CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken

J Fogelholm,N Huq,M Johnsson,R Lenz,P Jensen,R Henriksen,D Wright,A Höglund

doi:10.1038/s41598-020-57710-7

Abstract

Plumage colouration in birds is important for a plethora of reasons, ranging from camouflage, sexual signalling, and species recognition. The genes underlying colour variation have been vital in understanding how genes can affect a phenotype. Multiple genes have been identified that affect plumage variation, but research has principally focused on major-effect genes (such as those causing albinism, barring, and the like), rather than the smaller effect modifier loci that more subtly influence colour. By utilising a domestic × wild advanced intercross with a combination of classical QTL mapping of red colouration as a quantitative trait and a targeted genetical genomics approach, we have identified five separate candidate genes (CREBBP, WDR24, ARL8A, PHLDA3, LAD1) that putatively influence quantitative variation in red-brown colouration in chickens. By treating colour as a quantitative rather than qualitative trait, we have identified both QTL and genes of small effect. Such small effect loci are potentially far more prevalent in wild populations, and can therefore potentially be highly relevant to colour evolution.

Highlights

There are three main types of pigmentation in feathers – melanin, carotenoids and porphyrins[18]
In the case of the loci on chromosomes 2 and 10, the Red Junglefowl genotype led to an increase in red intensity, whilst for the chromosome 14 locus the White Leghorn genotype led to an increase in red intensity
An over-dominance interaction was seen with a homozygous Red Junglefowl genotype on the chromosome 15 locus and a homozygous White Leghorn genotype on the chromosome 26 locus leading to the biggest decrease in colour score, see Supplementary Fig. 1

Summary

Introduction

There are three main types of pigmentation in feathers – melanin, carotenoids and porphyrins[18]. In the case of coat colouration, domestic animals are markedly different to their wild ancestors This is for instance the case with chickens, where the wild ancestor the Red Junglefowl has a wide range of plumage colours ranging from dark red/ brown to light orange within a single individual. To identify genes that regulate quantitative variation in the intensity of red-brown colouration, we utilized an advanced intercross between wild Red Junglefowl and domestic White Leghorn (WL) chickens. By using a combination of targeted genetical genomics (whole genome transcriptomics of targeted individuals) to simultaneously map eQTL and correlate gene expression with intensity of red-brown colouration, we identify five putatively causal genes affecting quantitative variation in this plumage colouration trait in the chicken

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Conclusion