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.

中文翻译：

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贵州和云南地区八个古茶种群的基因组水平多样化确定了核心农艺性状的候选基因

古茶树作为珍贵的自然资源和茶树遗传多样性的来源，对于研究植物的进化机制、多样化和驯化具有重要价值。古代茶树的整体遗传多样性以及自然选择过程中发生的遗传变化仍然知之甚少。在这里，我们报告了由 120 种古茶树组成的八个不同组的基因组重测序：六组来自贵州省，两组来自云南省。基于 8,082,370 个已鉴定的高质量 SNP，我们构建了系统发育关系，评估了种群结构，并进行了全基因组关联研究 (GWAS)。我们的系统发育分析表明，120株古茶树主要聚集为3组5单枝，这与主成分分析（PCA）的结果一致。基于遗传结构分析，古代茶树被进一步划分为七个亚群。此外，发现古茶树的变异并未因外部自然环境的压力或人工育种而减少（非同义/同义= 1.05）。通过整合GWAS、选择信号和基因功能预测，4个候选基因与3个叶片性状显着相关，2个候选基因与植物类型显着相关。这些候选基因可用于茶树的进一步功能表征和遗传改良。研究发现，古茶树的变异并没有因外部自然环境的压力或人工育种而减少（非同义/同义= 1.05）。通过整合GWAS、选择信号和基因功能预测，4个候选基因与3个叶片性状显着相关，2个候选基因与植物类型显着相关。这些候选基因可用于茶树的进一步功能表征和遗传改良。研究发现，古茶树的变异并没有因外部自然环境的压力或人工育种而减少（非同义/同义= 1.05）。通过整合GWAS、选择信号和基因功能预测，4个候选基因与3个叶片性状显着相关，2个候选基因与植物类型显着相关。这些候选基因可用于茶树的进一步功能表征和遗传改良。并且两个候选基因与植物类型显着相关。这些候选基因可用于茶树的进一步功能表征和遗传改良。并且两个候选基因与植物类型显着相关。这些候选基因可用于茶树的进一步功能表征和遗传改良。