Fig 1.
Iris color variation in domestic pigeons.
(A) A pigeon with gravel eyes (wild type) exhibits a bright orange iris color; (B) A pigeon with pearl eyes exhibits a grayish-white iris color. The red background in both gravel and pearl irises is from capillaries. Photo credit: J. -O. Gao.
Fig 2.
Genomic mapping of the Tr locus.
(A) The Manhattan plot of the GWAS analysis for the Tr locus. The gray line indicates the Bonferroni-corrected critical value (P = 2.01×10−8). The scaffold with the strongest association signal is marked. (B) The genotypes of 92 pigeons across the mapped region associated with the pearl eye. Each row represents one individual, and each column represents an SNP/indel. Blue indicates homozygosity for the major allele in pearl-eyed pigeons, yellow indicates homozygosity for the minor allele in pearl-eyed pigeons, green indicates heterozygosity, and white indicates missing data. A shared haplotype (scaffold 30: 1,894,006–1,903,342) was identified. Genes located in and around the shared region are labeled.
Fig 3.
SLC2A11B mutations in avian species.
(A) Schematic diagram of the SLC2A11B protein with 12 transmembrane domains. The SLC2A11B mutations in birds are highlighted in red. (B) Validation of the SLC2A11B W49X mutation in domestic pigeons.
Fig 4.
The expression profile of SLC2A11B in pigeon tissues and genes with differential expression between pearl and gravel irises.
(A) Normalized expression of SLC2A11B in various tissues from wild-type pigeons as determined by qPCR analysis. Boxes span the first to third quartiles, bars extend to the minimum and maximum observed values, black lines indicate the medians, and circles represent the data points. (B) Normalized comparison of SLC2A11B expression between the pearl and gravel irises by transcriptome sequencing. Differentially expressed genes involved in xanthophore differentiation or pteridine synthesis are highlighted. (C) qPCR validation of differentially expressed genes (CSF1R, GCH1, and SLC2A11B) between pearl and gravel irises. *P < 0.05, **P < 0.01, ***P < 0.001.
Fig 5.
The origin of the pearl iris variant trmut in domestic pigeons.
(A) Neighbor-joining (NJ) trees of the 9 kb nonrecombining Tr region based on 81 haplotypes from 140 unrelated individuals comprising 139 domestic pigeons (35 fancy pigeons, two feral pigeons, and 102 racing pigeons) and one Columba rupestris (outgroup). All nodes had more than 60% support from 1,000 bootstrap replicates. Orange branches indicate trmut haplotypes, blue branches indicate Tr+ haplotypes, and the black branch indicates the outgroup. Different circle colors represent the seven traditional breeds of domestic pigeons and the outgroup. The red star indicates the time of origin of the Tr mutation. (B) Violin plots of the posterior distribution of the estimated TMRCA for the Tr locus in domestic pigeons. The generation time was set at one year. Two independent simulations were performed using the estimated recombination rates in 10 kb and 50 kb windows. In every simulation, 10 replicate MCMCs were plotted with transparency.
Fig 6.
Selection of the pearl iris variant trmut in domestic pigeons.
(A) The distribution of integrated haplotype score (iHS) values on scaffold AKCR02000030.1. The gray lines indicate the significance of the absolute iHS scores of 3 or greater. (B) Extended haplotype homozygosity (EHH) decay across the Tr locus region. Nucleotide diversity (π, Pi) (C) and Tajima’s D (D) were calculated in 10 kb windows with a 1 kb step size for trmut and Tr+ haplotypes.
Fig 7.
RELAX tests indicate consistent relaxation of selection in avian SLC2A11B but not TYR.
Three different schemes of test/reference branch designations were illustrated by color-labeled branches (red/dark blue for “basal”, red and orange/dark and intermediate blue for “internal”, all warm colors/all cool colors for “clade”) in the phylogeny and were tested separately (see Materials and Methods). The results with birds (warm-colored branches) as test branches are shown in the table below (see S6 Table for more results). The k values significantly smaller than 1, which indicate relaxation of selection, are highlighted in bold green font. The P-values shown are after Bonferroni correction for multiple testing.