Abstract
Genome-wide single-nucleotide polymorphisms (SNPs) are highly useful in unraveling genetic insights and are essential to accelerate selections for genetic improvement in tobacco. The discovery of genome-wide SNPs in tobacco is very complex due to its high level of repetitive genome and polyploidy. At present, publicly available genomic data on SNPs are very limited, which warrants the need for high-throughput SNPs for application in tobacco breeding. In this research paper, we describe our efforts on SNP discovery by whole genome resequencing of 18 flue-cured Virginia (FCV) tobacco genotypes and annotation of SNPs in the tobacco genome. A large amount of data of about 225 GB per genotype was generated, with an average read depth of 50× using paired-end next-generation sequencing (NGS) with the HiSeq 2500 platform. The discovery of a large number of SNPs and indels was attempted to assist mapping and, thus, the selection processes to develop superior tobacco breeding lines. Discovered SNPs, their functional annotation, mapping to the reference genome, and their relative positioning in the linkage group are discussed in this paper.
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Acknowledgements
The authors duly acknowledge the efforts of Nucleome Informatics Pvt Ltd., Hyderabad, for performing NGS of 12 genotypes and bioinformatics analysis. The authors also thank ITC’s IT division at LSTC and at ITC InfoTech for their timely support. The authors sincerely thank Dr. CC Lakshmanan, Chief Scientist, and Mr. Chittaranjan Dar, member of CMC & Head of Quality Assurance, LSTC, CPO & EHS, for their respective roles in mentoring, support, and inspiration.
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Thimmegowda, G.C., Ramadoss, S.K., Kaikala, V. et al. Whole genome resequencing of tobacco (Nicotiana tabacum L.) genotypes and high-throughput SNP discovery. Mol Breeding 38, 121 (2018). https://doi.org/10.1007/s11032-018-0876-0
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DOI: https://doi.org/10.1007/s11032-018-0876-0