Fig. 6: Genetic loci and a low-frequency/distantly evolved haplotype for early flowering in peach.
a Significantly associated loci and candidate genes (Pp.LH.01G06402 and Pp.LH.01G06403) for flowering time. Purple shading represents the IBD regions shared by Clr3 accessions. The horizontal line in the Manhattan plot denotes the Bonferroni-adjusted significance threshold. b Selection signature (XP-CLR) comparing Clr3 accessions with those from other clusters. Pp.LH.01G06402 and Pp.LH.01G06403, located within the putative selective regions, are labeled. c Haplotypes of the LD block (Chr1: 45,355,352-45,435,638 bp) associated with flowering time. Haplotype frequencies were calculated based on 489 peach accessions. d Box plot showing the distributions of the flowering dates among different haplotypes. Multiple comparisons were conducted using the least significant difference test. In the box plots, central line: median values; bounds of the box: 25th and 75th percentiles; whiskers: 1.5 x IQR (the interquartile range between the 25th and 75th percentiles). e The frequency distribution of the three haplotypes associated with peach flowering time across the six kinship clusters (Clr1–6). Different colored sections in each pie chart represent the proportion of each haplotype. f Haplotype network of the flowering trait. Median-joint network analysis was used to construct the haplotype network of the flowering haplotypes among the 489 accessions.
