Fig. 5: GWAS analysis identified SVs associated with the cauliflower/broccoli morphotype and details of SVs that change the expression of genes BoPNY and BoCKX3.

a, Manhattan plot showing the SV signals associated with cauliflower/broccoli (significance was calculated by two-tailed Fisher’s exact test. A Bonferroni-corrected P < 0.05 was interpreted as significant). The light red dots show the top 5% P values and deep red dots show the top 1% P values. b, One SV is associated with BoPNY. c, The number of accessions with presence or absence SV (associated with BoPNY) genotype for broccoli/cauliflower accessions and all the other accessions (statistical test: two-tailed Fisher’s exact test). d, Expression comparison of BoPNY between SV presence and absence accessions (two-sided Student’s t test; centerline, median; box limits, first and third quartiles; whiskers, 1.5× IQR). e, Sequence methylation level around BoPNY between absence and presence genotype groups, which is negatively associated with the expression level of the gene. f, Two SVs associated with BoCKX3. g, The number of accessions with presence or absence SV (associated with BoCKX3) genotypes for broccoli/cauliflower accessions and all other accessions (statistical test: two-tailed Fisher’s exact test). h, The four possible haplotype groups are formed by two SVs. Haplotype 4 was not detected in our population. i, Expression comparison of BoCKX3 between the three haplotype groups (two-sided Student’s t test; centerline, median; box limits, first and third quartiles; whiskers, 1.5× IQR). j, Expression of BoCKX3 in different tissues of cauliflower and cabbage, highlighting high expression of this gene in leaf 2 of cauliflower. Leaf 1 denotes fresh leaf before curd initiation; leaf 2 denotes fresh leaf during curd development; curd 1 denotes developing curd; curd 2 denotes mature curd. ‘N’ indicates a missing value as cabbage makes no curds.