Fig. 4
A 1.67-Mb heterozygous inversion is the causal variation for flat fruit shape. a, b Genome-wide (top) and regional (bottom) Manhattan plots using GWAS for fruit shape (round/flat) based on SNPs (a) and SVs (b). The regional plots showed the significant region (27.0–31.6 Mb) of Chr6. Each dot in plot (a) represents a SNP and in plot (b) represents the middle position of an SV. The black arrow in plot (a) points to the lead SNP (Chr6: 28,036,986) in this study, which was also reported in previous study [36]. The black arrow in plot (b) points to the middle position of the 1.67-Mb inversion (Chr6: 27,959,880–29,634,101). Horizontal dashed black lines correspond to the Bonferroni-corrected significance threshold for SNPs (5.94) and SVs (4.23) in (a) and (b), respectively. Vertical dashed blue lines correspond to the breakpoints of the inversion. c The heterozygous inversion in flat peach was formed by a NHEJ (non-homologous end-joining) mechanism accompanying two mis-repair events: the deletion of two base-pairs and the insertion of one base-pair respectively at the breakpoints highlighted in red dashed rectangles. d The association between the 1.67-Mb inversion and fruit shape was further verified in a diverse population that included 37 flat accessions (blue background) and 99 round accessions (orange background) using four pairs of primers (P1 for the sequences flanking the proximal breakpoint of the derived allele, and P2, P3, and P4 for those of the ancestral allele). The plus and minus signs represent the presence or absence of PCR products, respectively. e Linkage disequilibrium (LD) between the 1.67-Mb inversion and SNPs (left) or InDels (right) in the 23.00–31.98 Mb region of Chr6. Disequilibrium is measured as r2. The black arrow points to the lead SNP (Chr6: 28,036,986). Inversion breakpoints are depicted as vertical dashed blue lines. The color of SNPs and InDels with at least 5% minor allele frequency is shown as the P values of GWAS analysis, with red colors representing lower P values