Genome-wide SNP discovery and core marker sets for DNA barcoding and variety identification in commercial tomato cultivars

•A total of confident 10,615 SNPs was identified using the 48 F1 tomato cultivars.•Additional 94 cultivars were genotyped using the 288 filtered SNP markers.•Genetic variations between and within tomato market classes were investigated.• Fivecore SNP sets were effective for varity identification in the commerical cultivars.