Genetic fine‐mapping reveals single nucleotide polymorphism mutations in the MC1R regulatory region associated with duck melanism

Abstract

Birds are among the most colourful terrestrial vertebrates, with various plumage colours and patterns. We 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 52G > A (Chr11: 20,696,354G > A) and 376G > A (Chr11: 20,696,678G > 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 four novel single nucleotide polymorphisms in the MC1R regulator region (Chr11: 20,678,412G > A, Chr11: 20,679,236G > 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: 20,678,412G > A and Chr11: 20,679,236G > A led to significant promoter activity changes. Our research emphasizes the importance of MC1R regulatory region mutation in determining the duck black plumage phenotype, and these results expand our understanding of the genetic mechanism underlying duck plumage colour.

Unique feather color characteristics and transcriptome analysis of hair follicles in Liancheng White ducks

“…It activates the TYR core enhancer, which helps to regulate the tyrosinase gene in melanocytes ( Yun et al, 2019 ). At present, the predominant candidate genes related to duck feather color are TYR ( Sultana et al, 2018 ), TYRP1 ( Xi et al, 2020 ), DCT ( Sultana et al, 2018 ), MC1R ( Liu et al, 2023a ), EDNRB2 ( Guo et al, 2022 ), and MITF ( Zhou et al, 2018 ; Lin et al, 2019 ; Wang et al, 2022a ).…”

“…For these products, white feather ducks are favored by consumers. The variations of feather color in birds are related to the distribution, content and proportion of pigments ( Liu et al, 2023a ). Melanin is the main pigment, which mainly affects the color of feathers and the depth of skin color.…”

“…Duck is a good model to study the plumage color of birds, but there are only a few studies describing feather color. Researchers found MC1R are related to black feather in ducks, and single nucleotide polymorphism mutations in the MC1R regulatory region are found to be associated with duck melanism ( Liu et al, 2023a ). Some studies have shown that the dark spots in duck feathers are caused by the EDNRB2 gene ( Xi et al, 2021 ).…”

Common Ancestry of theIdLocus: Chromosomal Rearrangement and Polygenic Possibilities

“…For instance, in humans, an SNP in the promoter of the SLC45A2 gene has been linked to variations in skin color (Graf et al, 2007). In ducks, the black plumage phenotype is determined by a mutation within the regulatory region of the MC1R gene (Liu et al, 2023). Similarly, studies on different chicken breeds have revealed that mutations in the promoter regions of genes like MITF , TYR , ASIP, and GJA5 play a role in influencing skin color (Li et al, 2021; Wang et al, 2018; Yu et al, 2019, 2017).…”

Genomic basis of melanin‐associated phenotypes suggests colour‐specific environmental adaptations in tawny owls

“…Though the pleiotropic nature of the POMC gene has been posited to explain associations between melanin‐based pigmentation and other phenotypic traits, that is, melanin‐associated phenotypes, molecular evidence is largely absent (McNamara et al., 2021; San‐Jose & Roulin, 2018). What has been well described is structural genetic variation at MC1R and respective regulatory regions affecting melanin‐based pigmentation in several bird species including domestic breeds (Kerje et al., 2003; Liu et al., 2023; Mundy, 2005). However, a lack of associations has also been reported particularly after correcting for the effect of population structure (Avilés et al., 2019; Hoffman et al., 2014; MacDougall‐Shackleton et al., 2003).…”