Genome-wide association analysis identifies potential regulatory genes for eumelanin pigmentation in chicken plumage

Plumage color in chicken is determined by the proportion of eumelanin and pheomelanin pigmentation. As the main ingredient in plumage melanin, eumelanin plays a key role in the dark black, brown and grey coloration. However, very few studies have been performed to identify the related genes and mutations on a genome-wide scale. Herein, a resource family consisting of one backcross population and two F2 cross populations between a black roster and Yukou Brown I parent stockbreed was constructed for identification of genes related to eumelanin pigmentation. Chickens with eumelanin in their plumage were classified as the case group, and the rest were considered the control group. A genome-wide association study of this phenotype and genotypes using Affymetrix 600K HD SNP arrays in this F2 family revealed 13 significantly associated SNPs and in 10 separate genes on chromosomes 1, 2, 3 and 5. Based on previous studies in model species, we inferred that genes, including NUAK family kinase 1 (NUAK1) and sonic hedgehog (SHH), may play roles in the development of neural crest cells or melanoblasts during the embryonic period, which may also affect the eumelanin pigmentation. Our results facilitate the understanding of the genetic basis of eumelanin pigmentation in chicken plumage.

家鸡的羽色由真黑色素（eumelanin）与褐黑色素（pheomelanin）的沉积比例决定。作为羽毛黑色素的主要组分，真黑色素在深黑、棕褐与灰色羽色的形成过程中发挥关键调控作用。然而目前在全基因组层面开展的真黑色素相关基因与突变位点鉴定研究仍较为匮乏。本研究构建了由黑羽原种与裕口褐1号（Yukou Brown I）亲本品种杂交得到的1个回交群体及2个F2杂交群体组成的资源家系，用于鉴定真黑色素沉积相关基因。将羽部含有真黑色素的个体划分为病例组，其余个体作为对照组。本研究在该F2群体中利用Affymetrix 600K高密度单核苷酸多态性（SNP）芯片开展表型与基因型的全基因组关联分析，最终在1、2、3、5号染色体上的10个独立基因区域内筛选得到13个显著关联的SNP位点。结合模式物种已有研究结果，我们推测NUAK家族激酶1（NUAK1）与音猬因子（sonic hedgehog, SHH）等基因可能通过参与胚胎期神经嵴细胞或黑素母细胞的发育过程，进而影响真黑色素的沉积。本研究结果有助于加深学界对家鸡羽部真黑色素沉积遗传基础的理解。