Whole-genome sequencing of 2032 diverse tobacco accessions reveals genetic variation and population differentiation

Nicotiana tabacum is an allotetraploid hybrid and a widely used model organism in plant genetics. Despite its agricultural and biological significance, large-scale genomic studies and comprehensive analysis of population differentiation in tobacco remain limited. Here, we perform whole-genome resequencing of 2032 diverse tobacco accessions, identifying 59 million single-nucleotide polymorphisms and 8.3 million small insertions and deletions. These variants contribute to substantial genetic diversity both within and between populations. Population genetic structure analysis reveals two major genetic subpopulations, with the differentiation primarily driven by breeding practices. Notably, the genetic differentiation between varieties is greater than that observed between tobacco types. Shared divergent regions across six types are enriched in defense, epidermal development, and lipid metabolism pathways, reflecting selection for stress adaptation and plant growth. We further identify 302 accessions exhibiting strong signatures of selection in immune-related genes, highlighting their potential as parental lines in resistance breeding programs. Selective sweeps in major cultivars overlap with 19 previously identified quantitative trait loci, primarily associated with agronomic traits such as leaf morphology, disease resistance, and chemical traits. This study provides a high-resolution genomic resource for in-depth tobacco genomics research and offers valuable insights into precision breeding.