Fig. 4: Population structure of cherry accessions and selection signatures for blooming phenophase.

The neighbor-joining (NJ) phylogenetic tree (a), principal component analysis (PCA) (b), and admixture analysis (c) of 219 cherry accessions based on structural variation (SVs). d Manhattan plots showing the genomic regions under selection between early- and late-flowering groups based on the fixation index (F_ST) and nucleotide diversity (π) of SNPs. The dashed line represents the significant thresholds of π and F_ST values. e Local Manhattan plot (top) of the flowering-time association signals identified by genome-wide association analysis (GWAS) and the corresponding linkage disequilibrium (LD) heatmap (bottom) for the 44.71-kb interval on chromosome 7 (chr7: 28.10–28.15 Mb). Each dot represents an SNP, and the y-axis indicates the association significance as −log₁₀ P. Association P values were obtained using a GLM model implemented in TASSEL. The horizontal red dashed line indicates the significance threshold (−log₁₀ P = 6). Pairwise LD across this interval is shown in the lower panel and is measured as D′. Red dots indicate non-synonymous SNPs within chr7: 28.10–28.15 Mb. f Box plots showing haplotypes at the upstream locus of the candidate genes PAV07G053290 (+) and PAV07G053280 (−). Phenotypic differences among genotype classes at the upstream SNPs of these candidate genes are shown. Each point represents a biologically independent sample. Sample sizes were AA, n = 5; AT, n = 88; and TT, n = 126. Phenotypic values were obtained from single measurements per sample. Box plots show the median (center line), upper and lower quartiles (box limits), and whiskers extending to 1.5 × the interquartile range. Overall differences among genotype groups were assessed using a Kruskal–Wallis test (*P < 0.05, **P < 0.01, ns, P > 0.05), and pairwise comparisons were performed using two-sided Wilcoxon rank-sum tests. No conventional control group was included. g Zoom in on the selected region of the AGL9 gene.