In other species: Coscoroba swan , black swan , rock pigeon , helmeted guineafowl , chicken , king penguin , Arctic skua , pomarine skua , barn owl , brown booby , red-footed booby , zebra finch , Lesser snow goose , Bananaquit , gyrfalcon , ruff , Oriental honey-buzzard , Chestnut-bellied monarch , Eleonora's falcon

Categories: Pigmentation phene

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 266300 (trait) , 155555 (gene)

Mendelian trait/disorder: yes

Disease-related: no

Key variant known: no

Mapping: Liu et al. (2023) "conducted a genome-wide association study (GWAS) on an intercross F2 population of Pekin ducks and mallards (n=722) and identified a 1.57 Mb genetic region (Chr11: 20,176,480-21,750,101 bp) related to duck melanism. Fine mapping by linkage disequilibrium (LD) and Fst analysis narrowed the final candidate region to a region of 22,500 bp (Chr11: 20,677,500-20,700,000 bp) including three coding genes, TCF25, MC1R, and TUBB3. Combined with transcriptome and qRT-PCR analysis, MC1R was identified as the unique genetic locus responsible for black plumage in ducks, and it was significantly more highly expressed in the feather bulbs of black ducks. ... We also identified 52 G>A (Chr11: 20,696,354 G>A) and 376 G>A (Chr11: 20,696,678 G>A) mutations in the MC1R coding region that have been widely studied in ducks. In addition, structural variations (SVs) were screened by nanopore sequencing, and no significant SV was found to be associated with the duck black plumage trait. However, we identified 4 novel SNPs in the MC1R regulator region (Chr11: 20,678,412 G>A, Chr11: 20,679,236 G>A, Chr11: 20,692,496 A>G, and Chr11: 20,692,791 A>G) that had a strong association with the black plumage phenotype of ducks and combined with potential changes in transcription binding affinities. The luciferase reporter gene assay demonstrated that Chr11: 20,678,412 G>A and Chr11: 20,679,236 G>A led to significant promoter activity changes."

Markers: Yu et al. (2013) "performed a sequence characterization of the duck melanocortin 1 receptor (alpha-melanocyte stimulating hormone receptor) (MC1R) gene to analyze the relationship between MC1R polymorphism and the extended black variant in domestic ducks based on the extended black (E) and non-extended black (e+) allele hypothesis of the duck MC1R gene. Both c.52G>A and c.376G>A substitutions are highly associated with the duck extended black variant (P < 0.01), but the novel c.52G>A substitution is more of a fit for the allele hypothesis of the duck MC1R gene." Sultana et al. (2017) investigated "the effect of the MC1R gene on plumage coloration in duck breeds ... . ...Four non-synonymous SNPs, c.52A>G (p.Lys18Glu), and c.376 A>G (p.Ile126Val), c.409G>A (p.Ala137Thr) and c.649C>T (p.Arg217Cys), were associated with the two deduced genotypes (i.e., E/E and e+ /e+) based on plumage color phenotypes." Zhang et al. (2023) identified the same MC1R variants and reported an epistatic effect between MC1R and MITF: "Two non-synonymous SNPs in MC1R (c.52G>A and c.376G>A) were significantly related to duck black plumage, and three SNPs in MITF (chr13:15411658A>G, chr13:15412570T>C and chr13:15412592C>G) were associated with white plumage. Additionally, we also identified the epistatic interactions between causing loci. Some ducks with white plumage carry the c.52G>A and c.376G>A in MC1R, which also compensated for black and spotty plumage color phenotypes, suggesting that MC1R and MITF have an epistatic effect."

Associated gene: