Liu Xiayi, Wu Zhou, Li Junying, Bao Haigang, Wu Changxin
National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China.
Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands.
Front Genet. 2020 Dec 22;11:613078. doi: 10.3389/fgene.2020.613078. eCollection 2020.
The feather rate phenotype in chicks, including early-feathering and late-feathering phenotypes, are widely used as a sexing system in the poultry industry. The objective of this study was to obtain candidate genes associated with the feather rate in Shouguang chickens. In the present study, we collected 56 blood samples and 12 hair follicle samples of flight feathers from female Shouguang chickens. Then we identified the chromosome region associated with the feather rate by genome-wide association analysis (GWAS). We also performed RNA sequencing and analyzed differentially expressed genes between the early-feathering and late-feathering phenotypes using HISAT2, StringTie, and DESeq2. We identified a genomic region of 10.0-13.0 Mb of chromosome Z, which is statistically associated with the feather rate of Shouguang chickens at one-day old. After RNA sequencing analysis, 342 differentially expressed known genes between the early-feathering (EF) and late-feathering (LF) phenotypes were screened out, which were involved in epithelial cell differentiation, intermediate filament organization, protein serine kinase activity, peptidyl-serine phosphorylation, retinoic acid binding, and so on. The sperm flagellar 2 gene () and prolactin receptor () gene were the only two overlapping genes between the results of GWAS and differential expression analysis, which implies that and are possible candidate genes for the formation of the chicken feathering phenotype in the present study. Our findings help to elucidate the molecular mechanism of the feather rate in chicks.
雏鸡的羽速表型，包括早羽和晚羽表型，在 poultry 行业中被广泛用作一种性别鉴定系统。本研究的目的是获得与寿光鸡羽速相关的候选基因。在本研究中，我们采集了 56 份寿光鸡母鸡的血液样本和 12 份飞羽毛囊样本。然后我们通过全基因组关联分析（GWAS）鉴定了与羽速相关的染色体区域。我们还进行了 RNA 测序，并使用 HISAT2、StringTie 和 DESeq2 分析了早羽和晚羽表型之间差异表达的基因。我们鉴定出 Z 染色体上 10.0 - 13.0 Mb 的一个基因组区域，该区域与一日龄寿光鸡的羽速在统计学上相关。经过 RNA 测序分析，筛选出了早羽（EF）和晚羽（LF）表型之间 342 个差异表达的已知基因，这些基因参与上皮细胞分化、中间丝组织、蛋白质丝氨酸激酶活性、肽基丝氨酸磷酸化、视黄酸结合等过程。精子鞭毛 2 基因（）和催乳素受体（）基因是 GWAS 结果与差异表达分析结果中仅有的两个重叠基因，这意味着在本研究中 和 是鸡羽速表型形成的可能候选基因。我们的研究结果有助于阐明雏鸡羽速的分子机制。
