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

Abstract

World-wide grown and consumed tomato (Solanum lycopersicum) is used as model crop for newcultivar and fruit development. Genetic and genomic studieson Indian tomato cultivars will provide an insight that will enable development of breeding strategies and crop improvement. The present study aims to identifythe 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 and188 INDELs, we found 1,165 SNPs and 68 INDELs in genic regions. The genetic relationship among these cultivars suggested 4well-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.