Identification of Candidate Genomic Regions for Chicken Egg Production Traits Based on Genome Wide Association Study

Abstract Background: Since the domestication of chicken, various chicken 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 egg yielding differences 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 production traits or reproductive traits (57 significantly, 91 suggestively). Among them, 18 SNPs overlapped with previously reported quantitative trait loci (QTL), including 13 for egg production and 5 for reproductive traits. Three SNPs were significantly associated with multiple egg production traits, such as egg number, age at first egg, and egg production rate in chickens. 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, KITLG, GHRHR, NCOA1, ITPR1, GAMT, and CAMK4 deserve our attention and further study since they have been reported to be closely related to reproductive traits. In addition, the most significant genomic region obtained in this study was located at 48.61-48.84Mb on GGA5. In this region, we have repeatedly annotated four genes, in which YY1 and WDR25 have been shown to be related to oocytes and reproductive tissues, respectively, which implies that this region may be a candidate region underlying egg production traits. Conclusion: Our study utilized the genomic information from various chicken breeds or populations differed in egg production to understand the molecular genetic mechanisms involved in reproduction traits. We identified a series of SNPs, candidate genes, or genomic regions that associated with reproductive traits, which could help us in developing egg production in chickens.