Genome-wide association study and marker development for bacterial wilt resistance in tomato (Solanum lycopersicum L.)

•GWAS detected a total of eight marker-trait associations for bacterial wilt resistance.•Three major QTL were found on chromosomes 4, 6, and 12.•Four environment-specific QTL were suggested on chromosomes 1 and 8–10.•Molecular markers were developed for marker-assisted selection. Bacterial wilt (BW), caused by the soil-borne Ralstonia solanacearum, is a major disease in cultivated tomato (Solanum lycopersicum L.). Host resistance provides an environment-friendly and cost-effective strategy to control this disease. To investigate quantitative trait loci (QTL) for BW resistance, we conducted a genome-wide association study (GWAS) in a core collection of 191 tomato varieties. The 51 K Axiom® tomato array was used for genotyping and 38,541 confident SNPs were filtered for GWAS. We evaluated disease severity of the core collection in two independent seedling assays following inoculation with race 1 of R. solanacearum. A total of eight marker-trait associations (MTAs) for BW resistance was detected at P < 0.0005 using the compressed mixed linear model. Of these, the MTAs on chromosomes 4 and 12 were consistently found in both disease assays and their corresponding QTL (Bwr-4 and Bwr-12) explained 8.36–18.28% of total phenotypic variations. We also detected Bwr-6 on chromosome 6 at P < 0.0005 (the 1st assay) and P < 0.01 (the 2nd assay). Further analysis with 37 commercial F1 cultivars demonstrated that the resulting SNP markers for these major QTL were effective in identifying resistant tomatoes. The cultivars with two of three major QTL showed higher levels of resistance relative to those with a single QTL. In addition, four MTAs on chromosomes 1 and 8–10 were found from only one of two assays, suggesting the presence of environment-specific QTL. These results facilitate genetic dissection of BW resistance and marker-assisted selection for developing elite cultivars in tomato breeding programs.