resistance of cucumber core germplasms from four geographic groups at the seedling and adult stages. A total of 9 SNPs related to GSB resistance at the seedling stage and 26 SNPs at the adult stage were identified, of which some are co-localized to previously mapped Quantitative trait loci (QTLs) for GSB resistance (gsb3.2/gsb3.3, gsb5.1, and gsb-s6.2). Based on haplotype analysis and expression levels after inoculation, four candidate genes were identified within the region identified by both Genome-wide association study (GWAS) and previous identified QTL mapping, including Csa3G129470 for gsb3.2/gsb3.3, Csa5G606820 and Csa5G606850 for gsb5.1, and Csa6G079730 for gsb-s6.2. The novel GSB resistant accessions, significant SNPs, and candidate genes facilitate the breeding of GSB resistant cucumber cultivars and provide a novel idea for understanding GSB resistance mechanism in cucumber.