Population whole-genome resequencing reveals the phylogenetic relationships and population structure of four Hunan typical tea landraces

Hunan located at the evolutionary transitional zone edge of the Yunnan-Guizhou plateau, tea germplasms are abundant. At present, although morphological, enzymological and molecular markers have been used to study the genetic relationship of these tea germplasms. However, due to the complexity of the genetic background of tea germplasm resources, the evolution history and taxonomy of Hunan tea germplasm is still unclear. In this study, four Hunan tea landraces from the evolutionary transitional zone were collected, including 9 'Chengbu Dongcha' (CBDC), 8 'Jianghua Kucha' (JHKC), 11 'Rucheng Baimao' (RCBM) and 8 'Anhua Yuntai' (AHYT). We used whole-genome re-sequencing to identify genetic variation, phylogenetic placement, and population structure among the four tea landraces and then scanned the genome for regions related to population potential selective. Across the samples, we identified an average of 1.38 million (M) SNPs and 6.82 × 10³ INDELs. Based on the high-quality SNPs, we performed neighbor-joining phylogenetic tree, population structure, and principal component analysis, all of which supported that the 36 tea germplasms could been divided into two groups, CBDC and AHYT were clustered into a group, and RCBM and JHKC were clustered into another group. With CBDC, JHKC, and RCBM as control, 407, 380, and 147 selected genes were identified in AHYT, respectively, were in the top 5% of F_ST and Log₂^Ratioθπ scores. The identified genes are mainly involved in stress tolerance, biosynthesis of important secondary metabolites, adaptability, and yield. These results will be helpful in the classification of tea germplasms and investigating selection–related genes.