Genome-Wide Analysis Identifies Candidate Genes Encoding Feather Color in Ducks

Abstract

Comparative population genomics and genome-wide association studies (GWAS) offer opportunities to discover human-driven detectable signatures within the genome. From the point of view of evolutionary biology, the identification of genes associated with the domestication of traits is of interest for the elucidation of the selection of these traits. To this end, an F2 population of ducks, consisting of 275 ducks, was genotyped using a whole genome re-sequence containing 12.6 Mb single nucleotide polymorphisms (SNPs) and four plumage colors. GWAS was used to identify the candidate and potential SNPs of four plumage colors in ducks (white, spot, grey, and black plumage). In addition, FST and genetic diversity (π ratio) were used to screen signals of the selective sweep, which relate to the four plumage colors. Major genomic regions associated with white, spotted, and black feathers overlapped with their candidate selection regions, whereas no such overlap was observed with grey plumage. In addition, MITF and EDNRB2 are functional candidate genes that contribute to white and black plumage due to their indirect involvement in the melanogenesis pathway. This study provides new insights into the genetic factors that may influence the diversity of plumage color.

Genome-Wide Association Study Reveals the Genetic Basis of Duck Plumage Colors

“…Yang et al [ 25 ] have found that six SNPs of MITF are associated with plumage color in Kaiya–Liancheng F2 offspring. Guo et al [ 51 ] found that MITF is closely related to white plumage color. In this study, we identified three SNPs in MITF (chr13:15411658 A > G , chr13:15412570 T > C , and chr13:15412592 C > G ) in white-feathered ducks, which are located in the intron region.…”

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 ).…”

Genome-Wide Association Studies Reveal Candidate Genes Associated with Pigmentation Patterns of Single Feathers of Tianfu Nonghua Ducks

“…DENND4A ( DENN -domain-containing 4A) gene produces a protein that has a DENN domain and plays a role in releasing guanosine diphosphates (GDP) from the small guanine nucleotide-binding proteins (G-proteins) for the formation of guanosine triphosphates (GTP). Additionally, the protein activates ras-related proteins, particularly Rab-10, which regulates intracellular vesicle trafficking [ 45 , 46 ]. The DENND4A gene also contains molecules that are vital for antiviral responses and inflammation, and may play a key role in regulating avian beak and feather disease virus (BFDV) [ 47 ].…”