Deciphering the unique SNPs among leading Indian tomato cultivars using double Digestion Restriction Associated DNA sequencing

Worldwide grown and consumed tomato (Solanum lycopersicum L.) is used as model crop for new cultivar and fruit development. Genetic and genomic studies on Indian tomato cultivars will provide an insight that will enable development of breeding strategies and crop improvement. The present study aims to identify the high quality common and unique SNPs and INDELs, present in 9 different Indian tomato cultivars using double digest restriction site-associated DNA sequencing (ddRAD-seq). A total of 36.8 million raw reads were generated for selected cultivars and an average of 94% high quality reads of each were uniquely aligned to the reference tomato genome (SLv3.0). Out of 6, 957 SNPs and 188 INDELs, we found 1, 165 SNPs and 68 INDELs in genic regions. The genetic relationship among these cultivars suggested 4 well-differentiated groups of cultivars. Similarly, 7 and 33 SNPs were identified in chloroplast and mitochondrial genomes of tomato. SNPs markers were identified for common and specific genes associated with different pathways and their gene ontology (GO) annotated. These SNPs/INDELs could be useful as markers for variety identification for genetic purity analysis. Findings from this work will be useful to the research community, particularly plant breeders as a resource for SNP marker development.