Figure 2: Genetic mapping and genome-wide association analysis identify the genomic region determining ruff reproductive morphs.
From: A supergene determines highly divergent male reproductive morphs in the ruff
(a) The ruff linkage-mapping pedigree. Paternal links are shown as red lines, and maternal links are shown as blue lines. (b) Linkage maps (in cM) of the inversion region on ruff chromosome 11 support the presence of the inversion polymorphism, indicated by a ∼70% shorter linkage map when only independents are considered. SNPs on the same contig are shown in the same color. (c) Association between markers and morphs based on 41 unrelated males (ten faeder, ten satellite and 21 independent). Alternating shades of gray indicate different contigs, ordered on the basis of synteny with the chicken genome. The top panel shows −log10 (P values) of association across the entire ruff genome; the middle (Faeder) and bottom (Satellite) panels show enlarged views of the associated peak (0.703–0.713 Gb; indicated by dashed lines in the top panel) for comparisons with the independent locus. Red and blue dots represent genome-wide significant signals (P < 0.05, 1,000 permutations) for the Faeder and Satellite loci, respectively.
