Whole-genome resequencing reveals genetic differentiation in cigar tobacco population

Cigar tobacco is an important industrial crop and is widely cultivated all over the world. The genetic diversity of its population and patterns of genetic variation shaped by artificial selection have not been revealed. Here, we report a cigar tobacco genomic variation atlas of 2.12 million single-nucleotide polymorphisms (SNPs) from whole-genome resequencing of 185 samples covering 18 representative major agricultural regions and investigate their population structure and genetic diversity and architecture. Since its domestication, cigar tobacco has been subjected to artificial selection, and has thus differentiated into two types: filler cigar tobacco and wrapper cigar tobacco. This study describes the phenotypic and genetic differences between filler cigar tobacco and wrapper cigar tobacco populations, and provides 1225 genes and 1115 selective sweep regions related to artificial domestication. These genes were significantly enriched in biological processes related to monocarboxylic acid metabolism, indolebutyric acid metabolism, RNA processing, positive regulation of amide metabolism, cellular response to DNA damage stimuli, protein modification by small protein conjugation, secondary metabolite biosynthesis, aromatic compound biosynthesis, RNA 5′-ending, heat acclimation, cellular response to inorganic substance, developmental growth involved in yield, quality, ecological adaptability, and disease resistance. This study will be useful for elucidating the molecular basis of population differentiation during modern cigar tobacco breeding, providing suitable hybrid parents and a valuable resource for future cigar tobacco variety improvement.