Genomic variation of 363 diverse tea accessions unveils the genetic diversity, domestication, and structural variations associated with tea adaptation

文献类型： 外文期刊

第一作者： Tong, Wei

作者： Tong, Wei;Wang, Yanli;Li, Fangdong;Zhai, Fei;Su, Jingjing;Wu, Didi;Yi, Lianghui;Gao, Qijuan;Xia, Enhua;Li, Fangdong;Gao, Qijuan;Wu, Qiong

作者机构：

关键词： Camellia sinensis; cold tolerance; novel genes; population structure; presence-absence variation; structural variation

期刊名称：JOURNAL OF INTEGRATIVE PLANT BIOLOGY （ 影响因子：9.3； 五年影响因子：9.3 ）

ISSN： 1672-9072

年卷期： 2024 年

页码：

收录情况： SCI

摘要： 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 similar to 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.

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