Identification of candidate genomic regions for chicken egg number traits based on genome-wide association study

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.

A significant quantitative trait locus on chromosome Z and its impact on egg production traits in seven maternal lines of meat-type chicken

“…org/ cgi-bin/ QTLdb/ GG/ index). The regions identified in our study were 1.9 Mb apart from those reported by Zhao et al, which were carried out in more than a dozen breeds, including White Leghorn and Rhode Island Red chickens [23]. Although the results were different between the present study and that of Zhao et al, they suggest that GGA Z is an important genetic region involved in egg production.…”

Transcriptome Sequencing-Based Mining of Genes Associated With Pubertal Initiation in Dolang Sheep

“…Based on these results, a number of genes associated with puberty were identified. The GAMT gene plays an important role in embryonic development and the reproductive system ( Braissant et al, 2005 ; Zhao et al, 2021 ). SOHLH1 is a multifunctional regulator of the network required for oocyte maintenance and differentiation during early folliculogenesis ( Wang et al, 2020 ).…”

“…Ling et al (2014) identified 12 genes associated with high fecundity in Anhui white goats. Based on metabolomics, Zhou et al (2021) identified polymorphisms in IRS1 were associated with growth efficiency traits in Chinese black Tibetan sheep and Zhang et al found stallfeeding modified the content of protein and fat, tenderness, water holding capacity, and texture of the longissimus lumborum of Tibetan sheep (Zhang et al, 2021). Based on 16S rRNA gene pyrosequencing, Gui et al (2021) found that supplementation of concentrate in the cold season improved the rumen microbial abundance of Tibetan sheep.…”

Identification of selection signatures in Iranian dromedary and Bactrian camels using whole genome sequencing data

“…Since, brown adipose tissue acts as a thermal regulator and heat generator for the body upon cold exposure 28 , 29 , the positive selection of gene involved in the development of this tissue can be vital for Bactrian camels that have adapted to cold climates. The CAMK4 gene is known as a domestication-related gene in sheep 30 and has been shown to play an important role in the reproduction of mice 31 , sheep 32 , and chicken 33 , 34 . This gene is also associated with the formation of long-term memory 35 , 36 .…”