Fig. 1

Genome-wide relationship in cultivated apple and wild species. a Geographic distribution of apple accessions. The circle represents the sample size. b Principal component analysis (PCA) of apple accessions. c The phylogenetic tree and population structure of apple accessions. “RJ” represents “Ralls Janet,” “SD” represents “Starking Delicious,” “GD” represents “Golden Delicious” and “Jona” represents “Jonathan.” The accession orders and positions on the X-axis are the same. d Linkage disequilibrium (LD) decay patterns in M. sieversii, M. sylvestris, other wild, heirloom, and cultivar groups. e Nucleotide diversity (π) between different groups. Lowercase letters indicate the significant differences based on Fisher’s least significant difference (LSD) test at p ≤ 0.01