Fig. 3

SVs are deleterious and underwent preferential selection during improvement. a The proportion of SVs with different unfolded site frequency spectrum (SFS) frequencies compared to presumably neutral sSNPs (synonymous SNPs), nSNPs (non-synonymous SNPs), and SVs (DEL, INS, DUP, and INV) for landraces (top) (n = 41) and modern cultivars (bottom) (n = 108) compared with P. kansuensis accessions (n = 37) as the outgroup. b The inferred distribution of fitness effects for SVs and nSNPs in landraces (left) and modern cultivars (right) based on 100 bootstrap replicates. Error bars indicate the mean ± 95% CI. c Scatter plots showing gene occurrence frequencies in landraces and modern cultivars. The significantly selected genes harbored adjusted P values (FDR) smaller than 0.01. d Proportion of SVs overlapping with different regions relative to gene models, including intergenic, CDS, intronic, upstream (< 1 kb), and downstream (< 1 kb) regions for unfavorable and favorable SVs during improvement, respectively. NS (not significant) P > 0.05, *P < 0.05, ** P < 0.01 in Fisher’s exact test