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

Single nucleotide polymorphisms (SNPs) have been widely used as a molecular marker in crop species with advances in next-generation sequencing technology. The use of SNP markers for variety identification is a cost-effective strategy to protect breeder’s intellectual property rights. This study was conducted to identify genome-wide SNPs and develop core marker sets for assessing genetic variations in commercial tomato cultivars. A total of 10,615 confident SNPs was generated from genotyping by sequencing for 48 F1 cultivars representing four market classes (large-fruited fresh market, cherry, grape, and rootstock). Of these, 288 SNPs across 12 chromosomes were selected to genotype additional 94 F1 cultivars using the Fluidigm assay and 224 SNPs showed reliable polymorphisms in 91 F1 cultivars. Both model-based and hierarchical clustering analyses with these markers found that the large-fruited fresh market cultivars were significantly distinct from the cherry and grape cultivars. In addition, the cherry and grape cultivars showed higher levels of genetic diversity relative to the large-fruited fresh market cultivars. The 224 SNP markers were also effective in differentiating all 139 F1 cultivars and Heinz 1706 (an inbred for the tomato reference genome). Of the five subsets, the 192 and 96 markers identified all of these tomato cultivars, respectively. Furthermore, the other three subsets of 48, 24, and 12 markers showed 80.0–93.6 % of identification rates. These results demonstrate that all five subsets of SNP markers will be useful in developing a high-throughput DNA barcoding system for variety identification in commercial tomato cultivars.