Genetic insights into the population structure and adaptive evolution of tea germplasm in Guangxi, China

Abstract

Guangxi, China, is a critical region for tea plant genetic resources because of its proximity to the center of tea origin and its rich tea germplasm resources. However, the genetic background and evolutionary history of tea plant ( Camellia sinensis ) in this region remain poorly understood, which limits their utilization in tea breeding. We performed whole-genome resequencing on 179 tea accessions collected from 12 regions of Guangxi, generating 4.33 Tb of sequencing data with an average sequencing depth of 8.06× and identifying 84,827,998 high-quality SNPs. Phylogenetic and population structure analyses classified the accessions into five genetic groups. Notably, the ‘Fangchengcha’ ( C. fangchengensis ) population (GP1) occupied the most basal evolutionary position and exhibited the lowest genetic diversity (π = 0.162), suggesting its primitive and relatively isolated status. Selective sweep analysis identified distinct genomic selection signatures across different evolutionary stages. During the transition from non-domesticated to early domesticated germplasm, loci associated with primary metabolism and environmental responses gradually shifted toward loci related to secondary metabolite pathways associated with tea flavor traits (e.g., flavonoid and phenylpropanoid biosynthesis). Gene expression profiling further revealed stage-specific expression patterns of selected genes. Genes involved in epigenetic regulation and environmental responses were highly expressed in wild materials, whereas genes associated with lipid metabolism, energy metabolism, and substance transport showed progressively higher expression with increasing domestication. These patterns suggest coordinated changes between functional requirements and gene expression regulation during adaptive evolution. This study provides a systematic analysis of the genetic background and evolutionary dynamics of tea germplasm in Guangxi and may provide a useful basis for the conservation and molecular breeding of local tea germplasm.