Genome-Wide Association Study of Egg Production Traits in Shuanglian Chickens Using Whole Genome Sequencing

Egg production is the most important economic trait in laying hens. To identify molecular markers and candidate genes associated with egg production traits, such as age at first egg (AFE), weight at first egg (WFE), egg weight (EW), egg number (EN), and maximum consecutive egg laying days (MCD), a genome-wide analysis by whole genome sequencing was performed in Shuanglian chickens. Through whole genome sequencing and quality control, a total of 11,006,178 SNPs were obtained for further analysis. Heritability estimates ranged from moderate to high for EW (0.897) and MCD (0.632), and from low to moderate (0.193~0.379) for AFE, WFE, and EN. The GWAS results showed 11 genome-wide significant SNPs and 23 suggestive significant SNPs were identified to be associated with EN, MCD, WFE, and EW. Linkage disequilibrium analysis revealed twenty-seven SNPs associated with EN were located in a 0.57 Mb region on GGA10, and clustered into five blocks. Through functional annotation, three candidate genes NEO1, ADPGK, and CYP11A1, were identified to be associated with EN, while the S1PR4, LDB2, and GRM8 genes was linked to MCD, WFE, and EW, respectively. These findings may help us to better understand the molecular mechanisms underlying egg production traits in chickens and contribute to genetic improvement of these traits.

Differences in invitro responses of the hypothalamo-pituitary-gonadal hormonal axis between low- and high-egg-producing turkey hens

Low-egg-producing hens (LEPH) ovulate less frequently than high-egg-producing hens (HEPH) and exhibit differences in mRNA levels for components of the hypothalamo–pituitary–gonadal (HPG) axis, suggesting differential responsiveness to trophic stimulation. Ovulation frequency is governed by the production of the pituitary gonadotropins and feedback of the ovarian follicle steroid hormones, which are regulated by HPG axis stimulation and inhibition at the hypothalamic level. The pituitary and follicle cells from LEPH and HEPH were subjected to in vitro hormonal treatments to stimulate or inhibit the HPG axis, followed by expression analysis of mRNA levels for HPG axis genes and radioimmunoassays for steroid hormone production. Statistical analysis was performed using the mixed models procedure of SAS. The pituitary cells from HEPH showed upregulation of genes associated with ovulation stimulation, whereas cells from LEPH showed upregulation of genes associated with inhibition of ovulation. High-egg-producing hens’ follicle cells displayed a higher sensitivity and responsiveness to gonadotropin treatment. Level of egg production impacted ovulation-related gene expression in the pituitary cells as well as steroid hormone production in the follicle cells, with HEPH displaying a greater positive response to stimulation. These findings indicate that differences in egg production among turkey hens likely involve differential responsiveness of the cells within the HPG axis.

Endocrine and genetic factors affecting egg laying performance in chickens: a review

1. Egg-laying performance reflects the overall reproductive performance of breeding hens. The genetic traits for egg-laying performance have low or medium heritability, and, depending on the period involved, usually ranges from 0.16 to 0.64. Egg-laying in chickens is regulated by a combination of environmental, endocrine and genetic factors. 2. The main endocrine factors that regulate egg-laying are gonadotropin-releasing hormone (GnRH), prolactin (PRL), follicle-stimulating hormone (FSH) and luteinising hormone (LH). 3. In the last three decades, many studies have explored this aspect at a molecular genetic level. Recent studies identified 31 reproductive hormone-based candidate genes that were significantly associated with egg-laying performance. With the development of genome-sequencing technology, 64 new candidate genes and 108 single nucleotide polymorphisms (SNPs) related to egg-laying performance have been found using genome-wide association studies (GWAS), providing novel insights into the molecular genetic mechanisms governing egg production. At the same time, microRNAs that regulate genes responsible for egg-laying in chickens were reviewed. 4. Research on endocrinological and genetic factors affecting egg-laying performance will greatly improve the reproductive performance of chickens and promote the protection, development, and utilisation of poultry. This review summarises studies on the endocrine and genetic factors of egg-laying performance in chickens from 1972 to 2019.

Novel Polymorphisms in RAPGEF6 Gene Associated with Egg-Laying Rate in Chinese Jing Hong Chicken using Genome-Wide SNP Scan

The improvement of egg production is of vital importance in the chicken industry to maintain optimum output throughout the laying period. Because of the elongation of the egg-laying cycle, a drop in egg-laying rates in the late laying period has provoked great concern in the poultry industry. In this study, we calculated the egg-laying rate at weeks 61–69 (60 days) of Jing Hong chickens parent generation as the phenotype, and the genotype were detected by the chicken 600K Affymetrix Axiom High Density (HD) Single Nucleotide Polymorphisms (SNP)-array. The Genome-Wide Association Study (GWAS) result showed that the egg production trait is significantly associated with five SNPs (AX-75745366, AX-75745380, AX-75745340, AX-75745388, and AX-75745341), which are in the rap guanine nucleotide exchange factor 6 (RAPGEF6) gene on chicken chromosome 13. A total of 1676 Chinese commercial Jing Hong laying hens—including two populations, P1 population (858 hens) and P2 population (818 hens)—were genotyped using the Polymerase Chain Reaction-Restriction Fragments Length Polymorphisms (PCR-RFLP) method for the association analysis of egg-laying rates for the verification of the GWAS results. Genotypic and allelic frequencies of five SNPs were inconsistent with Hardy–Weinberg equilibrium, and the average population genetics parameters considering all the SNP values; i.e., gene homozygosity (Ho), gene heterozygosity (He), the effective number of alleles (Ne), and the polymorphism information content (PIC) were 0.75, 0.25, 1.40, and 0.20 in P1; 0.71, 0.29, 1.46, and 0.24 in P2; and 0.73, 0.27, 1.43, and 0.22 in P1 + P2 populations, respectively. The association analysis results revealed that out of the five polymorphisms, three of them (AX-75745366, AX-75745340, and AX-75745341; Patent applying No: 201810428916.5) had highly significant effects on egg-laying rates according to the GWAS results. Population-specific association analyses also showed similar significant association effects with this trait. Four haplotypes (AAGG, AAAG, AGGG, and AGAG) were inferred based on significant loci (AX-75745340 and AX-75745341) and also showed significant associations with the egg-laying rate, where haplotype AAGG had the highest egg-laying rate, with the exception of the egg-laying rate in P1 population, followed by other haplotypes. Furthermore, genotypes TT, AA, and GG showed the highest egg-laying rate compared to the corresponding genotypes at AX-75745366, AX-75745340, and AX-75745341 SNP loci in P1+P2, respectively. A similar result was found in the population-specific analysis except for the P1 population, in which TC genotype showed the highest egg-laying rate. No significant association was found in the egg-laying rate during the 60 days laying period for the SNPs (AX-75745380 and AX-75745388) in any group of population (p ≥ 0.05). Collectively, we report for the first time that 3 SNPs in the RAPGEF6 gene were significantly associated with the egg-laying rate during the later stage of egg production, which could be used as the potential candidate molecular genetic markers that would be able to facilitate in the selection and improvement of egg production traits through chicken breeding.

Molecular, cellular, morphological, physiological and behavioral aspects of gonadotropin-inhibitory hormone

Gonadotropin-inhibitory hormone (GnIH) is a hypothalamic neuropeptide that was isolated from the brains of Japanese quail in 2000, which inhibited luteinizing hormone release from the anterior pituitary gland. Here, we summarize the following fifteen years of researches that investigated on the mechanism of GnIH actions at molecular, cellular, morphological, physiological, and behavioral levels. The unique molecular structure of GnIH peptide is in its LPXRFamide (X=L or Q) motif at its C-terminal. The primary receptor for GnIH is GPR147. The cell signaling pathway triggered by GnIH is initiated by inhibiting adenylate cyclase and decreasing cAMP production in the target cell. GnIH neurons regulate not only gonadotropin synthesis and release in the pituitary, but also regulate various neurons in the brain, such as GnRH1, GnRH2, dopamine, POMC, NPY, orexin, MCH, CRH, oxytocin, and kisspeptin neurons. GnIH and GPR147 are also expressed in gonads and they may regulate steroidogenesis and germ cell maturation in an autocrine/paracrine manner. GnIH regulates reproductive development and activity. In female mammals, GnIH may regulate estrous or menstrual cycle. GnIH is also involved in the regulation of seasonal reproduction, but GnIH may finely tune reproductive activities in the breeding seasons. It is involved in stress responses not only in the brain but also in gonads. GnIH may inhibit male socio-sexual behavior by stimulating the activity of cytochrome P450 aromatase in the brain and stimulates feeding behavior by modulating the activities of hypothalamic and central amygdala neurons.