Replication Data for "Deciphering the unique SNPs among leading Indian Tomato Cultivars using Double Digestion Restriction Associated DNA sequencing"

Worldwide grown and consumed tomato (Solanum lycopersicum) crop is used as a model crop for new cultivar and fruit development. Genetic and genomic research of Indian tomato cultivars will provide an insight to develop new breeding strategies and crop improvement. The present study aimed 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 was generated for selected 9 samples 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, a total of 1,165 SNPs and 68 INDELs were found in genic regions. The genetic relationship among these cultivars suggested 4 well-differentiated groups of cultivars. Similarly, 7 and 33 SNPs were identified in the chloroplast and mitochondrial genome of tomato. GO terms and pathway associated with common and cultivar specific SNPs/INDELs containing genes along with cultivar specific SNPs/INDELs maker were identified. These SNPs/INDELs could be useful as markers for variety identification for genetic purity analysis. Findings from this work will be useful to plant breeders and research community as a resource for SNP marker development.