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

Xiong Zheng; Zhijun Tong; Asad Ullah; Tianle Zhu; Mingzhe Suo; Fangchan Jiao; Xingfu Wu; Haiming Xu; Feng Lin; Xuejun Chen; Bingguang Xiao

doi:10.1016/j.jgg.2026.02.025

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

doi: 10.1016/j.jgg.2026.02.025

a. Institute of Crop Science and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China;
b. Key Laboratory of Tobacco Biotechnological Breeding, National Tobacco Genetic Engineering Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan 650021, China

Funds:

We are grateful for the grants from the China National Tobacco Company (110202101038 [JY-15]), and Yunnan Tobacco Company (2024530000241003, 2022530000241009, 2025530000241005).

Received Date: 2025-09-01
Accepted Date: 2026-02-26
Rev Recd Date: 2026-02-24

Available Online: 2026-03-04

Abstract

Abstract

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 (SNPs) and 8.3 million small insertions and deletions (InDels). 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 QTLs, 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.
- Nicotiana tabacum,
- Germplasm resources,
- Whole-genome resequencing,
- Genetic differentiation,
- Disease resistance

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