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

ABSTRACT: 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 inserti

SUBMITTER: Tao L 

PROVIDER: S-EPMC12796203 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature