Identification of candidate genomic regions for chicken egg number traits based on genome-wide association study
Xiurong Zhao,
Changsheng Nie,
Jinxin Zhang,
Xinghua Li,
Tao Zhu,
Zi Guan,
Yu Chen,
Liang Wang,
Xue Ze Lv,
Weifang Yang,
Yaxiong Jia,
Zhonghua Ning,
Haiying Li,
Changqing Qu,
Huie Wang,
Lujiang Qu
Affiliations
Xiurong Zhao
Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University
Changsheng Nie
Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University
Jinxin Zhang
Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University
Xinghua Li
Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University
Tao Zhu
Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University
Zi Guan
Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University
Yu Chen
Beijing Municipal General Station of Animal Science
Liang Wang
Beijing Municipal General Station of Animal Science
Xue Ze Lv
Beijing Municipal General Station of Animal Science
Weifang Yang
Beijing Municipal General Station of Animal Science
Yaxiong Jia
Institute of Animal Sciences, Chinese Academy of Agricultural Sciences
Zhonghua Ning
Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University
Haiying Li
College of Animal Science, Xinjiang Agricultural University
Changqing Qu
Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University
Huie Wang
College of Animal Science, Tarim University
Lujiang Qu
Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University
Abstract Background Since the domestication of chicken, various breeds have been developed for food production, entertainment, and so on. Compared to indigenous chicken breeds which generally do not show elite production performance, commercial breeds or lines are selected intensely for meat or egg production. In the present study, in order to understand the molecular mechanisms underlying the dramatic differences of egg number between commercial egg-type chickens and indigenous chickens, we performed a genome-wide association study (GWAS) in a mixed linear model. Results We obtained 148 single nucleotide polymorphisms (SNPs) associated with egg number traits (57 significantly, 91 suggestively). Among them, 4 SNPs overlapped with previously reported quantitative trait loci (QTL), including 2 for egg production and 2 for reproductive traits. Furthermore, we identified 32 candidate genes based on the function of the screened genes. These genes were found to be mainly involved in regulating hormones, playing a role in the formation, growth, and development of follicles, and in the development of the reproductive system. Some genes such as NELL2 (neural EGFL like 2), KITLG (KIT ligand), GHRHR (Growth hormone releasing hormone receptor), NCOA1 (Nuclear receptor coactivator 1), ITPR1 (inositol 1, 4, 5-trisphosphate receptor type 1), GAMT (guanidinoacetate N-methyltransferase), and CAMK4 (calcium/calmodulin-dependent protein kinase IV) deserve our attention and further study since they have been reported to be closely related to egg production, egg number and reproductive traits. In addition, the most significant genomic region obtained in this study was located at 48.61–48.84 Mb on GGA5. In this region, we have repeatedly identified four genes, in which YY1 (YY1 transcription factor) and WDR25 (WD repeat domain 25) have been shown to be related to oocytes and reproductive tissues, respectively, which implies that this region may be a candidate region underlying egg number traits. Conclusion Our study utilized the genomic information from various chicken breeds or populations differed in the average annual egg number to understand the molecular genetic mechanisms involved in egg number traits. We identified a series of SNPs, candidate genes, or genomic regions that associated with egg number, which could help us in developing the egg production trait in chickens.
