Fig. 4

The population structure analysis based on all rice accessions. a Neighbor-joining tree of all rice accessions which was constructed from simple matching distance based on whole-genome SNP studies. Branch and circle block colors indicate different subgroup distributions. b Principal component (PCA) analysis plots of first and third components for all rice accessions, using the same colors as in a. c Cross-validation (CV) errors graph. d Population structure based on c (K = 6). e Genome-wide average LD decay analysis estimated from all rice accessions. f Histogram of kinship