Indian Society of Genetics & Plant Breeding

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

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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 welldifferentiated 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.
  

Keywords: Tomato, SNPs, INDELs, ddRAD-seq, Genomic resources

Info

Year: 2019
Volume: 79
Issue: 4
Article DOI: 10.31742/IJGPB.79.4.12
Print ISSN: 0019-5200
Online ISSN: 0975-6906

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