Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran.
Anim Genet. 2022 Feb;53(1):80-93. doi: 10.1111/age.13156. Epub 2021 Dec 1.
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 ) 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, TBC1D22A, RPL8, CACNA2D1, FZD4, SGMS1, IRF8, OPTN, LOC420362, TRABD, OvoDA1, DAD1, USP6, RBM12B, MIR1772, MIR1709 and MIR6696 and also 89 putative gene-gene combinations responsible for plumage color variation in chickens. Furthermore, several KEGG pathways including metabolic pathway, cytokine-cytokine receptor interaction, focal adhesion, melanogenesis, glycosaminoglycan biosynthesis-keratan sulfate and sphingolipid metabolism were enriched in the gene-set analysis. The results indicated that plumage color is a highly polygenic trait which, in turn, can be affected by multiple coding genes, regulatory genes and gene-gene epistasis interactions. In addition to genes with additive effects, epistatic genes with tiny individual effect sizes but significant effects in a pair have the potential to control plumage coloration in chickens.
羽色可以被视为鸡的一种社会信号，也是饲养者进行品种鉴定的一种工具。羽色与免疫、生长和繁殖性状群之间的关系仍然是一个有争议的问题。本研究旨在使用鸡的 Illumina 60k 高密度 SNP 芯片，确定影响鸡羽色变异的全基因组加性和上位性变异。使用所有 SNP 和独立 SNP 进行了全基因组加性关联研究的两种方案。为了进行上位性关联分析，采用 LD 修剪方法来降低分析的复杂性。我们在模型中使用所有 SNP 检测到了 7 个与羽色相关的新的显著位点，使用 LD 修剪方法检测到了 14 个 SNP。此外，在 25 条染色体上共鉴定到 89 个与羽色显著相关的 SNP-SNP 互作（P 值<10 ），表明所有信号共同影响羽色的数量变异。通过注释与 top SNP 相关的基因，我们区分出了 18 个潜在的候选基因，包括 HNF4beta、CKMT1B、TBC1D22A、RPL8、CACNA2D1、FZD4、SGMS1、IRF8、OPTN、LOC420362、TRABD、OvoDA1、DAD1、USP6、RBM12B、MIR1772、MIR1709 和 MIR6696，以及 89 个负责鸡羽色变异的潜在基因-基因组合。此外，在基因集分析中，几个 KEGG 通路，包括代谢途径、细胞因子-细胞因子受体相互作用、焦点黏附、黑色素生成、糖胺聚糖生物合成-角鲨烯硫酸盐和鞘脂代谢，被富集。结果表明，羽色是一个高度多基因性状，反过来又受到多个编码基因、调控基因和基因-基因上位性相互作用的影响。除了具有加性效应的基因外，具有微小个体效应但在一对中具有显著效应的上位性基因也有可能控制鸡的羽色。
