Fig. 3

Phylogenetic relationships and population structure of 415 tea accessions. (A) Inferred population structure of 415 accessions. Bar plot of individual membership coefficients for the genetic clusters is inferred by using ADMIXTURE (K = 5) base on 99,363 SNPs. Individual membership coefficients are sorted within each cluster. (B) Scatter diagram of the first three principal components. The first, second and third coordinates indicate PC1, PC2 and PC3. Each dot represents an accession. (C) A Neighbor-Joining (NJ) phylogenetic tree of all 415 tea accessions in Guizhou Plateau constructed using whole-genome SNP data based on the maximum composite likelihood (MCL) model. The NJ tree compared with indigenous communities (HR, DQ, BY, MM and PR indigenous communities) and ADMIXTURE software results (K = 5). The lines with different colors represent the indigenous communities (the black blocks in the middle represent accessions imported from other provinces), and the squares with different colors nearby represent the populations we divided according to the results of ADMIXTURE. GP01, GP02, GP03, GP04 and GP05 are pure populations and GP06 is admixture population. (D) The LD decay plot of 415 accessions and six inferred populations