Fig 1. The Duplex-comb phenotypes V-shaped and Buttercup are both associated with a novel 20 Kb duplication on chicken chromosome 2.

(A) Phenotypes associated with the Duplex-comb locus V-shaped (D*V), Buttercup (D*C) and wild-type (D*N) single comb alleles. (B) A 381 Kb haplotype is IBD in D*V individuals, SNP names in the region marked in red. Yellow shading represents heterozygous genotypes with blue/orange representing reciprocal homozygous genotypes. Genotype data is from the 60K SNP chip and color coded according to genotype with missing data shown in black. A single SNP GGaluGA142157 at 38,806,246 bp (marked in yellow) is heterozygous in all D*V individuals, suggestive of a duplication. A broader view of haplotypes in more individuals is available in S1 Fig. (C) A TaqMan assay was used to investigate the genomic copy number of the putative duplicated region, showing that a duplication is present in both D*V and D*C individuals. Each bar represents a single individual. Error bars represent the minimum and maximum estimated copy number as calculated from technical replicates of each sample by Copy Caller software (ABI). (D) The Duplex-comb alleles are associated with a tandem duplication with no sequence homology at the junction point. The middle line shows the sequence at the junction point with vertical dashes indicating sequence alignment to the 5’ (bottom line) and 3’ (top line) boundaries of the duplicated region. A LTR element is shaded in gray.