Pangenome analyses of tea plants reveal structural variations driving gene expression alterations and agronomic trait diversification
Tea plants, which are among the world's most economically important beverage crops, exhibit extensive genetic diversity and are rich in secondary metabolites. While structural variations (SVs) drive phenotypic diversification, their regulatory roles in transcriptional networks and agronomic traits remain underexplored in this perennial crop. Here, we construct a pangenome from 22 representative tea accessions and their wild relatives. Genomic SV analysis reveals that 22% of the gene promoters contain variants influencing flavonoid, amino acid, and terpenoid biosynthesis. Population SV analysis of 275 tea accessions reveals three haplotypes in the ANS3 promoter, with Hap1, containing a 192 bp insertion, predominantly found in wild relatives but largely lost in modern cultivars. This insertion increases CtANS3 expression and anthocyanin content in wild relatives. Additionally, a 159 bp insertion in the CtLRR1 promoter reduces resistance to Colletotrichum gloeosporioides in wild relatives. Our findings underscore SVs as pivotal regulators of flavor differentiation and adaptive evolution during tea plant domestication.
Authors
- Shengrui Liu (ORCID: https://orcid.org/0000-0003-3567-0218)
- Hongrong Chen
- Yanping Hu (ORCID: https://orcid.org/0009-0006-8820-7437)
- Kun Dong (ORCID: https://orcid.org/0009-0006-5155-5147)
- Enhua Xia (ORCID: https://orcid.org/0000-0003-3411-9117)
- L. Y. Tao (ORCID: https://orcid.org/0009-0000-8089-9850)
- Benying Liu (ORCID: https://orcid.org/0000-0001-9241-4240)
- Jianbing Hu (ORCID: https://orcid.org/0009-0006-2512-5055)
- Chaoling Wei (ORCID: https://orcid.org/0000-0003-0274-0910)
- Junyan Zhu (ORCID: https://orcid.org/0000-0001-7295-4768)
- Xiaochun Wan (ORCID: https://orcid.org/0000-0001-5294-786X)
- Youyong Li (ORCID: https://orcid.org/0000-0001-6641-3308)
- Fangdong Li (ORCID: https://orcid.org/0009-0002-6689-8944)
- Qi Xu (ORCID: https://orcid.org/0009-0000-0336-4924)
- Yuanyan Zhao
- Yongfeng Zhou (ORCID: https://orcid.org/0000-0003-0780-2973)
- Chunlin Chen
- Songyan Huang
- L. Chen (ORCID: https://orcid.org/0000-0001-6114-6837)
- Wu Jun
- Qianqian Zhou (ORCID: https://orcid.org/0009-0001-9077-8865)
Institutions
- Chinese Academy of Tropical Agricultural Sciences (CN)
- Anhui Agricultural University (CN)
- Agricultural Genomics Institute at Shenzhen (CN)
- Tropical Crops Genetic Resources Institute (CN)
- Yunnan Academy of Agricultural Sciences (CN)
- Puer University (CN)
- Tea Research Institute (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-12-06
- DOI
- https://doi.org/10.1038/s41467-025-67060-5
- Citations
- 3
- Primary Topic
- Tea Polyphenols and Effects
- Type
- article
- Field-Weighted Citation Impact
- 4.41