Fig. 2: Population structure and genetic divergence of primitive landraces and improved landraces.

a Phylogenetic tree and model-based clustering of 564 peach accessions, including 549 cultivated P. persica accessions and 15 close wild relative P. kansuensis accessions. The neighbor-joining (NJ) tree and model-based clustering (K = 3 and 4) were constructed based on a total of 337,386 SNPs. b PCA plot of the first two principal components for all P. persica accessions (n = 549) supported the classification of landraces (PLs and ILs), ECs, and WCs. Accessions with ambiguous/debatable geographic origins were excluded in subsequent analyses. c NJ tree for all PL and IL accessions supported the genetic divergence of PLs and ILs based on the same set of SNPs. The outer squares labeled with red and blue represent the accessions from eastern China and from central and western China, respectively. d Significant divergence of the pH and fructose content of the PL and IL accessions. The number (n) of individuals for each peach type is shown below. In the violin plots (significance was tested with Wilcoxon tests), central line: median values; bounds of box: 25th and 75th percentiles; whiskers: 1.5 * IQR (IQR: the interquartile range between the 25th and 75th percentile). e Demographic analysis for different groupings of peach accessions. A multiple sequentially Markovian coalescent (MSMC) model was used to infer their effective population fluctuations under a mutation rate μ = 7.7 × 10^–9 per site per generation¹¹² and the generation time of 3 years (and generation time of 4 years in Supplementary Fig. 7). f Linkage disequilibrium (LD) patterns and genetic diversity (θπ) for the four different types of P. persica. Source data underlying Fig. 2f are provided as a Source Data file.