Fig. 4: A region at the end of Chr3 controls important ornamental traits.

a, Major genes and QTLs that control continuous flowering, double flower, self-incompatibility and prickle density are shown together with candidate genes for each trait. Detailed analyses per locus are described in Supplementary Figs. 5, 7, 9 and 10, respectively. For prickle density in OW progeny (OW2017 and OW2016), the boxes represent the 1-LOD (log of the odds ratio) interval and the lines the 2-LOD interval. b,c, GWAS analysis showing the P values of the association between SNPs positioned along Chr3 and the number of petals, indicating regions that control the number of petals. The petal number is considered as a qualitative trait (simple versus double flowers; GLM) (b) or as a quantitative trait (MLM) (c). The horizontal red line shows Bonferroni-corrected significance levels (1.78 × 10^–6). Other significant associations detected by GWAS are shown in Supplementary Fig. 12. n = 96 cultivars with 3 flowers scored by cultivar. d,e, QTL analysis for prickle density in two F1 progenies using the OW mapping population based on scoring from 2016 and 2017, n = 151 individuals (d), and the YW mapping population, n = 174 individuals (e). Lod, log likelihood ratio.