SNP Genotyping of Tomato Cultivars

Genomic DNA of young leaf tissues of each line and parent were extracted using DNeasy Plant Mini Kit (Qiagen Inc., Valencia, CA, Spain). A Nano Drop (Model ND-2000, Thermo Scientific Inc., Wilmington, DE, USA) was used to quantify each DNA sample. Approximately 50 ng/µL of DNA was prepared from each sample for SNP genotyping. We used an optimized subset of 384 SNPs markers that were derived from the 7,725 SNP array developed by the Solanaceae Coordinated Agricultural Project (SolCAP) [36 (link),37 (link)]. The subset of markers was selected based on polymorphism rates among six fresh market tomato accessions including Fla.7776, Fla.8383, NC33EB-1, 091120-7, Fla. 7775, and NC 1CELBR. In addition, genetic position in the genome based on recombination [36 (link)] and physical position were considered as important selection criteria to insure genome coverage. These 384 SNPs were analyzed using the KASP genotyping platform (LGC Genomics, Beverly, MA, USA).