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

驯化 山茶 生物 遗传多样性 人口 遗传变异 植物 芳香 基因 遗传学 食品科学 社会学 人口学
作者
Wei Tong,Yan Li Wang,Fangdong Li,Fei Zhai,Jingjing Su,Didi Wu,Lianghui Yi,Qijuan Gao,Qiong Wu,Enhua Xia
出处
期刊:Journal of Integrative Plant Biology [Wiley]
标识
DOI:10.1111/jipb.13737
摘要

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.
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