Fig. 5

Candidate genes associated with selective sweeps in temperate maize. a Zoom in on the results of a GWAS for endosperm color using the maize genotypes included in this study focused on a 400 kilobase region containing the y1 gene. The dashed horizontal line indicates a 0.05 Bonferroni corrected p-value threshold. Each gray dot indicates a SNP in this interval and the red dot indicates the peak SNP. Blue column on the left indicates the position of the y1 gene. Lead SNP at position chr6:85,061,523 was highlighted as a purple diamond. b Difference in the distribution of endosperm color scores between temperate maize and tropical maize. This trait was quantified using the code: 1, white; 2, pale; 3, pale yellow; 4, yellow; 5, orange. c Difference in the distribution of flowering time (growing degree index from planting to 50% of anthesis) between temperate maize and tropical maize. d Difference in the distribution of upper kernel shape between temperate maize and tropical maize. This trait trait is quantified using the code: 1, shrunken; 2, indented; 3, level; 4, rounded; 5, pointed; 6, strongly pointed. e From left to right, selective sweep signals (XP-CLR and Fst), broad sense heritability of gene expression (H₂) in tropical and temperate maize, average expression level (in FPKM) in the roots of tropical and temperate maize and the allele frequency of the peak SNP of the cis-eQTL in both tropical and temperate maize for y1. Blue column on the left indicates the position of the y1 gene. f Display following the conventions of panel (e) for the sweet2 gene. g Display following the conventions of panel (e) for the mcm4 gene. h Display following the conventions of panel (e) for the aldolase gene