Whole genome resequencing analysis of tobacco K326 and its cold sensitive mutant M18

Introduction Low temperatures cause flower prematurely of tobacco sensitive variety, severely impacting its yield and quality. Methods To uncover the molecular mechanisms underlying cold-induced early flowering in tobacco, the whole-genome resequencing was performed on the wild-type K326 and its cold-sensitive mutant M18. Results Compared with the reference genome,1,155,183 and 1,724,339 single nucleotide polymorphisms (SNPs), 286,674 and 360,131 small fragment insertion/deletion sites (InDels) were detected in wild-type K326 and its mutant M18. There are 5,735 and 14,892 nonsynonymous mutations in the coding region, causing a total of 5,588 gene mutations. The GO classification annotation of genes containing SNP/Indel sites shows that a relatively large number of genes are annotated to categories such as plant reproduction, metal ion transport, plant systemic cell formation, nucleotide binding, kinase activity, and tRNA binding. KEGG analysis indicated that the genes were mainly involved in the pathways of plant metabolic pathway, oxidative phosphorylation and plant photosynthesis. Through comparative analysis of SNP and InDel differences between the two materials, 75 candidate genes associated with flowering and stress resistance were identified, including transcription factors (MYB, WRKY) and key kinases (14-3-3, MAPK, CDPK). Discussion These selected genes will not only facilitate understanding of genetic basis of cold stress response, but also accelerate genetic improvement through marker-assisted selection in tobacco.