Extended Data Fig. 6: Representative selected genes related to light signaling, flowering time regulation, biosynthesis or signaling of auxin.
From: Genome-wide selection and genetic improvement during modern maize breeding
Each plot group represents the results for a selected representative candidate gene, which includes XP-CLR plot (left), gene annotation (above the pie plot), nonsynonymous SNP frequency changes during the corresponding breeding process (pie plot) and nonsynonymous SNP information (below the pie plot). For XP-CLR plots, the XP-CLR scores for whole data panel and subgroups are plotted above and under the zero, respectively. Red arrows along the x-axis indicate the position of the candidate genes. The blue and red horizontal dashed lines above the zero represent the 80th quantile and genome-wide significant cutoff, respectively, for XP-CLR scores in whole data panel. The horizontal dashed lines under the zero represent the 80th quantile for XP-CLR scores in subgroups. Arabidopsis homologs were used for annotation of the candidate genes. The p-value of fisher’s exact test for allele frequency changes are shown above the pie plot. The nonsynonymous SNP information includes SNP location, variation from alleles in B73 to others and corresponding amino acid changes (separated by comma).
