Development of molecular markers for Ty-2 and Ty-3 selection in tomato breeding

Tomato yellow leaf curl virus (TYLCV) is a disease causing serious yield reduction of tomato in the world. An effective control strategy for this virus is required for stable tomato production. Six resistant genes, Ty-1 to Ty-6 were previously identified in several wild species. In this study, we investigated novel sequence variations associated with Ty-2 and Ty-3 resistance to develop gene-based or functional markers suitable for improving TYLCV resistance in tomato breeding programs. Two resistant and susceptible inbred varieties were used for sequence analysis of each gene. For a Ty-2 candidate gene, we found a total of 39 single nucleotide polymorphisms (SNPs) and seven insertion/deletions (InDels). Of these, three SNPs were derived from coding sequences but were synonymous mutations. The SNPs and InDels from intron sequences were not responsible for alternative splicing in this gene. In addition, three large InDels of 50 bp, 42 bp, and 15 bp were found in upstream sequences, which are located at 688 bp, 611 bp, and 499 bp from 5’ UTR. Using the 50 bp and 42 bp InDels, a molecular marker was developed for Ty-2 selection. Nine non-synonymous SNPs and a 12 bp InDel were detected on coding sequences of the Ty-3 gene. Three of these (two SNPs and an InDel) were used to develop cleaved amplified polymorphic sequence (CAPS) markers. The resulting markers for Ty-2 and Ty-3 selection were validated using 18 commercial F1 cultivars, nine inbred lines, and three wild species with known phenotypes against TYLCV. Furthermore, these markers were used for genetic analysis of Ty-2 and Ty-3 resistance in a collection of 171 germplasm. The InDel and CAPS markers will be a useful resource to facilitate marker-assisted selection for pyramiding Ty-2 and Ty-3 in elite tomato varieties.