Abstract：
Domestication has shaped the population structure and agronomic traits of tea plants, yet the complexity of tea population structure and genetic variation that determines these traits remains unclear. We here investigated the resequencing data of 363 diverse tea accessions collected extensively from almost all tea distributions and found that the population structure of tea plants was divided into eight subgroups, which were basically consistent with their geographical distributions. The genetic diversity of tea plants in China decreased from southwest to east as latitude increased. Results also indicated that Camellia sinensis var. assamica (CSA) illustrated divergent selection signatures with Camellia sinensis var. sinensis (CSS). The domesticated genes of CSA were mainly involved in leaf development, flavonoid and alkaloid biosynthesis, while the domesticated genes in CSS mainly participated in amino acid metabolism, aroma compounds biosynthesis, and cold stress. Comparative population genomics further identified ~730 Mb novel sequences, generating 6,058 full-length protein-encoding genes, significantly expanding the gene pool of tea plants. We also discovered 217,376 large-scale structural variations and 56,583 presence and absence variations (PAVs) across diverse tea accessions, some of which were associated with tea quality and stress resistance. Functional experiments demonstrated that two PAV genes (CSS0049975 and CSS0006599) were likely to drive trait diversification in cold tolerance between CSA and CSS tea plants. The overall findings not only revealed the genetic diversity and domestication of tea plants, but also underscored the vital role of structural variations in the diversification of tea plant traits.
摘要：
驯化塑造了茶树的种群结构和农艺性状,然而，决定这些性状的茶叶种群结构和遗传变异的复杂性仍不清楚。我们在这里调查了从几乎所有茶分布中广泛收集的363种不同茶树种的重新测序数据，发现茶树的种群结构分为八个亚组，与它们的地理分布基本一致。随着纬度的增加，中国茶树的遗传多样性从西南到东降低。结果还表明，茶树var。assamica（CSA）说明了山茶的不同选择特征。中华（CSS）。CSA的驯化基因主要参与叶片发育,类黄酮和生物碱的生物合成，而CSS中的驯化基因主要参与氨基酸代谢,芳香化合物生物合成，冷压力。比较群体基因组学进一步鉴定了约730Mb的新序列，产生6,058个全长蛋白质编码基因，显着扩大茶树的基因库。我们还发现了217,376个大规模的结构变化和56,583个存在和不存在的变化（PAV）在不同的茶叶品种，其中一些与茶叶品质和抗逆性有关。功能实验表明，两个PAV基因（CSS0049975和CSS0006599）可能会驱动CSA和CSS茶树之间耐寒性的性状多样化。总体发现不仅揭示了茶树的遗传多样性和驯化，但也强调了结构变化在茶树性状多样化中的重要作用。
