ddRAD sequencing of 1076 Camellia accessions reveals the genetic diversity and population introgression of the tea plant in China

doi:10.1016/j.pld.2025.09.002

Plant Diversity ›› 2026, Vol. 48 ›› Issue (03): 451-459.DOI: 10.1016/j.pld.2025.09.002

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ddRAD sequencing of 1076 Camellia accessions reveals the genetic diversity and population introgression of the tea plant in China

Xiao-Yan Tong^a, Jian-Bing Hu^a, Hui-Lin Wen^a, Chun-Lin Chen^b, Ling-Ling Tao^a, Jun Wu^a, Yi-Ping Tian^b, Hui-Ping Jiang^b, Lin-Bo Chen^b, Da-He Qiao^c, Ming-Tao Shu^a, En-Hua Xia^a, Kun Dong^a, Yue Fei^a, Sheng-Rui Liu^a, Chao-Ling Wei^a, Jun-Yan Zhu^a

a State Key Laboratory of Tea Plant Germplasm Innovation and Resource Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036, Anhui, China;
b Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650201, China;
c Guizhou Tea Research Institute, 1 Jin'nong Road, Guiyang 550006, Guizhou, China

Received:2025-02-24 Revised:2025-09-01 Online:2026-06-10 Published:2026-05-25
Contact: Chao-Ling Wei,E-mail:weichl@ahau.edu.cn;Jun-Yan Zhu,E-mail:zhujunyan1022@163.com
Supported by:
This study was funded by the National Natural Science Foundation of China (grant no. U20A2045) and the Science and Technology Project of Yunnan Province (grant no. 202102AE090038).

ddRAD sequencing of 1076 Camellia accessions reveals the genetic diversity and population introgression of the tea plant in China

a State Key Laboratory of Tea Plant Germplasm Innovation and Resource Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei 230036, Anhui, China;
b Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650201, China;
c Guizhou Tea Research Institute, 1 Jin'nong Road, Guiyang 550006, Guizhou, China

通讯作者: Chao-Ling Wei,E-mail:weichl@ahau.edu.cn;Jun-Yan Zhu,E-mail:zhujunyan1022@163.com
基金资助:
This study was funded by the National Natural Science Foundation of China (grant no. U20A2045) and the Science and Technology Project of Yunnan Province (grant no. 202102AE090038).

Abstract

Abstract: The tea plant (Camellia sinensis) is a widely cultivated and economically significant crop that originated from southwestern China. Owing to its high heterozygosity and complex genetic diversity, the evolutionary history of the tea plant and its domestication remain unclear. In this study, we used 1076 Camellia accessions to elucidate the phylogenetic relationships and population structure of Camellia accessions across 16 major tea-producing provinces in China. Six species-specific populations were classified based on these SNPs through phylogenetic trees and population structure. We found that C. taliensis populations have undergone divergent evolution compared to other wild relatives, such as C. kwangsiensis and C. crassicoluma. Population structure and introgression analyses further revealed frequent interspecific genetic exchanges between C. sinensis and its wild relatives. Thus, a transitional C. sinensis population that shared a genetic background with C. taliensis was characterized. Distinct genetic divergence was observed within the two main varieties of C. sinensis. Contrary to the relatively exclusive genetic background within the C. sinensis var. assamica population in southwestern China, extensive regional introgression and gene flow were observed in the C. sinensis var. sinensis population between southwestern and eastern China. Finally, we developed a core collection comprising 160 accessions based on our genetic diversity analyses. Our findings not only provide insights into the evolutionary history and genetic diversity of the tea plant but may facilitate the development of the conservation and utilization of tea plant resources.

Key words: Tea plant, Population structure, ddRAD-seq, Genetic diversity, Core collection, Introgression

摘要： The tea plant (Camellia sinensis) is a widely cultivated and economically significant crop that originated from southwestern China. Owing to its high heterozygosity and complex genetic diversity, the evolutionary history of the tea plant and its domestication remain unclear. In this study, we used 1076 Camellia accessions to elucidate the phylogenetic relationships and population structure of Camellia accessions across 16 major tea-producing provinces in China. Six species-specific populations were classified based on these SNPs through phylogenetic trees and population structure. We found that C. taliensis populations have undergone divergent evolution compared to other wild relatives, such as C. kwangsiensis and C. crassicoluma. Population structure and introgression analyses further revealed frequent interspecific genetic exchanges between C. sinensis and its wild relatives. Thus, a transitional C. sinensis population that shared a genetic background with C. taliensis was characterized. Distinct genetic divergence was observed within the two main varieties of C. sinensis. Contrary to the relatively exclusive genetic background within the C. sinensis var. assamica population in southwestern China, extensive regional introgression and gene flow were observed in the C. sinensis var. sinensis population between southwestern and eastern China. Finally, we developed a core collection comprising 160 accessions based on our genetic diversity analyses. Our findings not only provide insights into the evolutionary history and genetic diversity of the tea plant but may facilitate the development of the conservation and utilization of tea plant resources.

关键词: Tea plant, Population structure, ddRAD-seq, Genetic diversity, Core collection, Introgression

Xiao-Yan Tong, Jian-Bing Hu, Hui-Lin Wen, Chun-Lin Chen, Ling-Ling Tao, Jun Wu, Yi-Ping Tian, Hui-Ping Jiang, Lin-Bo Chen, Da-He Qiao, Ming-Tao Shu, En-Hua Xia, Kun Dong, Yue Fei, Sheng-Rui Liu, Chao-Ling Wei, Jun-Yan Zhu. ddRAD sequencing of 1076 Camellia accessions reveals the genetic diversity and population introgression of the tea plant in China[J]. Plant Diversity, 2026, 48(03): 451-459.

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ddRAD sequencing of 1076 Camellia accessions reveals the genetic diversity and population introgression of the tea plant in China

ddRAD sequencing of 1076 Camellia accessions reveals the genetic diversity and population introgression of the tea plant in China

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