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.
Highlights
The leaves of the tea plant Camellia sinensis (L.)O
90,502 nonsynonymous SNPs were identified in 19,793 genes, and 10,596 frameshift indels were identified in 26,943 genes (Fig. 1c, d)
This result showed that the proportion of nonsynonymous SNPs (nsSNPs) in the coding regions of ancient tea plants was significantly lower than that detected in pear (7.7%), apple (10.5%), and soybean (1.9%), suggesting that less genetic variation occurs in the coding regions of ancient tea plants than in that of fruit trees and some annual crops[22–24]
Summary
The leaves of the tea plant Camellia sinensis (L.)O. Kuntze var. sinensis (2n = 2x = 30) are used to produce different kinds of tea, making tea an important economic crop worldwide. The leaves of the tea plant Camellia sinensis (L.). Sinensis (Chinese type tea; CSS) and C. sinensis var. Analyses of genome-wide genetic diversity and the identification of genes associated with excellent traits that contribute to domestication and improvement play an essential role in the breeding of superior varieties[10–12]. Genome-wide association studies (GWAS) using wholegenome resequencing identified new genes influencing agronomic traits in crop plants[13–17]. The release of the tea genome database laid the foundation for genome resequencing and GWAS18. Resequencing dozens of tea cultivars has allowed preliminary understanding of the genetic variation patterns during tea plant domestication and varietal improvement; the high degree of heterozygosity in tea cultivars has hindered the correlation of selected loci with improvement and domestication related traits
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