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<p>Tea plants, which are among the world’s most economically important beverage crops, exhibit extensive genetic diversity and are rich in secondary metabolites. While structural variations (SVs) drive phenotypic diversification, their regulatory roles in transcriptional networks and agronomic traits remain underexplored in this perennial crop. Here, we construct a pangenome from 22 representative tea accessions and their wild relatives. Genomic SV analysis reveals that 22% of the gene promoters contain variants influencing flavonoid, amino acid, and terpenoid biosynthesis. Population SV analysis of 275 tea accessions reveals three haplotypes in the <i>ANS3</i> promoter, with Hap1, containing a 192 bp insertion, predominantly found in wild relatives but largely lost in modern cultivars. This insertion increases <i>CtANS3</i> expression and anthocyanin content in wild relatives. Additionally, a 159 bp insertion in the <i>CtLRR1</i> promoter reduces resistance to <i>Colletotrichum gloeosporioides</i> in wild relatives. Our findings underscore SVs as pivotal regulators of flavor differentiation and adaptive evolution during tea plant domestication.</p>

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Pangenome analyses of tea plants reveal structural variations driving gene expression alterations and agronomic trait diversification

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月6日

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  • Lingling Tao,
  • Junyan Zhu,
  • Jianbing Hu,
  • Qi Xu,
  • Jun Wu,
  • Chunlin Chen,
  • Youyong Li,
  • Fangdong Li,
  • Hongrong Chen,
  • Songyan Huang,
  • Qianqian Zhou,
  • Yuanyan Zhao,
  • Yanping Hu,
  • Shengrui Liu,
  • Kun Dong,
  • Linbo Chen,
  • Benying Liu,
  • Xiaochun Wan,
  • Enhua Xia,
  • Yongfeng Zhou,
  • Chaoling Wei

摘要

Tea plants, which are among the world’s most economically important beverage crops, exhibit extensive genetic diversity and are rich in secondary metabolites. While structural variations (SVs) drive phenotypic diversification, their regulatory roles in transcriptional networks and agronomic traits remain underexplored in this perennial crop. Here, we construct a pangenome from 22 representative tea accessions and their wild relatives. Genomic SV analysis reveals that 22% of the gene promoters contain variants influencing flavonoid, amino acid, and terpenoid biosynthesis. Population SV analysis of 275 tea accessions reveals three haplotypes in the ANS3 promoter, with Hap1, containing a 192 bp insertion, predominantly found in wild relatives but largely lost in modern cultivars. This insertion increases CtANS3 expression and anthocyanin content in wild relatives. Additionally, a 159 bp insertion in the CtLRR1 promoter reduces resistance to Colletotrichum gloeosporioides in wild relatives. Our findings underscore SVs as pivotal regulators of flavor differentiation and adaptive evolution during tea plant domestication.