New insights into genetics underlying of plumage color

Abstract

Plumage color can be considered as a social signal in chickens and a breeding identification tool among breeders. The relationship between plumage color and trait groups of immunity, growth and fertility is still a controversial issue. This research aimed to determine the genome-wide additive and epistatic variants affecting plumage color variation in chickens using the chicken Illumina 60k high-density SNP array. Two scenarios of genome-wide additive association studies using all SNPs and independent SNPs were carried out. To perform epistatic association analysis, the LD pruning approach was used to reduce the complexity of the analysis. We detected seven novel significant loci using all of the SNPs in the model and 14 SNPs using the LD pruning approach associated with plumage color. Moreover, 89 significantly associated SNP-SNP interactions (P-value <10 −6 ) distributed in 25 chromosomes were identified, indicating that all of the signals together putatively influence the quantitative variation of plumage color. By annotating genes relevant to top SNPs, we have distinguished 18 potential candidate genes comprising HNF4beta, CKMT1B,

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

“…A previous study on Swainson's thrush (Catharus ustulatus) confirmed that relevant regions, including TYRP1, were selected during evolution [47]. The findings related to chicken feather color confirmed 18 potential candidate regions, including HNF4BETA, CKMT1B, TBC1D22A, RPL8, CACNA2D1, FZD4, SGMS1, IRF8, OPTN, LOC420362, TRABD, OVODA1, DAD1, USP6, RBM12B, miR-1772, miR-1709, and miR-6696; 89 gene-gene combinations that may lead to changes in feather color may be primarily responsible for chicken feather color [48]. Additionally, the diversity of MC1R was associated with plumage color in pigeons [49].…”

Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens

“…Also, we identified the FZD4 as a candidate gene, which is associated with the pattern of phenotypic variation of plumage color (white, mixed and brown) in chicken. Plumage color is an important qualitative trait that can serve as marker for breed identification and can be considered indirectly as an economically important trait that is under the influence of multiple genes, gene–gene interactions, and environmental factors [ 53 ]. Several local Northern breeds show a white (Bianca di Saluzzo, Polverara Bianca, Ermellinata di Rovigo) or brown plumage color (Bionda Piemontese, Robusta Lionata, Padovana Camosciata).…”

A genome‐wide association study for eumelanin pigmentation in chicken plumage using a computer vision approach

“…In addition, plumage colour is considered an indirect economic trait because consumers prefer specific plumage colours for religious or nutritional reasons. Specifically, pure black and white chickens are preferred for religious reasons in Chad and the black‐boned chickens, which also have black plumage, are favoured in China for their nutritional value (Bibi et al, 2021; Davoodi et al, 2022; Yu et al, 2017).…”

“…In addition, plumage colour is considered an indirect economic trait because consumers prefer specific plumage colours for religious or nutritional reasons. Specifically, pure black and white chickens are preferred for religious reasons in Chad and the black-boned chickens, which also have black plumage, are favoured in China for their nutritional value (Bibi et al, 2021;Davoodi et al, 2022;Yu et al, 2017).In general, plumage colouration in birds serves a variety of functions such as camouflage or mimicry, interspecific communication, and protection from sunburns (Gomes et al, 2016;Prum, 2014;Rogalla et al, 2022). Plumage pigmentation exhibits various physiological and behavioural traits related to sexual selection and aids in the assessment of individual quality (Javůrková…”

“…Hua et al (2021) classified F 2 chicken colouration traits into seven groups based on the colour and pattern of body feathers, and Zhu et al (2022) divided the plumage colour into two categories: dark red and light yellow. Additionally, three discrete phenotypes (white, brown, and mixed) have been described in the genome-wide association study (GWAS) (Davoodi et al, 2022). These qualitative approaches are challenging to implement when describing phenotypes pertaining to colour variations and are likely to limit researchers to considering only the major genes that primarily affect feather colouration.…”