The genome and GeneBank genomics of allotetraploid Nicotiana tabacum provide insights into genome evolution and complex trait regulation
Nicotiana tabacum is an allotetraploid hybrid of Nicotiana sylvestris and Nicotiana tomentosiformis and a model organism in genetics. However, features of subgenome evolution, expression coordination, genetic diversity and complex traits regulation of N. tabacum remain unresolved. Here we present chromosome-scale assemblies for all three species, and genotype and phenotypic data for 5,196 N. tabacum germplasms. Chromosome rearrangements and epigenetic modifications are associated with genome evolution and expression coordination following polyploidization. Two subgenomes and genes biased toward one subgenome contributed unevenly to complex trait variation. Using 178 marker-trait associations, a reference genotype-to-phenotype map was built for 39 morphological, developmental and disease resistance traits, and a novel gene regulating leaf width was validated. Signatures of positive and polygenic selection during the process of selective breeding were detected. Our study provides insights into genome evolution, complex traits regulation in allotetraploid N. tabacum and the use of GeneBank-scale resources for advancing genetic and genomic research.
Authors
- Lingzhao Fang (ORCID: https://orcid.org/0000-0003-1103-3679)
- Guoyou Ye (ORCID: https://orcid.org/0000-0002-9943-4815)
- Yanjun Zan (ORCID: https://orcid.org/0000-0001-5571-4578)
- Yang Dong (ORCID: https://orcid.org/0000-0003-2117-538X)
- Ying Tong (ORCID: https://orcid.org/0000-0003-2356-8398)
- Caihong Jiang (ORCID: https://orcid.org/0000-0001-9818-0123)
- Yuanying Wang (ORCID: https://orcid.org/0009-0007-4253-5598)
- Aiguo Yang (ORCID: https://orcid.org/0000-0001-9491-8637)
- Guoxiang Liu (ORCID: https://orcid.org/0000-0001-8565-2363)
- Zhengwen Liu (ORCID: https://orcid.org/0000-0002-8540-9694)
- Ruimei Geng
- Yangyang Sun (ORCID: https://orcid.org/0000-0003-3232-2939)
- Huan Si (ORCID: https://orcid.org/0000-0003-2103-6136)
- Lirui Cheng (ORCID: https://orcid.org/0000-0003-3994-8782)
- Dan Liu (ORCID: https://orcid.org/0000-0002-1996-2627)
- Yu Han (ORCID: https://orcid.org/0009-0005-5713-2906)
- Shuai Chen (ORCID: https://orcid.org/0000-0002-6861-2682)
- Yao Zhang (ORCID: https://orcid.org/0000-0003-2789-6962)
- Xingwei Zhang (ORCID: https://orcid.org/0000-0003-2985-8177)
- Yuan Li (ORCID: https://orcid.org/0000-0002-4802-0305)
- Quanfu Feng
- Zhiliang Xiao
- Yan Ji
- Liuying Wen (ORCID: https://orcid.org/0009-0001-4487-9702)
- Min Ren (ORCID: https://orcid.org/0000-0003-1480-9962)
- Yong Chen (ORCID: https://orcid.org/0000-0002-2903-8753)
- Yutong Liu (ORCID: https://orcid.org/0009-0002-4216-6570)
Institutions
- International Rice Research Institute (PH)
- Chinese Academy of Sciences (CN)
- Aarhus University (DK)
- Sichuan University (CN)
- Beijing Botanical Garden (CN)
- Beijing Academy of Social Sciences (CN)
- Agricultural Genomics Institute at Shenzhen (CN)
- Tobacco Research Institute (CN)
- Umeå Plant Science Centre (SE)
- Chinese Academy of Agricultural Sciences (CN)
- Institute of Botany (CN)
- Beijing Academy of Science and Technology (CN)
- University of Chinese Academy of Sciences (CN)
- China National Botanical Garden
- Umeå University (SE)
Publication Details
- Journal
- Nature Genetics
- Published
- 2025-03-26
- DOI
- https://doi.org/10.1038/s41588-025-02126-0
- Citations
- 25
- Primary Topic
- Transgenic Plants and Applications
- Type
- article
- Field-Weighted Citation Impact
- 30.82
Funders
- National Science Foundation
- National Natural Science Foundation of China
- Ministry of Agriculture and Rural Affairs of the People's Republic of China
- Agricultural Science and Technology Innovation Program