High-throughput resequencing of four tobacco varieties (LY1306, Qinyan 96, Wanmao 3, Wufeng 1) of different tobacco types identifies genetic diversity and SSR markers

Purpose: The aim of this research was to employ genome re-sequencing to genetic variation of different tobacco varieties of different tobacco types and to identify genetic markers.Methods: Genome re-sequencing was performed on two tobacco varieties of Flue-cured tobacco type (LY1306 and Qinyan 96 (QY96)), one variety of sun-cured Tobacco type (Wanmao 3), and another Maryland Tobacco (variety Wufeng 1) which belongs to air-cured tobacco type, followed by a comparative analysis. The discovery of single nucleotide polymorphisms (SNPs), Indels, structural variation (SV), and copy-number variation (CNV) and functional analysis of mutative genes were then carried out. In addition, the identified SSR-based markers were varified by PCR amplification.Results: In-depth comparative analysis of genomes of the tobacco varieties of different tobacco types identified the genome variations of a number of SNPs, InDel, SVs, CNVs, and SSRs. Functional analysis of mutative genes containing these differential SNPs, InDel, SVs and CNVs showed that mutative genes were mainly involved in diffenent functions, such as carbohydrate metabolism. We mainly focused on those genes that were involved in the biosynthesis of secondary metabolites and nicotine metabolism.Conclusion: Our study provides more understanding of the genetic difference between different tobacco types or varieties and identifies five simple sequence repeats (SSRs) markers to classify tobacco varieties or tobacco types.