Pituitary whole transcriptome analysis reveals key genes regulating reproduction in Hy-Line Brown hens and the construction of their ceRNA molecular regulatory network

BACKGROUND

The development and egg-laying performance of hens are precisely regulated by hormones secreted by the pituitary. In this study, we performed comprehensive transcriptome sequencing of pituitary from Hy-Line Brown hens at 15, 20, 30 and 68 W of age. Through association analysis, we identified key genes and ceRNA regulatory networks related to pituitary development and egg production.

RESULTS

Based on the comprehensive transcriptome data, we identified 470 differentially expressed lncRNAs (DE-lncRNAs), 38 differentially expressed miRNAs (DE-miRNAs), and 2,449 differentially expressed mRNAs (DE-mRNAs). Time-series analysis pinpointed genes and signaling pathways that significantly influence pituitary hormone secretion at various stages. At 15 W, the high expression of GHRHR, NPY1R, and TSHR in the pituitary supports growth. At 20 and 30 W, elevated GNRHR expression sustains continuous egg production. In the late laying period, the expression of PRL may lead to a decline in egg production. Additionally, association analysis enabled the construction of a ceRNA regulatory network involving non-coding RNAs that regulate the development and reproduction of hens.

CONCLUSION

This study elucidated the comprehensive transcriptome expression profiles of the pituitary gland during the development and egg-laying processes in Hy-Line Brown hens and constructed the associated molecular regulatory networks. These findings lay the foundation for investigating the mechanisms by which non-coding RNAs regulate pituitary hormone secretion.

Effects of ferritin heavy chain on oxidative stress, cell proliferation and apoptosis in geese follicular granulosa cells

1. The ferritin heavy chain (FHC) has a vital impact on follicular development in geese, due to its ability to regulate apoptosis of granulosa cells (GCs) and follicular atresia. However, its specific regulatory mechanisms remain unclear. The present study characterised how FHC regulates oxidative stress, cell proliferation and apoptosis in goose GCs by interfering with and overexpressing the FHC gene.2. After 72 h of interference with FHC expression, the activity of GCs decreased remarkably (p < 0.05), reactive oxygen species (ROS) levels and the expression levels of antioxidant enzyme genes catalase (CAT), superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) increased significantly (p < 0.05). The overexpression of FHC for 72 h was found to significantly reduce the expression of CAT and SOD genes (p < 0.05).3. Interfering with FHC expression revealed that the expression levels of the cell proliferation gene Aurora kinase A (AURORA-A) were significantly decreased (p < 0.05), while the expression levels of the apoptosis genes B-cell lymphoma-2 (BCL-2) and cysteine aspartate-specific protease 8 (CASPASE 8) increased (p < 0.05). Further research has shown that, when interfering with FHC expression for 72 h, apoptosis rate increased by 1.19-fold (p < 0.05), but the current data showed a lower apoptosis rate after FHC overexpression by 59.41%, 63.39%, and 52.31% at three different treatment times (p < 0.05).4. In conclusion, FHC improved the antioxidant capacity of GCs, promotes GCs proliferation, and inhibits GCs apoptosis of ovarian follicles in Sichuan white geese.

Integration of Whole-Genome Resequencing and Transcriptome Sequencing Reveals Candidate Genes in High Glossiness of Eggshell

Eggshell gloss is an important characteristic for the manifestation of eggshell appearance. However, no study has yet identified potential candidate genes for eggshell gloss between high-gloss (HG) and low-gloss (LG) chickens. The aim of this study was to perform a preliminary investigation into the formation mechanism of eggshell gloss and to identify potential genes. The eggshell gloss of 300-day-old Rhode Island Red hens was measured from three aspects. Uterine tissues of the selected HG and LG (n = 5) hens were collected for RNA-seq. Blood samples were also collected for whole-genome resequencing (WGRS). RNA-seq analysis showed that 150 differentially expressed genes (DEGs) were identified in the uterine tissues of HG and LG hens. These DEGs were mainly enriched in the calcium signaling pathway and the neuroactive ligand-receptor interaction pathway. Importantly, these two pathways were also significantly enriched in the WGRS analysis results. Further joint analysis of WGRS and RNA-seq data revealed that 5-hydroxytryptamine receptor 1F (HTR1F), zinc finger protein 536 (ZNF536), NEDD8 ubiquitin-like modifier (NEDD8), nerve growth factor (NGF) and calmodulin 1 (CALM1) are potential candidate genes for eggshell gloss. In summary, our research provides a reference for the study of eggshell gloss and lays a foundation for improving egg glossiness in layer breeding.

Integrating genomics and transcriptomics to identify candidate genes for high egg production in Wulong geese (Anser cygnoides orientalis)

BACKGROUND

Wulong geese (Anser cygnoides orientalis) are known for their excellent egg-laying performance. However, they show considerable population differences in egg-laying behavior. This study combined genome-wide selection signal analysis with transcriptome analysis (RNA-seq) to identify the genes related to high egg production in Wulong geese.

RESULTS

A total of 132 selected genomic regions were screened using genome-wide selection signal analysis, and 130 genes related to high egg production were annotated in these regions. These selected genes were enriched in pathways related to egg production, including oocyte meiosis, the estrogen signaling pathway, the oxytocin signaling pathway, and progesterone-mediated oocyte maturation. Furthermore, a total of 890 differentially expressed genes (DEGs), including 340 up-regulated and 550 down-regulated genes, were identified by RNA-seq. Two genes - GCG and FAP - were common to the list of selected genes and DEGs. A non-synonymous single nucleotide polymorphism was identified in an exon of FAP.

CONCLUSIONS

Based on genome-wide selection signal analysis and transcriptome data, GCG and FAP were identified as candidate genes associated with high egg production in Wulong geese. These findings could promote the breeding of Wulong geese with high egg production abilities and provide a theoretical basis for exploring the mechanisms of reproductive regulation in poultry.

Ferritin heavy chain participated in ameliorating 3-nitropropionic acid-induced oxidative stress and apoptosis of goose follicular granulosa cells

Oxidative stress is the major culprits responsible for ovarian dysfunction by damaging granulosa cells (GCs). Ferritin heavy chain (FHC) may participate in the regulation of ovarian function by mediating GCs apoptosis. However, the specific regulatory function of FHC in follicular GCs remains unclear. Here, 3-nitropropionic acid (3-NPA) was utilized to establish an oxidative stress model of follicular GCs of Sichuan white geese. To explore the regulatory effects of FHC on oxidative stress and apoptosis of primary GCs in geese by interfering or overexpressing FHC gene. After transfection of siRNA-FHC to GCs for 60 h, the expressions of FHC gene and protein decreased significantly (P < 0.05). After FHC overexpression for 72 h, the expressions of FHC mRNA and protein upregulated considerably (P < 0.05). The activity of GCs was impaired after interfering with FHC and 3-NPA coincubated (P < 0.05). When overexpression of FHC combined with 3-NPA treatment, the activity of GCs was remarkably enhanced (P < 0.05). After interference FHC and 3-NPA treatment, NF-κB and NRF2 gene expression decreased (P < 0.05), the intracellular reactive oxygen species (ROS) level increased greatly (P < 0.05), BCL-2 expression reduced, BAX/BCL-2 ratio intensified (P < 0.05), the mitochondrial membrane potential decreased notably (P < 0.05), and the apoptosis rate of GCs aggravated (P < 0.05). While overexpression of FHC combined with 3-NPA treatment could promote BCL-2 protein expression and reduce BAX/BCL-2 ratio, indicating that FHC regulated the mitochondrial membrane potential and apoptosis of GCs by mediating the expression of BCL-2. Taken together, our research manifested that FHC alleviated the inhibitory effect of 3-NPA on the activity of GCs. FHC knockdown could suppress the expression of NRF2 and NF-κB genes, reduce BCL-2 expression and augment BAX/BCL-2 ratio, contributing to the accumulation of ROS and jeopardizing mitochondrial membrane potential, as well as exacerbating GCs apoptosis.

Integrative analyses of the mRNA expression profile reveal the involvement of STC1 in chicken folliculogenesis

Efficient ovarian follicle development, maturation, and ovulation are critical for egg production performance. Previous research has underscored the importance of messenger RNAs (mRNAs) in regulating development and folliculogenesis in chicken ovarians. However, the molecular mechanism is not fully understood, especially in the late period of the laying cycle. In the present study, ovarian tissues from 80-week-old Hy-Line Brown layers (three with high and three with low rates of egg laying) were collected for transcriptome sequencing. A total of 306 differentially expressed genes (DEGs) were identified in this study, at a false discovery rate (FDR)-corrected P-value < 0.05 and a log2|fold change| (log2|FC|) ≥1.5. Among these DEGs, stanniocalcin 1 (STC1) was mainly related to cellular processes, single-organism processes, biological regulation, metabolic processes, developmental processes, and reproductive processes. Then, we further investigated the regulation of STC1 during chicken follicle development and found that STC1 inhibited the proliferation and stimulated the apoptosis of follicular granulosa cells (GCs), and decreased the expression of progesterone (P4) and estradiol (E2). Collectively, these results suggest that STC1 plays an important role in chicken follicle development by decreasing GC proliferation and steroidogenesis and stimulating GC apoptosis. This study contributes to the understanding of the reproductive biology of laying hens in the late period of the laying cycle and further lays a foundation for the improvement of egg production in poultry breeding.

Embryonic transcriptome unravels mechanisms and pathways underlying embryonic development with respect to muscle growth, egg production, and plumage formation in native and broiler chickens

Background: Muscle development, egg production, and plumage colors are different between native and broiler chickens. The study was designed to investigate why improved Aseel (PD4) is colorful, stronger, and grew slowly compared with the control broiler (CB).

Methods: A microarray was conducted using the 7th-day embryo (7EB) and 18th-day thigh muscle (18TM) of improved Aseel and broiler, respectively. Also, we have selected 24 Gallus gallus candidate reference genes from NCBI, and total RNA was isolated from the broiler, improved Aseel embryo tissues, and their expression profiles were studied by real-time quantitative PCR (qPCR). Furthermore, microarray data were validated with qPCR using improved Aseel and broiler embryo tissues.

Results: In the differential transcripts screening, all the transcripts obtained by microarray of slow and fast growth groups were screened by fold change ≥ 1 and false discovery rate (FDR) ≤ 0.05. In total, 8,069 transcripts were differentially expressed between the 7EB and 18TM of PD4 compared to the CB. A further analysis showed that a high number of transcripts are differentially regulated in the 7EB of PD4 (6,896) and fewer transcripts are differentially regulated (1,173) in the 18TM of PD4 compared to the CB. On the 7th^- and 18th-day PD4 embryos, 3,890, 3,006, 745, and 428 transcripts were up- and downregulated, respectively. The commonly up- and downregulated transcripts are 91 and 44 between the 7th- and 18th-day of embryos. In addition, the best housekeeping gene was identified. Furthermore, we validated the differentially expressed genes (DEGs) related to muscle growth, myostatin signaling and development, and fatty acid metabolism genes in PD4 and CB embryo tissues by qPCR, and the results correlated with microarray expression data.

Conclusion: Our study identified DEGs that regulate the myostatin signaling and differentiation pathway; glycolysis and gluconeogenesis; fatty acid metabolism; Jak-STAT, mTOR, and TGF-β signaling pathways; tryptophan metabolism; and PI3K-Akt signaling pathways in PD4. The results revealed that the gene expression architecture is present in the improved Aseel exhibiting embryo growth that will help improve muscle development, differentiation, egg production, protein synthesis, and plumage formation in PD4 native chickens. Our findings may be used as a model for improving the growth in Aseel as well as optimizing the growth in the broiler.

Associations of CALM1 and DRD1 polymorphisms, and their expression levels, with Taihang chicken egg-production traits

Egg production by hens is an important reproductive performance index in the poultry industry. To investigate the effects of the CALM1 and DRD1 genes on egg production in chicken, their mRNA expression and single nucleotide polymorphisms (SNP) levels were investigated, and bioinformatics and egg-production association analyses were performed. Three SNPs (g.44069941G > A and g.44069889A > G in CALM1 and g.10742639C > T in DRD1) were detected in the exons and introns of CALM1 and DRD1 in 400 Taihang chickens. Among them, g.44069941G > A was significantly associated with Taihang chicken egg production on the 500th day (p < 0.05), whereas g.10742639C > T was significantly associated with the 300th day (p < 0.05). The expression levels of CALM1 and DRD1 in ovarian tissues of a high-yielding Taihang group were greater than in a low-yielding group (p < 0.05). The bioinformatics analysis revealed that the mutations influenced the mRNA secondary structures of CALM1 and DRD1. This study provides new insights into the potential effects of CALM1 and DRD1 polymorphisms on chicken egg production. The two SNPs g.44069941G > A and g.10742639C > T are potential molecular markers for improving the reproductive traits of Taihang chicken.

Ovarian transcriptome profile from pre-laying period to broody period of Xupu goose

Xupu goose, a breed from Hunan province, produces high quality and quantity of meat and liver. However, its egg production rate is low, with poor reproductive traits but strong broody performance. These characteristics decrease the economic value of Xupu goose significantly. Here, RNA-seq was used to analyze the transcriptome changes of ovaries of Xupu goose at different stages to explore the molecular mechanism of reproduction from the pre-laying period to the broody period. A total of 258 genes were differentially expressed in the 3 stages. These genes are associated with inflammation, reproduction, mutual recognition and adhesion between cells, and cytoskeleton formation, and so on. In particular, we report, for the first time, the expression patterns of MRP126, serglycin, TXNIP, and FZD2 during the pre-laying, egg-laying, and broody periods of goose ovaries. Functional analysis by GO annotation revealed that GO terms were mainly involved in actin, cell signal transduction and regulation, and cellular components. Three pathways, including focal adhesion (gga04510), ECM-receptor interaction (gga04512), and N-Glycan biosynthesis (gga00510), were significantly enriched in the three groups. These findings provide a basis for further exploration of profiles of goose ovaries to improve egg production of Xupu goose.

Transcriptome analysis of ovary tissues from low- and high-yielding Changshun green-shell laying hens

Background

Changshun green-shell laying hens are unique to Guizhou Province, China, and have high egg quality. Improving egg production performance has become an important breeding task, and in recent years, the development of high-throughput sequencing technology provides a fast and exact method for genetic selection. Therefore, we aimed to use this technology to analyze the differences between the ovarian mRNA transcriptome of low and high-yield Changshun green-shell layer hens, identify critical pathways and candidate genes involved in controlling the egg production rate, and provide basic data for layer breeding.

Results

The egg production rates of the low egg production group (LP) and the high egg production group (HP) were 68.00 ± 5.56 % and 93.67 ± 7.09 %, with significant differences between the groups (p < 0.01). Moreover, the egg weight, shell thickness, strength and layer weight of the LP were significantly greater than those of the HP (p < 0.05). More than 41 million clean reads per sample were obtained, and more than 90 % of the clean reads were mapped to the Gallus gallus genome. Further analysis identified 142 differentially expressed genes (DEGs), and among them, 55 were upregulated and 87 were downregulated in the ovaries. KEGG pathway enrichment analysis identified 9 significantly enriched pathways, with the neuroactive ligand-receptor interaction pathway being the most enriched. GO enrichment analysis indicated that the GO term transmembrane receptor protein tyrosine kinase activity, and the DEGs identified in this GO term, including PRLR, NRP1, IL15, BANK1, NTRK1, CCK, and HGF may be associated with crucial roles in the regulation of egg production.

Conclusions

The above-mentioned DEGs may be relevant for the molecular breeding of Changshun green-shell laying hens. Moreover, enrichment analysis indicated that the neuroactive ligand-receptor interaction pathway and receptor protein tyrosine kinases may play crucial roles in the regulation of ovarian function and egg production.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07688-x.

Transcriptome Analysis of Ovarian Follicles Reveals Potential Pivotal Genes Associated With Increased and Decreased Rates of Chicken Egg Production

Egg production is an important economic trait in the commercial poultry industry. Ovarian follicle development plays a pivotal role in regulation of laying hen performance and reproductive physiology. However, the key genes and signaling pathways involved in the various-stages of laying hen follicular development remain poorly understood. In this study, transcriptomes of ovarian follicles at three developmental stages, the large white follicle (LWF), small yellow follicle (SYF), and large yellow follicle (LYF), were comparatively analyzed in hens with high (HR) and low (LR) egg-laying rates by RNA-sequencing. Eighteen cDNA libraries were constructed and a total of 236, 544, and 386 unigenes were significantly differentially expressed in the LWF, SYF, and LYF follicles of HR and LR hens, respectively. Among them, 47 co-transcribed differentially expressed genes (DEGs) in LWF and SYF, 68 co-expressed DEGs in SYF and LYF, and 54 co-expressed DEGs in LWF and LYF were mined. Thirteen co-expressed DEGs were found in LWF, SYF, and LYF follicles. Eighteen candidate genes, including P2RX1, CAB39L, BLK, CSMD3, GPR65, ADRB2, CSMD1, PLPP4, ATF3, PRLL, STMN3, RORB, PIK3R1, PERP1, ACSBG1, MRTO4, CDKN1A, and EDA2R were identified to be potentially related to egg production. Furthermore, Kyoto Encyclopedia of Genes and Genomes analysis indicated neuroactive ligand-receptor interaction, cell adhesion molecules, peroxisome proliferator-activated receptor pathway, and cAMP signaling pathway might elicit an important role in formation of egg-laying traits by influencing ovarian follicle development. This study represents the first transcriptome analysis of various-sized follicles between HR and LR hens. These results provide useful molecular evidence for elucidating the genetic mechanism underlying ovarian follicle development associated with egg production in chicken.

Expression and analysis of ESR1, IGF-1, FSH, VLDLR, LRP, LH, PRLR genes in Pekin duck and Black Muscovy duck

In order to explore the influence of egg-laying regulatory genes on egg production in ducks at different laying stages, Pekin duck and Black Muscovy duck were used in this study, including early laying stage (20-30 weeks old), peak laying period (31-48 weeks old) and late laying stage (49-66 weeks old). Relative quantitative RT-PCR was used to detect the mRNA transcription level of selected egg-laying regulatory genes in the ovary tissues of ducks at different laying stages. Study shows: during the laying period of Pekin duck, ESR1, LRP1, IGF-1 and LHR were involved in the regulation of egg-laying, and the high expression of LRP1 in the late stage could inhibit egg production. Still, the expression products of the other three genes showed promoting effect. During the laying period of Black Muscovy duck, FSH, VLDLR, IGF-1, PRLR, LHR and LRP1 participated in the regulation of egg-laying, in which the expression products of the first five genes could promote egg production, while LRP1 showed inhibitory effect. Through our experiments, these data will provide strong theoretical support for the breeding of Pekin duck and Black Muscovy duck.

The Attenuating Effect of the Intraovarian Bone Morphogenetic Protein 4 on Age-Related Endoplasmic Reticulum Stress in Chicken Follicular Cells

In the poultry, only less than 5% primordial follicles in the ovary can develop into the prehierarchical follicles (PHFs) leading to progressive development, ovulation, and egg formation. This low rate of recruitment indicates a huge potential for improvement of the laying performance. A great reduction in egg production is caused by aging with extensive follicular atresia. In this study, age-related changes in the laying performance and ovarian status were compared between the peak-lay (D280) and aged (D580) chickens. Subsequently, a cross coculture of PHFs and granulosa cells (GCs) from D280 or D580 hens was adopted to reveal the mechanism of declined follicle development. Results showed that persistent endoplasmic reticulum (ER) stress in GCs of the aged hens was accompanied with intensified apoptosis. Bone morphogenetic protein 4 (BMP4) secreted by GCs of PHFs in D280 hens was capable of relieving ER stress and improving follicular dominance for selection in D580 hens. During this action, BMP4 reduced free calreticulin (CALR, an ER marker) content and attenuated cell apoptosis in PHFs of D580 hens via the PERK-CHOP-BCL2/caspase3 or CALR-Ca²⁺-BCL2-caspase12 pathway. Furthermore, BMP4 prevented follicular atresia by promoting production of steroid hormones to improve survival of GCs in PHFs from the aged hens. In conclusion, intensified ER stress and apoptosis occurred in GCs of PHFs in aged chickens, while BMP4 secreted by GCs was capable of improving follicular viability by alleviating ER stress to promote follicular development.

Transcriptome analysis reveals differentially expressed genes associated with high rates of egg production in chicken hypothalamic-pituitary-ovarian axis

The hypothalamic-pituitary-ovarian (HPO) axis regulates the breeding process cycle of laying hens. However, the key regulatory genes of the HPO axis and pathways that drive chicken egg laying performance remain elusive. A total of 856 Chinese Luhua chicken was raised and the highest two hundred and the lowest two hundred chicken egg production were considered as high egg production (HEP) and low egg production (LEP) according to the total egg number at 300 days of age, respectively. RNA-seq sequencing (RNA-Seq) was conducted to explore the chicken transcriptome from the hypothalamus, pituitary gland and ovary tissue of 6 Chinese Luhua chicken with 3 high and low-rate egg production. In total, 76.09 Gb RNA-seq sequences were generated from 15 libraries with an average of 5.07 Gb for each library. Further analysis showed that 414, 356 and 10 differentially expressed genes (DEGs) were identified in pituitary gland, ovary and hypothalamus between HEP and LEP chickens, respectively. In pituitary gland, DEGs were involve in regulation of cellular glucose homeostasis, Ras protein signal transduction, negative regulation of hormone secretion. In Ovary DEGs were mainly involved in embryonic organ development, regulation of canonical Wnt signaling, response to peptide hormone. Our study identified DEGs that regulate mTOR signaling pathway, Jak-STAT signaling pathway, Tryptophan metabolism and PI3K-Akt signaling pathways at HPO-axis in laying hens. These important data contribute to improve our understanding of reproductive biology of chicken and isolating effective molecular markers that can be used for genetic selection in Chinese domestic Luhua chicken.

Effects of α-enolase Gene Silencing on Reproductive-related Hormone Receptor Expression and Steroid Hormone Synthesis of Primary Granulosa Cells from Goose F1 Follicles

Introduction

Enolases are enzymes in the glycolytic pathway, which catalyse the reversible conversion of D-2-phosphoglycerate into phosphoenol pyruvate in the second half of the pathway. In this research, the effects of α-enolase (ENO1) on steroid reproductive-related hormone receptor expression and on hormone synthesis of primary granulosa cells from goose F1 follicles were studied.

Material and Methods

Primary granulosa cells from the F1 follicles of eight healthy 8-month-old Zi geese were separated and cultured. An ENO1 interference expression vector was designed, constructed and transfected into primary cultured granulosa cells. The mRNA expression levels of follicle-stimulating hormone receptor (FSHR), luteinising hormone receptor (LHR), oestrogen receptor α (ER α), oestrogen receptor β (ER β), growth hormone receptor (GHR) and insulin-like growth factor binding protein-1 (IGFBP-1) in the cells were evaluated as were the secretion levels of oestradiol, activin, progesterone, testosterone, inhibin and follistatin in cell supernatant.

Results

α-enolase gene silencing reduced the expression of FSHR, LHR, ERα, ERβ, GHR, and IGFBP-1 mRNA, potentiated the secretion of oestrogen, progesterone, testosterone, and follistatin of granulosa cells, and hampered the production of activin and inhibin.

Conclusion

ENO1 can regulate the reactivity of granulosa cells to reproductive hormones and regulate cell growth and development by adjusting their hormone secretion and reproductive hormone receptor expression. The study provided a better understanding of the functional action of ENO1 in the processes of goose ovary development and egg laying.

A Functional Mutation in KIAA1462 Promoter Decreases Glucocorticoid Receptor Affinity and Affects Egg-Laying Performance in Yangzhou Geese

The identification of genetic markers is valuable for improving the egg-laying performance in goose production. The single-nucleotide polymorphism (SNP) rs1714766362 in an intron of the goose KIAA1462 gene was found to be relevant to laying performance in our previous study. However, its function remains unclear. In this study, the full-length coding sequence of KIAA1462 gene was firstly characterized in Yangzhou geese. Q-PCR (Quantitative Real Time Polymerase Chain Reaction) results showed that KIAA1462 was highly expressed in the liver, ovary, and mature F1 follicles. For SNP rs1714766362, geese with the AA genotype showed better laying performance than the TT ones and exhibited a higher KIAA1462 expression level in the ovary. Gain- and loss-of function experiments in granulosa cells revealed that KIAA1462 affected the expression of the apoptosis marker gene caspase-3. Considering that rs1714766362 locates in an intron area, we compared the KIAA1462 promoter regions of AA and TT individuals and identified the SNP c.-413C>G (Genbank ss2137504176), which was completely linked to SNP rs1714766362. According to the transcription factor prediction results, the glucocorticoid receptor (GR) would bind to the SNP site containing the C but not the G allele. In this study, we proved this hypothesis by an electrophoretic mobility shift assay (EMSA). In summary, we identified a novel mutation in the promoter of KIAA1462 gene which can modulate GR binding affinity and affect the laying performance of geese.

Comparative proteomic analysis of pituitary glands from Huoyan geese between pre-laying and laying periods using an iTRAQ-based approach

In this study, we performed a comprehensive evaluation of the proteomic profile of the pituitary gland of the Huoyan goose during the laying period compared to the pre-laying period using an iTRAQ-based approach. Protein samples were prepared from pituitary gland tissues of nine pre-laying period and nine laying period geese. Then the protein samples from three randomly selected geese within each period were pooled in equal amounts to generate one biological sample pool. We identified 684 differentially expressed proteins, including 418 up-regulated and 266 down-regulated proteins. GO annotation and KEGG pathway analyses of these proteins were conducted. Some of these proteins were found to be associated with hormone and neurotransmitter secretion and transport, neuropeptide signalling and GnRH signalling pathways, among others. Subsequently, the modification of the abundance of three proteins (prolactin, chromogranin-A and ITPR3) was verified using western blotting. Our results will provide a new source for mining genes and gene products related to the egg-laying performance of Huoyan geese, and may provide important information for the conservation and utilization of local goose breeds.

OAZ1 knockdown enhances viability and inhibits ER and LHR transcriptions of granulosa cells in geese

An increasing number of studies suggest that ornithine decarboxylase antizyme 1 (OAZ1), which is regarded as a tumor suppressor gene, regulates follicular development, ovulation, and steroidogenesis. The granulosa cells in the ovary play a critical role in these ovarian functions. However, the action of OAZ1 mediating physiological functions of granulosa cells is obscure. OAZ1 knockdown in granulosa cells of geese was carried out in the current study. The effect of OAZ1 knockdown on polyamine metabolism, cell proliferation, apoptosis, and hormone receptor transcription of primary granulosa cells in geese was measured. The viability of granulosa cells transfected with the shRNA OAZ1 at 48 h was significantly higher than the control (p<0.05). The level of putrescine and spermidine in granulosa cells down-regulating OAZ1 was 7.04- and 2.11- fold higher compared with the control, respectively (p<0.05). The CCND1, SMAD1, and BCL-2 mRNA expression levels in granulosa cells down-regulating OAZ1 were each significantly higher than the control, respectively (p<0.05), whereas the PCNA and CASPASE 3 expression levels were significantly lower than the control (p<0.05). The estradiol concentration, ER and LHR mRNA expression levels were significantly lower in granulosa cells down-regulating OAZ1 compared with the control (p<0.05). Taken together, our results indicated that OAZ1 knockdown elevated the putrescine and spermidine contents and enhanced granulosa cell viability and inhibited ER and LHR transcriptions of granulosa cells in geese.

Ovarian transcriptomic analysis of Shan Ma ducks at peak and late stages of egg production

Objective

To assess the differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production, and to obtain new transcriptomic data of these egg-producing ducks.

Methods

The Illumina HiSeq 2000 system was used for high throughput sequencing of ovarian transcriptomes from Shan Ma ducks at their peak or late stages of egg production.

Results

Greater than 93% of the sequencing data had a base quality score (Q score) that was not less than 20 (Q20). From ducks at their peak stage of egg production, 42,782,676 reads were obtained, with 4,307,499,083 bp sequenced. From ducks at their late stage of egg production, 45,316,166 reads were obtained, with 4,562,063,363 bp sequenced. A comparison of the two datasets identified 2,002 differentially expressed genes, with 790 upregulated and 1,212 downregulated. Further analysis showed that 1,645 of the 2,002 differentially expressed genes were annotated in the non-redundant (NR) database, with 646 upregulated and 999 downregulated. Among the differentially expressed genes with annotations in the NR database, 696 genes were functionally annotated in the clusters of orthologous groups of proteins database, involving 25 functional categories. One thousand two hundred four of the differentially expressed genes with annotations in the NR database were functionally annotated in the gene ontology (GO) database, and could be divided into three domains and 56 categories. The three domains were cellular component, molecular function, and biological process. Among the genes identified in the GO database, 451 are involved in development and reproduction. Analysis of the differentially expressed genes with annotations in the NR database against the Kyoto encyclopedia of genes and genomes database revealed that 446 of the genes could be assigned to 175 metabolic pathways, of which the peroxisome proliferator-activated receptor signaling pathway, insulin signaling pathway, fructose and mannose metabolic pathways, gonadotropin releasing hormone signaling pathway and transforming growth factor beta signaling pathway were significantly enriched.

Conclusion

The differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production were elucidated, which greatly enriched the ovarian transcriptomic information of egg-producing ducks.

Expressed microRNA associated with high rate of egg production in chicken ovarian follicles

MicroRNA (miRNA) is a highly conserved class of small noncoding RNA about 19-24 nucleotides in length that function in a specific manner to post-transcriptionally regulate gene expression in organisms. Tissue miRNA expression studies have discovered a myriad of functions for miRNAs in various aspects, but a role for miRNAs in chicken ovarian tissue at 300 days of age has not hitherto been reported. In this study, we performed the first miRNA analysis of ovarian tissues in chickens with low and high rates of egg production using high-throughput sequencing. By comparing low rate of egg production chickens with high rate of egg production chickens, 17 significantly differentially expressed miRNAs were found (P < 0.05), including 11 known and six novel miRNAs. We found that all 11 known miRNAs were involved mainly in pathways of reproduction regulation, such as steroid hormone biosynthesis and dopaminergic synapse. Additionally, expression profiling of six randomly selected differentially regulated miRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR). Some miRNAs, such as gga-miR-34b, gga-miR-34c and gga-miR-216b, were reported to regulate processes such as proliferation, cell cycle, apoptosis and metastasis and were expressed differentially in ovaries of chickens with high rates of egg production, suggesting that these miRNAs have an important role in ovary development and reproductive management of chicken. Furthermore, we uncovered that a significantly up-regulated miRNA-gga-miR-200a-3p-is ubiquitous in reproduction-regulation-related pathways. This miRNA may play a special central role in the reproductive management of chicken, and needs to be further studied for confirmation.

SNP analysis reveals estrogen receptor 1 (<i>ESR1</i>) gene variants associated with laying traits in quails

Abstract. In this study, the estrogen receptor 1 (ESR1) gene was studied as a candidate gene for laying traits of two quail populations (the yellow-feather quail and chestnut-feather quail). Five pairs of primers were designed to detect single-nucleotide polymorphisms (SNPs) of exon 1, 2, 4, 8 and intron 1 of the ESR1 gene by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) and sequencing methods. Only the products amplified from exon 8 displayed polymorphism. The results showed one novel variation: a variation in exon 8 of ESR1 gene (g.91C > T, KC977991 and KC977992). It was associated with some laying traits in two quail populations including egg weight, the age of first egg and egg number at 20 weeks. And the CC genotype was associated with superior egg number at 20 weeks. Therefore, we speculated that the variation in exon 8 of ESR1 gene may have an effect on laying traits in the abovementioned quail populations.

Evidence for a role of ferritin heavy chain in mediating reproductive processes of geese

Ferritin heavy chain (FHC), which exhibits ferroxidase activity and mediates the primary functions of ferritin, plays a role in regulating reproduction in animals. However, the changes in the FHC mRNA and protein levels in the HPG axis of geese remain to be determined. In the current study, FHC mRNA expression level was quantitatively monitored in the hypothalamus, anterior pituitary and ovary stroma in prelaying and laying geese. In addition, the levels of FHC mRNA and protein were determined in follicles and ovarian stroma of laying geese. In comparison to prelaying geese, the FHC mRNA expression were 2.4, 1.8, and 13 times higher in the hypothalamus, anterior pituitary and ovarian stroma of laying geese, respectively (p<0.05). FHC mRNA and protein were detected in all examined follicles and ovarian stroma. FHC mRNA expression was higher in postovulatory follicles (POFs) and atretic follicles than in developing follicles and ovarian stroma. Furthermore, the FHC protein concentration in POF3 and atretic follicles were, respectively, 1.45 and 1.7 times higher compared with that of F1 (p<0.05). In conclusion, the presented results provided evidence of a link between FHC and goose reproduction, and supplied a theoretical foundation and a new approach for studying reproduction, in particular ovarian follicular development in birds.

Identification of Promising Mutants Associated with Egg Production Traits Revealed by Genome-Wide Association Study

Egg number (EN), egg laying rate (LR) and age at first egg (AFE) are important production traits related to egg production in poultry industry. To better understand the knowledge of genetic architecture of dynamic EN during the whole laying cycle and provide the precise positions of associated variants for EN, LR and AFE, laying records from 21 to 72 weeks of age were collected individually for 1,534 F2 hens produced by reciprocal crosses between White Leghorn and Dongxiang Blue-shelled chicken, and their genotypes were assayed by chicken 600 K Affymetrix high density genotyping arrays. Subsequently, pedigree and SNP-based genetic parameters were estimated and a genome-wide association study (GWAS) was conducted on EN, LR and AFE. The heritability estimates were similar between pedigree and SNP-based estimates varying from 0.17 to 0.36. In the GWA analysis, we identified nine genome-wide significant loci associated with EN of the laying periods from 21 to 26 weeks, 27 to 36 weeks and 37 to 72 weeks. Analysis of GTF2A1 and CLSPN suggested that they influenced the function of ovary and uterus, and may be considered as relevant candidates. The identified SNP rs314448799 for accumulative EN from 21 to 40 weeks on chromosome 5 created phenotypic differences of 6.86 eggs between two homozygous genotypes, which could be potentially applied to the molecular breeding for EN selection. Moreover, our finding showed that LR was a moderate polygenic trait. The suggestive significant region on chromosome 16 for AFE suggested the relationship between sex maturity and immune in the current population. The present study comprehensively evaluates the role of genetic variants in the development of egg laying. The findings will be helpful to investigation of causative genes function and future marker-assisted selection and genomic selection in chickens.

Molecular cloning and mRNA expression analysis of antizyme inhibitor 1 in the ovarian follicles of the Sichuan white goose

Antizyme inhibitor 1 (Azin1) plays critical roles in various cellular pathways, including ornithine decarboxylase regulation, polyamine anabolism and uptake and cell proliferation. However, the molecular characteristics of the AZIN1 gene and its expression profile in goose tissues and ovarian follicles have not been reported. In this study, the AZIN1 cDNA of the Sichuan white goose (Anser cygnoides) was cloned, and analyzed for its phylogenetic and physiochemical properties. The expression profile of AZIN1 mRNA in geese tissues and ovarian follicles were examined using quantitative real-time PCR. The results showed that the open reading frame of the AZIN1 cDNA is 1,353 bp in length, encoding a 450 amino acid protein with a molecular weight of 50 kDa. Out of all tissues examined, AZIN1 expression was highest in the adrenal gland and lowest in breast muscle. There was also a high expression of AZIN1 in the cerebellum and isthmus of oviduct. With follicular development, AZIN1 gene expression gradually increased, and its expression in F1 was significantly higher than in F5 (P<0.05). AZIN1 expression was also significantly higher in the POF1 than in the other follicles (P<0.05), and there was a low mRNA expression of AZIN1 in atretic follicles. The results of AZIN1 expression profiling in ovarian follicles suggest that AZIN1 may play an important role in the progression of follicular development, potentially through regulating polyamine levels.

Transcriptome profiling identifies differentially expressed genes in Huoyan goose ovaries between the laying period and ceased period

The Huoyan goose is famous for its high egg-laying performance and is listed as a nationally protected domestic animal by the Chinese government. To elucidate the key regulatory genes involved in Huoyan goose egg laying, RNA from ovarian tissue during the ceased and laying periods was sequenced using the Illumina HiSeq 2000 sequencing platform. More than 12 million reads were produced in ceased and laying libraries that included 11,896,423 and 12,534,799 clean reads, respectively. More than 20% of the reads were matched to the reference genome, and 23% of the reads were matched to reference genes. Genes with a false discovery rate (FDR) ≤0.001 and log₂ratio ≧1 or ≤−1 were characterized as differentially expressed, and 344 up-regulated and 344 down-regulated genes were classified into functional categories. Twelve genes that are mainly involved in pathways for reproduction regulation, such as steroid hormone biosynthesis, GnRH signaling pathways, oocyte meiosis, progesterone-mediated oocyte maturation, steroid biosynthesis, calcium signaling pathways, and G-protein coupled receptor signaling pathway were selected for validation by a quantitative real-time polymerase chain reaction (qRT-PCR) analysis, the qRT-PCR results are consistent with the general expression patterns of those genes from the Illumina sequencing. These data provide comprehensive gene expression information at the transcriptional level that might increase our understanding of the Huoyan goose's reproductive biology.

Gene expression profiling in the pituitary gland of laying period and ceased period huoyan geese

Huoyan goose is a Chinese local breed famous for its higher laying performance, but the problems of variety degeneration have emerged recently, especially a decrease in the number of eggs laid. In order to better understand the molecular mechanism that underlies egg laying in Huoyan geese, gene profiles in the pituitary gland of Huoyan geese taken during the laying period and ceased period were investigated using the suppression subtractive hybridization (SSH) method. Total RNA was extracted from pituitary glands of ceased period and laying period geese. The cDNA in the pituitary glands of ceased geese was subtracted from the cDNA in the pituitary glands of laying geese (forward subtraction); the reverse subtraction was also performed. After sequencing and annotation, a total of 30 and 24 up and down-regulated genes were obtained from the forward and reverse SSH libraries, respectively. These genes mostly related to biosynthetic process, cellular nitrogen compound metabolic process, transport, cell differentiation, cellular protein modification process, signal transduction, small molecule metabolic process. Furthermore, eleven genes were selected for further analyses by quantitative real-time PCR (qRT-PCR). The qRT-PCR results for the most part were consistent with the SSH results. Among these genes, Synaptotagmin-1 (SYT1) and Stathmin-2 (STMN2) were substantially over-expressed in laying period compared to ceased period. These results could serve as an important reference for elucidating the molecular mechanism of higher laying performance in Huoyan geese.

Selection of Reliable Reference Genes for Real-time qRT-PCR Analysis of Zi Geese (Anser anser domestica) Gene Expression

Zi geese (Anser anser domestica) belong to the white geese and are excellent layers with a superior feed-to-egg conversion ratio. Quantitative gene expression analysis, such as Real-time qRT-PCR, will provide a good understanding of ovarian function during egg-laying and consequently improve egg production. However, we still don’t know what reference genes in geese, which show stable expression, should be used for such quantitative analysis. In order to reveal such reference genes, the stability of seven genes were tested in five tissues of Zi geese. Methodology/Principal Findings: The relative transcription levels of genes encoding hypoxanthine guanine phosphoribosyl transferase 1 (HPRT1), β-actin (ACTB), β-tubulin (TUB), glyceraldehyde-3-phosphate-dehydrogenase (GADPH), succinate dehydrogenase flavoprotein (SDH), 28S rRNA (28S) and 18S rRNA (18S) have been quantified in heart, liver, kidney, muscle and ovary in Zi geese respectively at different developmental stages (1 d, 2, 4, 6 and 8 months). The expression stability of these genes was analyzed using geNorm, NormFinder and BestKeeper software. Conclusions: The expression of 28S in heart, GAPDH in liver and ovary, ACTB in kidney and HPRT1 in muscle are the most stable genes as identified by the three different analysis methods. Thus, these genes are recommended for use as candidate reference genes to compare mRNA transcription in various developmental stages of geese.

Comprehensive analysis of Sichuan white geese (Anser cygnoides) transcriptome

High-throughput RNA sequencing was performed for comprehensively analyzing the transcriptome of geese. A total of 28,803,759 bp of raw sequence data was generated by 454 GS Flx+. After removal of adaptor sequences, 28,730,361 bp remained and 117,279 reads were obtained, with an average length of 244 bases. Simultaneously, complementary DNA samples from two different reproductive stages of goose ovarian, hypothalamus and pituitary tissue were sequenced separately using Illumina MiSeq platform. A total of 12 688 673 148 bp of raw sequence data were generated by Illumina MiSeq. After removal of adaptor sequences, 8 198 126 562 bp remained and 60 382 786 clean reads were obtained, with an average length of 135 bases. Assembly of all the reads from both 454 Flx+ and Illumina platforms formed 56,839 contigs. The sequence size ranges from 38 to 28,206 bp in size, with an average size of 2584 bp and an N50 of 4624. The assembly produced a substantial number of large contigs: 35,545 (62.5%) were longer than 1 kb, of which 8850 (15.6%) were longer than 5 kb. The sequencing depth was 85 X on average. We performed comprehensive function annotations on unigenes including protein sequence similarity, gene ontology (GO) term classification, and Kyoto Encylcopedia of Genes and Genomes (KEGG) pathway enrichment. GO analysis showed that approximately 63% of the contigs had annotation information, among the 35,953 annotated isotigs in Nr database, 24,783 (68.9%) sequences were assigned with one or more GO terms. There were 14,634 (40.7%) isotigs for biological processes, 10,557(29.3%) isotigs for cellular component, 22,607 (62.9%) isotigs for molecular function. The result of KEGG pathway mapping 8926 sequences had the pathway annotation, and took part in 477 pathways. Additionally, 10,685 simple sequence repeat (SSR) markers were identified from the assembled sequences. The most frequent repeat motifs were trinucleotides, which accounted for 53.03% of all SSRs, followed by dinucleotides (39.9%), tetranucleotides (5.08%), pentanucleotides (1.68%) and hexanucleotides (0.32%). Transcriptome sequencing on mixture issue of the geese yielded substantial transcriptional sequences and potentially useful SSR markers which provide an important data source for geese research.

Molecular characterisation and expression profiling of the ENO1 gene in the ovarian follicle of the Sichuan white goose

The ENO1 gene encodes a multifunctional enzyme that has been identified as a key component of the glycolytic pathway. Our previous studies demonstrated that ENO1 gene expression was higher in the ovaries of laying geese compared with prelaying geese. However, the molecular characterisation and expression profiling of the ENO1 gene in geese tissues and ovarian follicles remain to be determined. In this study, ENO1 cDNA (1,445 bp long) of the Sichuan white goose was cloned and characterised. The ORF of ENO1 cDNA is 1,305 bp in length and encodes a 434 amino acid protein with a molecular weight of 47.27 kDa. ENO1 expression in all of the examined tissues was the highest in spleen and the lowest in breast muscle. High expression of ENO1 appeared in the kidney, liver, adrenal gland, and retina. With increasing follicle growth, ENO1 gene expression began to decrease from the small white follicle to F5, which was followed by a sharp increase in expression in F4 and then a gradual decrease in expression from F3 to F1. Furthermore, in the postovulatory follicles (POF), the levels of ENO1 gene expression decreased gradually from POF1 to POF4. In conclusion, the ENO1 transcript was widely distributed in various tissues of the Sichuan white goose, but ENO1 expression was tissue-specific. Furthermore, the results of the ENO1 expression profiling of ovarian follicles suggest that ENO1 may play an important dual role in the progress of follicular development, where ENO1 acts as a glycolytic enzyme and also mediates apoptosis.

Transcriptome profiling of the goose (Anser cygnoides) ovaries identify laying and broodiness phenotypes

Background

The geese have strong broodiness and poor egg performance. These characteristics are the key issues that hinder the goose industry development. Yet little is known about the mechanisms responsible for follicle development due to lack of genomic resources. Hence, studies based on high-throughput sequencing technologies are needed to produce a comprehensive and integrated genomic resource and to better understand the biological mechanisms of goose follicle development.

Methodology/Principal Findings

In this study, we performed de novo transcriptome assembly and gene expression analysis using short-read sequencing technology (Illumina). We obtained 67,315,996 short reads of 100 bp, which were assembled into 130,514 unique sequences by Trinity strategy (mean size = 753bp). Based on BLAST results with known proteins, these analyses identified 52,642 sequences with a cut-off E-value above 10⁻⁵. Assembled sequences were annotated with gene descriptions, gene ontology and clusters of orthologous group terms. In addition, we investigated the transcription changes during the goose laying/broodiness period using a tag-based digital gene expression (DGE) system. We obtained a sequencing depth of over 4.2 million tags per sample and identified a large number of genes associated with follicle development and reproductive biology including cholesterol side-chain cleavage enzyme gene and dopamine beta-hydroxylas gene. We confirm the altered expression levels of the two genes using quantitative real-time PCR (qRT-PCR).

Conclusions/Significance

The obtained goose transcriptome and DGE profiling data provide comprehensive gene expression information at the transcriptional level that could promote better understanding of the molecular mechanisms underlying follicle development and productivity.