Whole genome re-sequencing to reveal genetic diversity and to develop snp array in common tobacco

The common tobacco (Nicotiana tabacum) is an important model plant applied in basic life science. In this study, we re-sequenced 391 diverse tobacco germplasms with mean genome coverage of 11.6 x . A total of 17.9 M single nucleotide polymorphisms (SNPs) were identified which revealed the average SNP frequency 6 SNP/Kb and diversity (pi) about 0.4 x 10-3. Compared the genetic diversity and divergence between tobaccos from China (TChina) and from USA (TUSA), significant differences were found in Nt01 and Nt05, and selective sweeps revealed the regional selections for genes enriched in pathways of photosynthesis and sesquiterpenoids and triterpenoids biosynthesis. Genomic transmission and conservation patterns along chromosomes were also evaluated for 10 tobacco cultivars which highlighted genome blocks under selection in the past. Based on the millions of SNPs, a high density tobacco SNP array Nt660YN was designed and validated, which was composed of 588,553 PolyHighResolution SNPs with an average 3.5 SNPs per gene. The millions of SNPs and Nt660YN SNP array will facilitate genetic researches in Nicotiana as well as all Solanaceae crops.