Genetic insights into the population structure and adaptive evolution of tea germplasm in Guangxi, China
- 1State Key Laboratory of Tea Plant Germplasm Innovation and Resource Utilization, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008 China
- 2Guangxi South Subtropical Agricultural Research Institute, Chongzuo, 532415 China
- 3Yunnan Key Laboratory of Tea Germplasm Conservation and Utilization in the Lancang River Basin, West Yunnan University, Lincang, 677000 China
Abstract
Background: Guangxi, China, is a critical region for tea plant genetic resources because of its proximity to the center of tea origin and its rich tea germplasm resources. However, the genetic background and evolutionary history of tea plant (Camellia sinensis) in this region remain poorly understood, which limits their utilization in tea breeding.
Results: We performed whole-genome resequencing on 179 tea accessions collected from 12 regions of Guangxi, generating 4.33 Tb of sequencing data with an average sequencing depth of 8.06× and identifying 84,827,998 high-quality SNPs. Phylogenetic and population structure analyses classified the accessions into five genetic groups. Notably, the ‘Fangchengcha’ (C. fangchengensis) population (GP1) occupied the most basal evolutionary position and exhibited the lowest genetic diversity (π = 0.162), suggesting its primitive and relatively isolated status. Selective sweep analysis identified distinct genomic selection signatures across different evolutionary stages. During the transition from non-domesticated to early domesticated germplasm, loci associated with primary metabolism and environmental responses gradually shifted toward loci related to secondary metabolite pathways associated with tea flavor traits (e.g., flavonoid and phenylpropanoid biosynthesis). Gene expression profiling further revealed stage-specific expression patterns of selected genes. Genes involved in epigenetic regulation and environmental responses were highly expressed in wild materials, whereas genes associated with lipid metabolism, energy metabolism, and substance transport showed progressively higher expression with increasing domestication. These patterns suggest coordinated changes between functional requirements and gene expression regulation during adaptive evolution.
Conclusion: This study provides a systematic analysis of the genetic background and evolutionary dynamics of tea germplasm in Guangxi and may provide a useful basis for the conservation and molecular breeding of local tea germplasm.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12870-026-09720-2.
Related
- Elucidating the evolution of litchi: insights into the population genomics of ancient trees on origin, dispersal, and adaptive genetic basis
- Evolution of lake microbial structure and function under climatic and anthropogenic forcings: Insights from sedimentary ancient DNA
- Seasonal population structure and adaptive signatures across long-term marine microbial time series
- Integrating genome-wide neutral and putatively adaptive variation resolves population structure and differentiation in a recently diverged albatross complex
- Genomic insights into population structure, resistome, virulome, and mobilome of multidrug-resistant Pseudomonas aeruginosa
BibTeX
@article{li2026genetic,
title = {{Genetic insights into the population structure and adaptive evolution of tea germplasm in Guangxi, China}},
author = {Fang Li and Zhilu Fu and Shuran Zhang and Qin Xiao and Yuanquan Chen and Liang Chen and Jiedan Chen},
journal = {BMC Plant Biology},
year = {2026},
month = aug,
doi = {10.1186/s12870-026-09720-2},
url = {https://doi.org/10.1186/s12870-026-09720-2},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Genetic insights into the population structure and adaptive evolution of tea germplasm in Guangxi, China
AU - Fang Li
AU - Zhilu Fu
AU - Shuran Zhang
AU - Qin Xiao
AU - Yuanquan Chen
AU - Liang Chen
AU - Jiedan Chen
PY - 2026
DA - 2026/08/11
JO - BMC Plant Biology
DO - 10.1186/s12870-026-09720-2
UR - https://doi.org/10.1186/s12870-026-09720-2
AB - Background: Guangxi, China, is a critical region for tea plant genetic resources because of its proximity to the center of tea origin and its rich tea germplasm resources. However, the genetic background and evolutionary history of tea plant (Camellia sinensis) in this region remain poorly understood, which limits their utilization in tea breeding. Results: We performed whole-genome resequencing on 179 tea accessions collected from 12 regions of Guangxi, generating 4.33 Tb of sequencing data with an average sequencing depth of 8.06× and identifying 84,827,998 high-quality SNPs. Phylogenetic and population structure analyses classified the accessions into five genetic groups. Notably, the ‘Fangchengcha’ (C. fangchengensis) population (GP1) occupied the most basal evolutionary position and exhibited the lowest genetic diversity (π = 0.162), suggesting its primitive and relatively isolated status. Selective sweep analysis identified distinct genomic selection signatures across different evolutionary stages. During the transition from non-domesticated to early domesticated germplasm, loci associated with primary metabolism and environmental responses gradually shifted toward loci related to secondary metabolite pathways associated with tea flavor traits (e.g., flavonoid and phenylpropanoid biosynthesis). Gene expression profiling further revealed stage-specific expression patterns of selected genes. Genes involved in epigenetic regulation and environmental responses were highly expressed in wild materials, whereas genes associated with lipid metabolism, energy metabolism, and substance transport showed progressively higher expression with increasing domestication. These patterns suggest coordinated changes between functional requirements and gene expression regulation during adaptive evolution. Conclusion: This study provides a systematic analysis of the genetic background and evolutionary dynamics of tea germplasm in Guangxi and may provide a useful basis for the conservation and molecular breeding of local tea germplasm. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s12870-026-09720-2.
SN - 1471-2229
ER -