Fig. 3

SNPs associated with the AGRs. A GWAS between genotypes and AGRs (left) and QQ plots (right). The red lines represent the Bonferroni corrected significance threshold (-log10P = 8.59). And the red dots were the significant SNPs that crossed the threshold. GWAS results of AGRs from S1 – S5 were shown from inside to outside. B The KEGG pathways (diamonds) and GO functions (circles) in which significant related SNPs-related genes are enriched. Each node represents an enriched term, and the node colour represents different clusters. The higher the enriched factors, the smaller the node sizes are. Same as Fig. 2, only the first 5 terms with highest enrich ratios in each cluster were marked with text. C The shared significant SNPs between the AGRs and RGRs GWAS results. D Phenotypic comparisons between different genotypes based on the most significant SNP, Chr2: 42508231 G>A. The X-axis represents the different genotypes, and the Y-axis shows the AGR and RGR in the S5 growth stage. E Changes in the binding sites of Chr2: 42508231 G>A were demonstrated. The sequence used in the analysis was 5 bp of the left and right flanks of the mutation site