Fig. 3. Population structure and genetic divergence of rice bean landraces.

a The geographic distributions of 440 rice bean landraces. SSA South & Southeast Asia, SC South China, NC North China. The size and color of each pie chart represent the sample size in a specific geographic location. The map was created using the map_data() function in the R package ggplot2. b Phylogenetic tree and model-based clustering (K = 2–4) of 440 sequenced landraces. c Scores plot from a principal component analysis, supporting the division of the landraces into three geographical groups (SSA, SC, and NC). d Summary of nucleotide diversity (π) and population divergence (F_ST) across the three geographical groups. Values in parentheses represent measures of nucleotide diversity of each group, and values between pairs indicate population divergence. e Decay of linkage disequilibrium (LD), measured by r², in the three geographical groups. The upper and lower black dots with numerical values in the lines represented maximum and median values of the r² and the corresponding physical distances. Source data are provided as a Source Data file.