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Indian Journal of Genetics and Plant Breeding (The)
Year : 2019, Volume : 79, Issue : 4
First page : ( 732) Last page : ( 740)
Print ISSN : 0019-5200. Online ISSN : 0975-6906.
Article DOI : 10.31742/IJGPB.79.4.12

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

Bodanapu Reddaiah, Vasudevan Sreehari V., Chakravartty Navajeet, Lalam Krishna, Lekkala Sivarama Prasad, Kuriakose Boney1, Bhanot Chetan, Kokkonda Navitha1, Thomas George1, Gupta Saurabh**, Lachagari Vijaya Bhasker Reddy*

AgriGenome Labs Pvt. Ltd., BTIC, MN iHub, Genome Valley, Hyderabad, 500 078

1AgriGenome Labs Pvt. Ltd., Infopark Road, Kakkanad, 682 042, Kerala

*Corresponding author's e-mail: vb.reddy@aggenome.com

**saurabh.g@aggenome.com

Online published on 11 February, 2020.

Abstract

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.

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Keywords

Tomato, SNPs, INDELs, ddRAD-seq, Genomic resources.

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