The genetic effects of the dopamine D1 receptor gene on chicken egg production and broodiness traits

Comprehensive analysis of mRNA and miRNA differential expression profiles in the hypothalamus-pituitary-gonadal axis in laying and broodiness period of Wanxi white geese

The hypothalamus-pituitary-gonadal (HPG) axis is an important neuroendocrine regulatory center involved in egg-laying process in poultry. However, its mechanism of regulating broodiness behavior and laying performance in geese remains unclear. This study explored the molecular mechanism by which the HPG axis regulates brooding behavior in Wanxi white geese (WWG). The hypothalamus, pituitary, and ovarian tissues of Wanxi white geese were collected at laying and brooding periods for transcriptome sequencing analysis. A total of 240 (BH vs. LH), 319 (BP vs. LP), and 445 (BO vs. LO) differentially expressed genes, and 56 (BH vs. LH), 82 (BP vs. LP), and 48 (BO vs. LO) differentially expressed miRNAs were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis showed that differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were significantly enriched in hormone level regulation, cell communication, calcium signaling pathway, GnRH signaling pathway, MAPK signaling pathway, Wnt signaling pathway, and other processes. Six DEGs and four DEMs were randomly selected for real-time fluorescence quantitative reverse transcription PCR (RT-qPCR). The results showed that the transcriptome sequencing data were accurate and reliable. In addition, 22 potential hub miRNAs were screened. Dual luciferase reporter assays confirmed the targeting relationship between miR-144-y and DIO3. The results showed that the miRNAs mainly regulated the laying performance and brooding behavior of WWG by mediating the expression of target genes. In this study, we systematically elucidated the mechanisms by which the HPG axis regulates the broodiness behavior and laying performance of WWG at the post-transcriptional level. Several miRNAs and mRNAs associated with the reproductive performance of WWG were identified, providing a crucial reference for the subsequent use of gene editing technologies to breed new varieties and advance the development of WWG breeding industry.

Hypothalamic transcriptome profile from laying period to incubation period of Changshun green-shell laying hens

Incubation behavior in chickens is closely associated with hypothalamus. Here, RNA sequencing of hypothalamus from Changshun green-shell laying hens, an indigenous chicken breed from China, in egg-laying period (LP) and incubation period (BP) was conducted to identify critical pathways and candidate genes involved in controlling the incubation behavior in hypothalamus. A total of 637 up-regulated and 305 down-regulated differently expressed genes (DEGs) were identified in chicken hypothalamus between LP and BP groups. Gene ontology term (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further revealed that neuroactive ligand-receptor interaction, hippo signaling pathway, and focal adhesion were significantly enriched. Five candidate genes (POMC, IGF1R, CHAD, VCL, and MYL9) were suggested to play crucial roles in the regulation of chicken incubation behavior. Our results further indicated the complexity of reproductive behavior of different chicken breeds.

Exploring Evolutionary Adaptations and Genomic Advancements to Improve Heat Tolerance in Chickens

Climate change poses a significant threat to the poultry industry, especially in hot climates that adversely affect chicken growth, development, and productivity through heat stress. This literature review evaluates the evolutionary background of chickens with the specific genetic characteristics that can help chickens to cope with hot conditions. Both natural selection and human interventions have influenced the genetic characteristics of the breeds used in the current poultry production system. The domestication of chickens from the Red junglefowl (Gallus gallus) has resulted in the development of various breeds with distinct genetic differences. Over the past few years, deliberate breeding for desirable traits (such as meat production and egg quality) in chickens has resulted in the emergence of various economically valuable breeds. However, this selective breeding has also caused a decrease in the genetic diversity of chickens, making them more susceptible to environmental stressors like heat stress. Consequently, the chicken breeds currently in use may possess a limited ability to adapt to challenging conditions, such as extreme heat. This review focuses on evaluating potential genes and pathways responsible for heat tolerance, including heat shock response, antioxidant defense systems, immune function, and cellular homeostasis. This article will also discuss the physiological and behavioral responses of chicken varieties that exhibit genetic resistance to heat, such as the naked neck and dwarf traits in different indigenous chickens. This article intends to review the current genomic findings related to heat tolerance in chickens that used methods such as the genome-wide association study (GWAS) and quantitative trait loci (QTL) mapping, offering valuable insights for the sustainability of poultry in the face of global warming.

Genetic parameter estimation and molecular foundation of chicken egg-laying trait

The age of first egg (AFE) in chicken can affect early and even life-time egg production performance to some extent, and therefore is an important economic trait that affects production efficiency. To better understand the genetic patterns of AFE and other production traits including body weight at first egg (BWA), first egg weight (FEW), and total egg number from AFE to 58 wk of age (total-EN), we recorded the production performance of 2 widely used layer breeds, white leghorn (WL) and Rhode Island Red (RIR) and estimated genetic parameters based on pedigree and production data. The results showed that the heritability of AFE in both breeds ranged from 0.4 to 0.6, and AFE showed strong positive genetic and phenotypic correlations to BWA as well as FEW, while showing strong negative genetic and phenotypic correlations with total-EN. Furtherly, by genome-wide association analysis study (GWAS), we identified 12 and 26 significant SNPs to be related to AFE in the 2-layer breeds, respectively. A total of 18 genes were identified that could affect AFE based on the significant SNP annotations obtained, but there were no gene overlapped in the 2 breeds indicating the genetic foundation of AFE could differ from breed to breed. Our results provided a deeper understanding of genetic patterns and molecular basement of AFE in different breeds and could help in the selection of egg production traits.

Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

This study was designed to perform an association analysis and identify SNP markers associated with production traits of Japanese quail using restriction-site-associated DNA sequencing. Weekly body weight data from 805 quail were collected from hatching to 16 weeks of age. A total number of 3990 eggs obtained from 399 female quail were used to assess egg quality traits. Egg-related traits were measured at the beginning of egg production (first stage) and at 12 weeks of age (second stage). Five eggs were analyzed at each stage. Traits, such as egg weight, egg length and short axes, eggshell strength and weight, egg equator thickness, yolk weight, diameter, and colour, albumen weight, age of first egg, total number of laid eggs, and egg production rate, were assessed. A total of 383 SNPs and 1151 associations as well as 734 SNPs and 1442 associations were identified in relation to quail production traits using general linear model (GLM) and mixed linear model (MLM) approaches, respectively. The GLM-identified SNPs were located on chromosomes 1-13, 15, 17-20, 24, 26-28, and Z, underlying phenotypic traits, except for egg and albumen weight at the first stage and yolk yellowness at the second stage. The MLM-identified SNPs were positioned on defined chromosomes associated with phenotypic traits except for the egg long axis at the second stage of egg production. Finally, 35 speculated genes were identified as candidate genes for the targeted traits based on their nearest positions. Our findings provide a deeper understanding and allow a more precise genetic improvement of production traits of Galliformes, particularly in Japanese quail.

Transcriptome analysis reveals mRNAs and long non-coding RNAs associated with fecundity in the hypothalamus of high-and low-fecundity goat

As an important organ that coordinates the neuroendocrine system, the hypothalamus synthesizes and secretes reproductive hormones that act on the goat organism, thereby precisely regulating follicular development and reproductive processes in goats. However, it is still elusive to explore the mechanism of hypothalamic effects on goat fertility alone. Therefore, RNA-seq was used to analyze the gene expression in hypothalamic tissues of goats in high fertility group (HFG: litter size per litter ≥2) and low fertility group (LFG: litter size per litter = 1), and identified the differential lncRNAs and mRNAs and their associated pathways related to their fertility. The results showed that a total of 23 lncRNAs and 57 mRNAs were differentially expressed in the hypothalamic tissue of high and low fertility goats. GO terms and KEGG functional annotation suggest that DE lncRNAs and DE mRNAs were significantly enriched in hormone-related pathways regulating ovarian development, hormone synthesis and secretion, regulation of reproductive processes, Estrogen signaling pathway, Oxytocin signaling pathway and GnRH signaling pathway. And we constructed a co-expression network of lncRNAs and target genes, and identified reproduction-related genes such as NMUR2, FEZF1, and WT1. The sequencing results of the hypothalamic transcriptome have broadened our understanding of lncRNA and mRNA in goat hypothalamic tissue and provided some new insights into the molecular mechanisms of follicle development and regulation of its fertility in goats.

Transcriptome Analysis Reveals miR-302a-3p Affects Granulosa Cell Proliferation by Targeting DRD1 in Chickens

Egg production is an important economic trait in laying chickens as higher yields bring higher profits. Small yellow follicle (SYFL) development is a key determinant of chicken reproductive performance; however, the majority of SYFLs are not selected during the process of chicken reproduction and thus, atresia occurs. Although there have been numerous omic studies focused on egg production, the molecular mechanisms involved are still not well-understood. In this study, we used high-throughput technology to analyze the differences between the SYFL mRNA transcriptomes of high– (H) and low–egg-yielding (L) Taihang layer hens, with the aim of identifying the potential candidate genes involved in controlling the rate of egg production. We constructed six cDNA libraries, three from H and three from L Taihang hens and then performed high-throughput sequencing. Comparison of the H and L groups showed 415 differentially expressed genes (DEGs). In the high-yield group, 226 were upregulated and 189 were downregulated. Differentially enriched biological functions and processes were identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis. Ten of the candidate DEGs we identified (DRD1, MC5R, PCK1, CTSA, TGFBR3, AGO4, SLIT2, RGS1, SCNN1B, and ZP3) have been identified in previous studies as being involved in the development of small yellow follicles. DRD1 was significantly enriched in the gap junction pathway, which is an important pathway in chicken granulosa cells (GCs) to pass nutrition to an oocyte. Homology analysis showed that DRD1 was highly conserved in numerous species, indicating that it may be a productive target for improving egg production. Evidence from bioinformatics analysis revealed that gga-miR-302a-3p putatively targets the 3′UTR region of DRD1. We then identified the functions of gga-miR-302a-3p in follicular granulosa cell proliferation by targeting DRD1. RT-qPCR analysis showed that DRD1 and miR-302a-3p expression were inversely related in the SYLs of high and low egg-yielding chickens. Luciferase assays showed that miR-302a-3p targets the 3′UTR of DRD1, and overexpression of miR-302a-3p significantly inhibits the expression of DRD1 in chicken GCs (p < 0.01). Functional experiments revealed that by targeting DRD1, miR-302a-3p acts as an inhibitor of GC proliferation. Taken together, we concluded that miR-302a-3p affects chicken GC proliferation by targeting DRD1. Our data expanded the knowledge base of genes whose functions are important in egg production and the molecular mechanisms of high-yield egg production in chicken small yellow follicles.

A test of context and sex-dependent dopaminergic effects on the behavior of a gregarious bird, the common waxbill Estrilda astrild

The Dopaminergic (DAergic) system has well known influences on behavioral and cognitive functions. Previous work with common waxbills (Estrilda astrild) reported context-specific DAergic effects that could have been due to social environment. Manipulating the dopamine D2-like receptor family (D2R) pathways had opposed effects on behavior depending on whether waxbills were tested alone or in a small cage with a mirror as social stimulus. Since waxbills are highly gregarious, it was hypothesized that being alone or perceiving to have a companion might explain this context-dependence. To test context-dependent DAergic effects, we compared behavioral effects of D2R manipulation in waxbills in the same familiar environment, but either alone or with a familiar, same-sex companion. We found that D2R agonism decreased movement and feeding, similarly to previous results when testing waxbills alone. However, contrary to the hypothesis of dependence on social context, we found that the behavioral effects of the D2R agonist were unchanged when waxbills were tested with a companion. The context-dependence reported earlier might thus be due to other factors, such as the stress of being in a novel environment (small cage) or with an unfamiliar social stimulus (mirror image). In tests with a companion, we also found a sex-specific social effect of D2R manipulation: D2R blocking tended to decrease aggression in males but to increase in females. Together with past work, our results suggest that DAergic effects on behavior involve different types of context- or sex-dependence.

Mediatory role of the dopaminergic system through D1 receptor on glycine-induced hypophagia in neonatal broiler-type chickens

The present study aimed to examine the mediatory role of the dopaminergic system in the food intake induced by intracerebroventricular (ICV) injection of glycine in neonatal 3-h feed-deprived (FD3) meat-type chickens. In the first and second experiments, birds were ICV injected using low and high doses of glycine (50, 100 and 200 nmol) and strychnine (50, 100 and 200 nmol), respectively. In experiments 3-9, the behaviorally subeffective doses of dopamine (10 nmol), 6-OHDA (2.5 nmol), SCH 23,390 (D1 antagonist; 5 nmol), AMI-193 (D2 antagonist; 5 nmol), NGB2904 (D3 antagonist; 6.4 nmol) and L-741,742 (D4 antagonist; 6 nmol) were, respectively, co-administrated with glycine (200 nmol) in FD3 5-day-old chicks to investigate possible interplay of dopamine receptors in glycine-induced feeding behavior. Then, cumulative food intake based on body weight percentage (%BW) was determined at 30, 60 and 120 min after the injection. According to the results, dopamine significantly boosted the hypophagia induced by glycine at all-time intervals (p ≤ 0.001). These results combined with the previous findings suggest an interplay between dopamine and glycine in chicken's brain in which D1 receptor-mediated food intake induced by glycine.

High dietary copper induces oxidative stress and leads to decreased egg quality and reproductive performance of Chinese Yellow broiler breeder hens

The objective of this study was to investigate the effects of dietary copper (Cu) on production, egg quality, and hatchability of Chinese Yellow broiler breeder hens and growth performance of their offspring. A total of 576 30-week-old hens were randomly allotted into 6 groups, each with 6 replicates (8 cages for each replicate with 2 birds per cage). The basal diet contained 3.50 mg/kg Cu, and the other 5 treatment diets contained 8.5, 13.5, 23.5 43.5, and 83.5 mg/kg Cu, respectively, additionally supplemented with Cu on the basal diet. The trial lasted for 15 wk. Qualified egg rate of birds fed 23.5 or 83.5 mg/kg Cu was significantly decreased (P < 0.05) compared with those given 3.5, 8.5, or 13.5 mg/kg Cu. Plasma malondialdehyde concentration showed quadratic effect (P = 0.002) which that decreased first then increased with dietary Cu increased. Highest values of Cu content and hepatic activity of Cu-ATPase occurred in hens fed 83.5 mg/kg dietary Cu with linear (P = 0.001) and quadratic (P = 0.001) effects. Shell strength and proportion on 18th day of live embryos of hens fed 13.5 mg/kg Cu were the greatest compared with other groups respectively (P < 0.05); rate of qualified eggs for hatch and hatchability of fertilized eggs of hens fed 83.5 mg/kg Cu were the least (P < 0.05). In conclusion, both inadequate (3.5 mg/kg diet) and excess (83.5 mg/kg) of dietary Cu can induce oxidative stress in hens and lead to decreased egg quality. Hatchability and growth performance of offspring were decreased when breeder hens were fed excess Cu in spite of greater hatching weight. The appropriate dietary Cu level for Chinese Yellow broiler breeder hens during the egg-laying period is 15.7 to 21.2 mg/kg (1.81-2.44 mg Cu fed per day) when based on Cu level and Cu-ATPase activity in the liver. This dietary Cu requirement is approximately doubled (∼40 mg/kg, ∼4.60 mg Cu per bird per day) for maximal response of eggshell thickness.

Secretion and Function of Pituitary Prolactin in Evolutionary Perspective

The hypothalamo-pituitary system developed in early vertebrates. Prolactin is an ancient vertebrate hormone released from the pituitary that exerts particularly diverse functions. The purpose of the review is to take a comparative approach in the description of prolactin, its secretion from pituitary lactotrophs, and hormonal functions. Since the reproductive and osmoregulatory roles of prolactin are best established in a variety of species, these functions are the primary subjects of discussion. Different types of prolactin and prolactin receptors developed during vertebrate evolution, which will be described in this review. The signal transduction of prolactin receptors is well conserved among vertebrates enabling us to describe the whole subphylum. Then, the review focuses on the regulation of prolactin release in mammals as we have the most knowledge on this class of vertebrates. Prolactin secretion in response to different reproductive stimuli, such as estrogen-induced release, mating, pregnancy and suckling is detailed. Reproduction in birds is different from that in mammals in several aspects. Prolactin is released during incubation in avian species whose regulation and functional significance are discussed. Little information is available on prolactin in reptiles and amphibians; therefore, they are mentioned only in specific cases to explain certain evolutionary aspects. In turn, the osmoregulatory function of prolactin is well established in fish. The different types of pituitary prolactin in fish play particularly important roles in the adaptation of eutherian species to fresh water environments. To achieve this function, prolactin is released from lactotrophs in hyposmolarity, as they are directly osmosensitive in fish. In turn, the released prolactin acts on branchial epithelia, especially ionocytes of the gill to retain salt and excrete water. This review will highlight the points where comparative data give new ideas or suggest new approaches for investigation in other taxa.

Gene Expression Profiling in Ovaries and Association Analyses Reveal HEP21 as a Candidate Gene for Sexual Maturity in Chickens

Simple Summary

Chicken meat and egg productions are essential for human beings. Sexual maturity is important for both egg production and meat flavor. It is necessary to elucidate the genetic mechanism of chicken sexual maturity. In current study, we used digital gene expression (DGE) RNA-sequencing analysis to investigate differential expression of genes in pre-pubertal and post-pubertal ovaries in two different sub-breeds of chicken with different onsets of sexual maturity. After the analysis of RNA-sequencing data, numerous differentially expressed genes were found in both comparisons (32 day old, early-sexual-maturity pre-laying hens (P-F-O1) vs. 103 day old early-sexual-maturity laying hens (P-F-O2), and 32 day old late-sexual-maturity pre-laying hens (L-F-O1) vs. 153 day old late-sexual-maturity pre-laying hens (L-F-O2)). With the bioinformatic analysis, hen egg protein 21 kDa (HEP21) was chosen as the candidate gene to conduct following experiment. The variations in HEP21 were screened and association analyses between rs315156783 and reproductive traits were investigated in fifth-generation Ningdu Yellow chickens from a closely bred population. These results demonstrated that HEP21 is a candidate gene for sexual maturity and ovary development in chickens. However, the underlying mechanism of how HEP21 regulates chicken sexual maturity needs further focused studies.

Abstract

The age of onset of sexual maturity is an important reproductive trait in chickens. In this study, we explored candidate genes associated with sexual maturity and ovary development in chickens. We performed DGE RNA-sequencing analyses of ovaries of pre-laying (P-F-O1, L-F-O1) and laying (P-F-O2, L-F-O2) hens of two sub-breeds of Ningdu Yellow chicken. A total of 3197 genes were identified in the two comparisons, and 966 and 1860 genes were detected exclusively in comparisons of P-F-O1 vs. P-F-O2 and L-F-O1 vs. L-F-O2, respectively. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that genes involved in transmembrane signaling receptor activity, cell adhesion, developmental processes, the neuroactive ligand–receptor interaction pathway, and the calcium signaling pathway were enriched in both comparisons. Genes on these pathways, including growth hormone (GH), integrin subunit beta 3 (ITGB3), thyroid stimulating hormone subunit beta (TSHB), prolactin (PRL), and transforming growth factor beta 3 (TGFB3), play indispensable roles in sexual maturity. As a gene unique to poultry, hen egg protein 21 kDa (HEP21) was chosen as the candidate gene. Differential expression and association analyses were performed. RNA-seq data and qPCR showed that HEP21 was significantly differentially expressed in pre-pubertal and pubertal ovaries. A total of 23 variations were detected in HEP21. Association analyses of single nucleotide polymorphisms (SNPs) in HEP21 and reproductive traits showed that rs315156783 was significantly related to comb height at 84 and 91 days. These results indicate that HEP21 is a candidate gene for sexual maturity in chickens. Our results contribute to a more comprehensive understanding of sexual maturity and reproduction in chickens.

Transcriptomic Analyses of the Hypothalamic-Pituitary-Gonadal Axis Identify Candidate Genes Related to Egg Production in Xinjiang Yili Geese

The study was conducted to investigate the transcriptomic differences of the hypothalamic-pituitary-gonadal axis between Xinjiang Yili geese with high and low egg production and to find candidate genes regulating the egg production of Xinjiang Yili geese. The 8 selected Xinjiang Yili Geese with high or low egg production (4 for each group) were 3 years old, with good health, and under the same feeding condition. High-throughput sequencing technology was used to sequence cDNA libraries of the hypothalami, pituitary glands, and ovaries. The sequencing data were compared and analyzed, and the transcripts with significant differences were identified and analyzed with bioinformatics. The study showed that the transcriptome sequencing data of the 24 samples contained a total of 1,176,496,146 valid reads and 176.47 gigabase data. Differential expression analyses identified 135, 56, and 331 genes in the hypothalami, pituitary glands, and ovaries of Xinjiang Yili geese with high and low egg production. Further annotation of these differentially expressed genes in the non-redundant protein sequence database (Nr) revealed that 98, 52, and 309 genes were annotated, respectively. Through the annotations of GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases, 30 candidate genes related to the egg production of Xinjiang Yili geese were preliminarily selected. The gap junction, focal adhesion, and ECM-receptor interaction signaling pathways were enriched with the hypothalamic, pituitary, and ovarian differentially expressed genes, and the calcium signaling pathway was enriched with the pituitary and ovarian differentially expressed genes. Thus, these pathways in the hypothalamic-pituitary-gonadal axis may play an important role in regulating egg production of Xinjiang Yili geese. The results provided the transcriptomic information of the hypothalamic-pituitary-gonadal axis of Xinjiang Yili geese and laid the theoretical basis for revealing the molecular mechanisms regulating the egg-laying traits of Xinjiang Yili geese.

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.

Genomic Approaches Identify Novel Gene Associations with Out of Season Lambing in Sheep

Sheep are seasonally polyestrous, traditionally breeding when the day length shortens in the autumn. The changing photoperiod stimulates reproductive hormones through a series of chemical pathways, ultimately leading to cyclicity. Some breeds of sheep, such as the Polypay and Dorset, have been selected for reduced seasonality and can lamb year-round. Despite this selection, there is still variation within these breeds in the ability to lamb out of season. The identification of out of season lambing quantitative trait loci has the potential to improve genetic progress using genomic selection schemes. Association studies, fixation index (FST), and runs of homozygosity (ROH) were evaluated to identify regions of the genome that influence the ability of ewes to lamb out of season. All analyses used genotypic data from the Illumina Ovine HD beadchip. Genome-wide associations were tested both across breeds in 257 ewes and within the Dorset and Polypay breeds. FST was measured across breeds and between UK and US Dorsets to assess population differences. ROH were estimated in ewes to identify homozygous regions contributing to out of season lambing. Significant associations after multiple testing correction were found through these approaches, leading to the identification of several candidate genes for further study. Genes involved with eye development, reproductive hormones, and neuronal changes were identified as the most promising for influencing the ewe’s ability to lamb year-round. These candidate genes could be advantageous for selection for improved year-round lamb production and provide better insight into the complex regulation of seasonal reproduction.

Genetic variations for egg quality of chickens at late laying period revealed by genome-wide association study

With the extension of the egg-laying cycle, the rapid decline in egg quality at late laying period has aroused great concern in the poultry industry. Herein, we performed a genome-wide association study (GWAS) to identify genomic variations associated with egg quality, employing chicken 600 K high-density SNP arrays in a population of 1078 hens at 72 and 80 weeks of age. The results indicated that a genomic region spanning from 8.95 to 9.31 Mb (~0.36 Mb) on GGA13 was significantly associated with the albumen height (AH) and the haugh unit (HU), and the two most significant SNPs accounted for 3.12 ~ 5.75% of the phenotypic variance. Two promising genes, MSX2 and DRD1, were mapped to the narrow significant region, which was involved in embryonic and ovary development and found to be related to egg production, respectively. Moreover, three interesting genes, RHOA, SDF4 and TNFRSF4, identified from three significant loci, were considered to be candidate genes for egg shell colour. Findings in our study could provide worthy theoretical basis and technological support to improve late-stage egg quality for breeders.

Whole-transcriptome analysis of atrophic ovaries in broody chickens reveals regulatory pathways associated with proliferation and apoptosis

Broodiness in laying hens results in atrophy of the ovary and consequently decreases productivity. However, the regulatory mechanisms that drive ovary development remain elusive. Thus, we collected atrophic ovaries (AO) from 380-day-old broody chickens (BC) and normal ovaries (NO) from even-aged egg-laying hens (EH) for RNA sequencing. We identified 3,480 protein-coding transcripts that were differentially expressed (DE), including 1,719 that were down-regulated and 1,761 that were up-regulated in AO. There were 959 lncRNA transcripts that were DE, including 56 that were down-regulated and 903 that were up-regulated. Among the116 miRNAs that were DE, 79 were down-regulated and 37 were up-regulated in AO. Numerous DE protein-coding transcripts and target genes for miRNAs/lncRNAs were significantly enriched in reproductive processes, cell proliferation, and apoptosis pathways. A miRNA-intersection gene-pathway network was constructed by considering target relationships and correlation of the expression levels between ovary development-related genes and miRNAs. We also constructed a competing endogenous RNA (ceRNA) network by integrating competing relationships between protein-coding genes and lncRNA transcripts, and identified several lncRNA transcripts predicted to regulate the CASP6, CYP1B1, GADD45, MMP2, and SMAS2 genes. In conclusion, we discovered protein-coding genes, miRNAs, and lncRNA transcripts that are candidate regulators of ovary development in broody chickens.

Molecular characterization, expression profile of the FSHRgene and its association with egg production traits in muscovy duck

Follicle-stimulating hormone (FSH) and its receptor play a key role in the follicular development and regulation of steroidogenesis in the ovary and spermatogenesis in the testis. The purpose of this study was to characterize themuscovy duck FSHR gene, identify SNPs and their association with egg production traits in muscovy ducks. Here, we cloned the complementary DNA (cDNA) sequence of FSHR, and examined the expression patterns of FSHR gene in adult female muscovy duck tissues. The cloned cDNA of the muscovy duck FSHR gene shared high similarity to those of pekin duck (Anas platyrhynchos) (95.7%) and chicken (93.2%). Three different muscovy duck FSHR transcripts were identified. Quantitative real-time PCR (RT-qPCR) results showed that the FSHR gene was expressed in all the 14 tested tissues, and the highest expression level was seen in the ovary. A total of 16 SNPs were identified, among which, four SNPs were located in the coding region of FSHR. The SNP C320T is significantly associated with egg production at 59 weeks of age (P < 0.05), whereas the SNP A227G is significantly associated with age at first egg stage (P < 0.05). These results suggest that the two SNPs (A227G and C320T) of FSHR gene are associated with egg production traits and could be potential markers that can be used for marker-assisted selection programmes to increase egg production in muscovy duck.

Genetic effects of the transcription factors-sal-like 1 and spalt-like transcription factor 3 on egg production-related traits in Chinese Dagu hens

Transcription factors (TFs) encoded by SALL1 and SALL3 genes play central roles in the regulation of ovarian development in hens. The present study aimed to examine polymorphisms of these two genes in Chinese Dagu chickens, and to identify the effects of TFs on the laying performance. Among the population, two novel single-nucleotide polymorphisms (SNPs) were identified by single-strand conformation polymorphism (SSCP) in the amplicons of the candidate genes. The effect of the SNP (729C > A) in exon 2 of SALL1 gene on egg production at 43, 57, and 66 weeks and EW at 30 and 43 weeks were the most significant in the 360 samples (P < 0.05). Moreover, for the SNP 1014T > A (in exon 2 of SALL3), the TT genotype was significantly correlated with higher egg production and EW (P < 0.05). Furthermore, four combined genotypes were reconstructed based on the two SNPs. The combined genotype TATT was correlated with the highest egg production at 43-66 weeks and with higher EW at 30, 43 weeks (P < 0.05). The polymorphisms of the two TFs studied are potential molecular genetic markers for chicken breeding, which might help in understanding the genetic structure of laying performance and improving these traits directly by marker-assisted selection (MAS).

Dopamine D2-like receptors (DRD2 and DRD4) in chickens: Tissue distribution, functional analysis, and their involvement in dopamine inhibition of pituitary prolactin expression

Dopamine (DA) D2-like (and D1-like) receptors are suggested to mediate the dopamine actions in the anterior pituitary and/or CNS of birds. However, the information regarding the structure, functionality, and expression of avian D2-like receptors have not been fully characterized. In this study, we cloned two D2-like receptors (cDRD2, cDRD4) from chicken brain using RACE PCR. The cloned cDRD4 is a 378-amino acid receptor, which shows 57% amino acid (a.a.) identity with mouse DRD4. As in mammals, two cDRD2 isoforms, cDRD2L (long isoform, 437 a.a.) and cDRD2S (short isoform, 408 a.a.), which differ in their third intracellular loop, were identified in chickens. Using cell-based luciferase reporter assays or Western blot, we demonstrated that cDRD4, cDRD2L and cDRD2S could be activated by dopamine and quinpirole (a D2-like receptor agonist) dose-dependently, and their activation inhibits cAMP signaling pathway and stimulates MAPK/ERK signaling cascade, indicating that they are functional receptors capable of mediating dopamine actions. Quantitative real-time PCR revealed that cDRD2 and cDRD4 are widely expressed in chicken tissues with abundant expression noted in anterior pituitary, and their expressions are likely controlled by their promoters near exon 1, as demonstrated by dual-luciferase reporter assays in DF-1 cells. In accordance with cDRD2/cDRD4 expression in the pituitary, DA or quinpirole could partially inhibit vasoactive intestinal peptide-induced prolactin expression in cultured chick pituitary cells. Together, our data proves the functionality of DRD2 and DRD4 in birds and aids to uncover the conserved roles of DA/D2-like receptor system in vertebrates, such as its action on the pituitary.

Transcriptome sequencing reveals genetic mechanisms underlying the transition between the laying and brooding phases and gene expression changes associated with divergent reproductive phenotypes in chickens

Transition from laying to incubation behavior in chicken is an interesting topic in reproductive biology. The decline of incubation behavior in chicken population has led to considerable phenotypic differences in reproductive traits between breeds. However, the exact genetic mechanism of the reproductive phase transition still largely unknown and little is known about the gene expression changes that contribute to the phenotypic differences. We performed mRNA sequencing to investigate the molecular mechanism underlying the transition from laying to brooding and to detect difference in gene regulation underlying the phenotypic diversification using two chicken breeds. The majority of gene expression changes during phase transition were steroidogenesis and hormone-releasing genes. Brooding chickens shared a conservative pattern of greatly inhibited steroidogenic enzyme genes in the pituitary gland, therefore, low levels of steroidogenic enzymes might result in reproductive defects such as ovary regression and brooding onset. The conserved network responsible for brooding behavior was maintained by steroid biosynthesis and hormonal interactions. Interestingly, three transcription factors, SREBF2, NR5A1 and PGR, act as central signal modulators of steroid biosynthesis and hormonal interactions during the transition from laying to brooding modes at the molecular level. Furthermore, Genes correlated with protein synthesis and accumulation showed expression variation between breeds, which might result in different concentrations of and sensitivities to reproduction-related hormones. This study provided a new insight in neuroendocrine system at the molecular level, and helps to understand the genetic and hormonal responses that ultimately translate into behavior in chicken.

Association of novel polymorphisms of forkhead box L2 and growth differentiation factor-9 genes with egg production traits in local Chinese Dagu hens

Transcription factor forkhead box L2 (FOXL2) and growth differentiation factor-9 (GDF9) genes have critical roles in the regulation of hen ovarian development. In the present study, these genes were explored as possible molecular markers associated with BW, hen-housed egg production, and egg weight in Chinese Dagu hens. Samples were analyzed using the PCR-single strand conformation polymorphism (PCR-SSCP) technique followed by sequencing analysis, and two novel single nucleotide polymorphisms (SNPs) were identified within these candidate genes. Among them, an A/G transition at base position 238 in the coding region of the FOXL2 gene and a G/T transversion at base position 1609 in exon 2 of the GDF9 gene were found to be polymorphic and named SNPs A238G and G1609T, respectively. The SNP A238G (FOXL2) leads to a nonsynonymous substitution (isoleucine77-to-valine), and when the 360 Dagu hen samples were divided into genotypes AA and AB, allele A was found to be present at a higher frequency. Furthermore, the AA genotype correlated with significantly higher hen-housed egg production at 30, 43, 57, and 66 wk of age and with a higher egg weight at 43 wk (P<0.05). For the SNP G1609T (GDF9), the hens were typed into TT and TC genotypes, with the T allele shown to be dominant. The TC genotype was also markedly correlated with higher hen-housed egg production and a higher egg weight (P<0.05). Moreover, four haplotypes were reconstructed based on these two SNPs, with the AATC haplotype found to be correlated with the highest hen-housed egg production at 30 to 66 wk of age and with higher egg weights at 43 wk (P<0.05). Collectively, the two SNPs identified in this study might be used as possible genetic molecular markers to aid in the improvement of egg production traits in chicken breeding.

The effect of perch access during pullet rearing and egg laying on physiological measures of stress in White Leghorns at 71 weeks of age

Egg laying strains of chickens have a strong motivation to perch. Providing caged chickens with perches allows them to perform their natural perching behavior and also improves their musculoskeletal health due to exercise. Little is known about the effect of perch access for hens on physiological measures of stress. Our hypothesis was that denying chickens access to perches would elicit a stress response. The objective of this study was to determine the effect of perch access during all or part of life cycle on physiological homeostasis in caged 71-wk-old White Leghorn hens. A total of 1,064 chicks were assigned randomly to cages with and without perches (n = 14 pullet cages/perch treatment) on day of hatch. As pullets aged, chicks were removed from cages to provide more space. At 17 wk of age, 324 chickens in total were assigned to laying cages consisting of 4 treatments with 9 replicates per treatment. Treatment 1 chickens never had access to perches during their life cycle. Treatment 2 chickens had access to perches only from 17 to 71 wk of age (laying phase). Treatment 3 chickens had access to perches only from hatch to 16.9 wk of age (pullet phase). Treatment 4 chickens always had access to perches during their life cycle. At 71 wk of age, chickens were sampled for measurement of plasma catecholamines (epinephrine, norepinephrine, and dopamine) and corticosterone; blood serotonin and Trp; fluctuating asymmetry of shank length and width; and adrenal weight. Only shank width differed among treatments. Chickens with previous exposure to perches during the pullet phase had wider shanks than chickens without access to perches (P = 0.006), suggesting that early perching promoted skeletal development. These results suggest that a stress response was not elicited in 71-wk-old White Leghorn hens that always had access to perches compared with hens that never had access to perches during all or part of their life cycle.

QTL analysis of behavior in nine-spined sticklebacks (Pungitius pungitius)

The genetic architecture of behavioral traits is yet relatively poorly understood in most non-model organisms. Using an F2-intercross (n = 283 offspring) between behaviorally divergent nine-spined stickleback (Pungitius pungitius) populations, we tested for and explored the genetic basis of different behavioral traits with the aid of quantitative trait locus (QTL) analyses based on 226 microsatellite markers. The behaviors were analyzed both separately (viz. feeding activity, risk-taking and exploration) and combined in order to map composite behavioral type. Two significant QTL-explaining on average 6 % of the phenotypic variance-were detected for composite behavioral type on the experiment-wide level, located on linkage groups 3 and 8. In addition, several suggestive QTL located on six other linkage groups were detected on the chromosome-wide level. Apart from providing evidence for the genetic basis of behavioral variation, the results provide a good starting point for finer-scale analyses of genetic factors influencing behavioral variation in the nine-spined stickleback.

Genetic effect of the prolactin receptor gene on egg production traits in chickens

The identification and utilization of potential candidate genes with significant effects on economically important traits have become increasingly important in poultry breeding programs. The prolactin (PRLR) receptor is a specific receptor for prolactin, which is an anterior pituitary peptide hormone involved in various physiological activities and is essential for reproductive success. In chickens, the PRLR gene resides on the Z chromosome. We used a pooled DNA sequencing approach for identifying SNPs of the PRLR gene. Three hundred and nine-six Erlang Mountainous chicken hens were genotyped for six SNPs using PCR-SSCP and PCR-sequencing methods; the association with chicken egg production traits was studied using general linear model procedures. Three linked SNPs (G14952A, A14969C and G14984A) at the P1 locus, two linked SNPs (G17560A and T17626A) at the P2 locus, and one SNP (T20868C) at the P3 locus were identified. Eight haplotypes were reconstructed on the basis of the six SNPs. The general linear model analysis indicated that there were significant associations of certain genotypes and haplotypes with some egg production traits. We conclude that chicken PRLR gene polymorphisms are associated with egg production traits and have potential as molecular markers for chicken breeding.

Molecular cloning, expression profile, polymorphism and the genetic effects of the dopamine D1 receptor gene on duck reproductive traits

The dopamine D1 receptor (DRD1), a member of the dopamine receptor (DR) gene family, participates in the regulation of reproductive behaviors in birds. In this study, a 1,390 bp fragment covering the complete coding region (CDS) of duck DRD1 gene was obtained. The cDNA (GenBank: JQ346726) contains a 1,353 bp CDS and a 37 bp 3'- UTR including a TGA termination codon (nucleotides 1,354-1,356 bp). The duck DRD1 shares about 76-96 % nucleic acid identity and 82-98 % amino acid identity with their counterparts in other species. A phylogenetic tree based on amino acid sequences displays that duck DRD1 protein is closely related with those of chicken and zebra finch. The quantitative real-time PCR analysis indicates that the DRD1 mRNA is widely expressed in all examined tissues. Five single nucleotide polymorphisms (SNPs) (c.189A > T, c.507C > T, c.681C > T, c.765A > T, c.1044A > G) in the CDS of duck DRD1 gene were indentified, c.681C > T and c.765A > T were genotyped and analyzed in a two generations duck population by using of PCR-RFLP. Association analysis demonstrated that the c.681C > T genotypes were significantly associated with body weight at sexual maturity (when laying their first egg) (P < 0.01), egg production within 360 days (P < 0.05) and 420 days (P < 0.01); the c.765A > T genotypes were significantly associated with egg shape index and egg shell strength (P < 0.05). Those results suggest that the DRD1 gene may be a potential genetic marker to improve some reproductive traits in ducks.

The GTPase activating Rap/RanGAP domain-like 1 gene is associated with chicken reproductive traits

Background

Abundant evidence indicates that chicken reproduction is strictly regulated by the hypothalamic-pituitary-gonad (HPG) axis, and the genes included in the HPG axis have been studied extensively. However, the question remains as to whether any other genes outside of the HPG system are involved in regulating chicken reproduction. The present study was aimed to identify, on a genome-wide level, novel genes associated with chicken reproductive traits.

Methodology/Principal Finding

Suppressive subtractive hybridization (SSH), genome-wide association study (GWAS), and gene-centric GWAS were used to identify novel genes underlying chicken reproduction. Single marker-trait association analysis with a large population and allelic frequency spectrum analysis were used to confirm the effects of candidate genes. Using two full-sib Ningdu Sanhuang (NDH) chickens, GARNL1 was identified as a candidate gene involved in chicken broodiness by SSH analysis. Its expression levels in the hypothalamus and pituitary were significantly higher in brooding chickens than in non-brooding chickens. GWAS analysis with a NDH two tail sample showed that 2802 SNPs were significantly associated with egg number at 300 d of age (EN300). Among the 2802 SNPs, 2 SNPs composed a block overlapping the GARNL1 gene. The gene-centric GWAS analysis with another two tail sample of NDH showed that GARNL1 was strongly associated with EN300 and age at first egg (AFE). Single marker-trait association analysis in 1301 female NDH chickens confirmed that variation in this gene was related to EN300 and AFE. The allelic frequency spectrum of the SNP rs15700989 among 5 different populations supported the above associations. Western blotting, RT-PCR, and qPCR were used to analyze alternative splicing of the GARNL1 gene. RT-PCR detected 5 transcripts and revealed that the transcript, which has a 141 bp insertion, was expressed in a tissue-specific manner.

Conclusions/Significance

Our findings demonstrate that the GARNL1 gene contributes to chicken reproductive traits.

Polymorphisms associated with egg number at 300 days of age in chickens

We looked for variations that could be associated with chicken egg number at 300 days of age (EN300) in seven genes of the hypothalamic-pituitary-gonadal axis, including gonadotrophin-releasing hormone-I (GnRH-I), GnRH receptor (GnRHR), neuropeptide Y (NPY), dopamine D2 receptor (DRD2), vasoactive intestinal polypeptide (VIP), VIP receptor-1 (VIPR-1), prolactin (PRL), and the QTL region between 87 and 105 cM of the Z chromosome. Ten mutations in the seven genes were chosen to do marker-trait association analyses in a population comprising 1310 chickens, which were obtained from a company located in Guangdong Province of China. The C1704887T of VIPR-1 was found to have a highly significant association with EN300. The T5841629C of DRD2 and the C1715301T of VIPR-1 were significantly associated with EN300. A highly significant association was also found between the C1704887T-C1715301T haplotypes of VIPR-1 and EN300. H1H3 had the highest EN300. Four PCR-RFLP variations in the candidate QTL region were selected to investigate their genetic effects on EN300. The haplotypes of T32742468C-G32742603A in this region showed a highly significant association with EN300. Bioinformatics analyses showed that both T32742468C and G32742603A were located in intron 1 of the SH3-domain GRB2-like 2 (SH3GL2) gene. We conclude that five SNPs, including C1704887T and C1715301T of VIPR-1, T5841629C of DRD2, and T32742468C and G32742603A of SH3GL2, would be useful as markers for breeding to increase chicken EN300.

Genetic effects of polymorphisms in candidate genes and the QTL region on chicken age at first egg

Background

The age at first egg (AFE), an important indicator for sexual maturation in female chickens, is controlled by polygenes. Based on our knowledge of reproductive physiology, 6 genes including gonadotrophin releasing hormone-I (GnRH-I), neuropeptide Y (NPY), dopamine D2 receptor (DRD2), vasoactive intestinal polypeptide (VIP), VIP receptor-1 (VIPR-1), and prolactin (PRL), were selected as candidates for influencing AFE. Additionally, the region between ADL0201 and MCW0241 of chromosome Z was chosen as the candidate QTL region according to some QTL databases. The objective of the present study was to investigate the effects of mutations in candidate genes and the QTL region on chicken AFE.

Results

Marker-trait association analysis of 8 mutations in those 6 genes in a Chinese native population found a highly significant association (P < 0.01) between G840327C of the GnRH-I gene with AFE, and it remained significant even with Bonferroni correction. Based on the results of the 2-tailed χ² test, mutations T32742394C, T32742468C, G32742603A, and C33379782T in the candidate QTL region of chromosome Z were selected for marker-trait association analysis. The haplotypes of T32742394C and T32742468C were significantly associated (P < 0.05) with AFE. Bioinformatics analysis indicated that T32742394C and T32742468C were located in the intron region of the SH3-domain GRB2-like 2 (SH3GL2) gene, which appeared to be associated in the endocytosis and development of the oocyte.

Conclusion

This study found that G840327C of the GnRH-I gene and the haplotypes of T32742394C-T32742468C of the SH3GL2 gene were associated with the chicken AFE.