Fig. 3

Population structure and LD of 159 accessions. A Inferred population structure of 159 accessions. Bar plot of individual membership coefficients for the genetic clusters was inferred using ADMIXTURE (K = 2) based on 98,241 SNPs. Individual membership coefficients (Q) were sorted within each cluster. GP01 and GP02 are shown in red and blue, respectively. B Principal component analysis (PCA). The three PCA scatter diagram was made by the first and second principal components. Three inferred populations were identified in ADMIXTURE, GP01 is shown in red, GP02 in blue, and GP03 in yellow. C ML tree comparing the classification of inferred populations, Species C. tachangensis and C. gymnogyna, altitude: H1, H2, and H3 corresponding to the first (> 1400 m), second (1400–1100 m), and third (< 1100 m) altitude gradient, respectively. D LD decay plot of 159 accessions and three inferred populations