Genome-level diversification of eight ancient tea populations in the Guizhou and Yunnan regions identifies candidate genes for core agronomic traits

Abstract

The ancient tea plant, as a precious natural resource and source of tea plant genetic diversity, is of great value for studying the evolutionary mechanism, diversification, and domestication of plants. The overall genetic diversity among ancient tea plants and the genetic changes that occurred during natural selection remain poorly understood. Here, we report the genome resequencing of eight different groups consisting of 120 ancient tea plants: six groups from Guizhou Province and two groups from Yunnan Province. Based on the 8,082,370 identified high-quality SNPs, we constructed phylogenetic relationships, assessed population structure, and performed genome-wide association studies (GWAS). Our phylogenetic analysis showed that the 120 ancient tea plants were mainly clustered into three groups and five single branches, which is consistent with the results of principal component analysis (PCA). Ancient tea plants were further divided into seven subpopulations based on genetic structure analysis. Moreover, it was found that the variation in ancient tea plants was not reduced by pressure from the external natural environment or artificial breeding (nonsynonymous/synonymous = 1.05). By integrating GWAS, selection signals, and gene function prediction, four candidate genes were significantly associated with three leaf traits, and two candidate genes were significantly associated with plant type. These candidate genes can be used for further functional characterization and genetic improvement of tea plants.

Genetic analyses reveal regional structure and demographic expansion of the predominant tea pest Empoasca onukii (Hemiptera: Cicadellidae) in China

“…These findings suggest that E. onukii spatially expanded to its currently distributed regions in the post‐LGM era, similar to many species in temperate North America and Europe 1,87 . Archaeological records showed that the western parts of China might be the region in which tea was first cultivated outside the native location of tea trees, dated to 2000 years ago (the Western Han Dynasty) 16,81–83,88 . Tea was disseminated to the north and east of its native region approximately 1000 years ago (from the Three Kingdoms to the Tang Dynasty) 88 .…”

Evaluating the productivity of ancient Pu’er tea trees (Camellia sinensis var. assamica): a multivariate modeling approach

“…Tea is consumed by over three billion people across 160 countries, making it one of the world’s most popular beverages [ 9 , 10 ]. Its management as a cash crop plays an important role in rural poverty reduction [ 2 , 11 ] and economic growth.…”

“…Some trees in tea gardens regrow from the original ancient trunks. According to Lu et al [ 9 ], there is no official definition of ancient tea trees, but natural trees over 100 years of age are often considered ancient. Hence, we define wild trees over 100 years or trees regrown from trunks over 100 years of age as ancient in this study.…”

The Future Potential Distribution and Sustainable Management of Ancient Pu’er Tea Trees (Camellia sinensis var. assamica (J. W. Mast.) Kitam.)

“…Tea from ancient trees fetches high prices because of its rarity and flavor. "Ancient" trees are often defined as trees over 100 years of age or regrown trees from trunks over 100 years of age [10]. Tea from ancient trees has unique properties.…”

“…According to Zhao et al [11], ancient tea is rich in nutrients, and the genetic diversity of these ancient trees significantly contributes to tea cultivation. Lu et al [10] indicated that the study of the genes of ancient trees under natural selection can provide insights into the evolutionary mechanisms, diversification, and domestication of trees and aid the functional characterization and genetic improvement of trees. A photochemical analysis of ancient Pu'er tea trees suggests that their high polyphenol concentration has detoxifying and elastin-protecting properties, which slows skin aging [12].…”