ddRAD sequencing of 1076 Camellia accessions reveals the genetic diversity and population introgression of the tea plant in China

The tea plant ( Camellia sinensis ) is a widely cultivated and economically significant crop that originated from southwestern China. Owing to its high heterozygosity and complex genetic diversity, the evolutionary history of the tea plant and its domestication remain unclear. In this study, we used 1076 Camellia accessions to elucidate the phylogenetic relationships and population structure of Camellia accessions across 16 major tea-producing provinces in China. Six species-specific populations were classified based on these SNPs through phylogenetic trees and population structure. We found that C. taliensis populations have undergone divergent evolution compared to other wild relatives, such as C. kwangsiensis and C. crassicoluma . Population structure and introgression analyses further revealed frequent interspecific genetic exchanges between C. sinensis and its wild relatives. Thus, a transitional C. sinensis population that shared a genetic background with C. taliensis was characterized. Distinct genetic divergence was observed within the two main varieties of C. sinensis . Contrary to the relatively exclusive genetic background within the C. sinensis var. assamica population in southwestern China, extensive regional introgression and gene flow were observed in the C. sinensis var. sinensis population between southwestern and eastern China. Finally, we developed a core collection comprising 160 accessions based on our genetic diversity analyses. Our findings not only provide insights into the evolutionary history and genetic diversity of the tea plant but may facilitate the development of the conservation and utilization of tea plant resources. • ddRAD-seq analysis of 1,076 Camellia accessions revealed the phylogenetic relationships and population structure of tea plants in China. • Population structure analysis identified frequent interspecific introgression between C. sinensis and wild relatives. • A core collection of 160 accessions was developed to characterize the genetic diversity of tea plants in China.