Transcriptome analysis of follicles reveals the importance of autophagy and hormones in regulating broodiness of Zhedong white goose

Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson)

BACKGROUND

Broodiness significantly impacts poultry egg production, particularly notable in specific breeds such as the black-boned Silky, characterized by pronounced broodiness. An understanding of the alterations in ovarian signaling is essential for elucidating the mechanisms that influence broodiness. However, comparative research on the characteristics of long non-coding RNAs (lncRNAs) in the ovaries of broody chickens (BC) and high egg-laying chickens (GC) remains scant. In this investigation, we employed RNA sequencing to assess the ovarian transcriptomes, which include both lncRNAs and mRNAs, in eight Taihe Black-Bone Silky Fowls (TBsf), categorized into broody and high egg-laying groups. This study aims to provide a clearer understanding of the genetic underpinnings associated with broodiness and egg production.

RESULTS

We have identified a total of 16,444 mRNAs and 18,756 lncRNAs, of which 349 mRNAs and 651 lncRNAs exhibited significantly different expression (DE) between the BC and GC groups. Furthermore, we have identified the cis-regulated and trans-regulated target genes of differentially abundant lncRNA transcripts and have constructed an lncRNA-mRNA trans-regulated interaction network linked to ovarian follicle development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses have revealed that DE mRNAs and the target genes of DE lncRNAs are associated with pathways including neuroactive ligand-receptor interaction, CCR6 chemokine receptor binding, G-protein coupled receptor binding, cytokine-cytokine receptor interaction, and ECM-receptor interaction.

CONCLUSION

Our research presents a comprehensive compilation of lncRNAs and mRNAs linked to ovarian development. Additionally, it establishes a predictive interaction network involving differentially abundant lncRNAs and differentially expressed genes (DEGs) within TBsf. This significantly contributes to our understanding of the intricate interactions between lncRNAs and genes governing brooding behavior.

Posthatch developmental changes in the ovary with emphasis on follicular development and atresia in the native chicken (Uttara fowl) of Uttarakhand, India

This experiment was designed to investigate the postnatal development of the ovary in the Uttara fowl chicken and was conducted on 54 apparently healthy female birds divided into different age groups, namely Day 1 and Weeks 1, 4, 8, 12, 16, 20, 24, 28 with six birds each. During postnatal development, the left ovary gradually increased in size and complexity. The segmentation of the ovary started by 4 weeks, follicular eruption by 8 weeks, small liquor follicles (1-5 mm) appeared by 16 weeks, pre-hierarchical follicles by 20 weeks and hierarchical follicles by 24 weeks of age. The cortex was distinctly differentiated from the medulla in the early stage of ovarian development. However, the division between cortex and medulla was gradually obscured with age (transitional stage) and distinction was completely lost in the mature ovary. The different stages of follicular development in the chicken ovary were classified as primordial, primary, growing at Stage I, II and III stromal follicles besides pre-hierarchical and hierarchical surface follicles. The primordial and primary follicles showed cytoplasmic sudanophilic substances, especially in the Balbiani's yolk body, indicating the presence of lipids (Sudan Black B) with no activity for neutral polysaccharides (periodic acid Schiff method). It was observed that apoptotic changes may affect any stage of developing follicle resulting in arrested growth and atrophy. An early form of follicular atresia was the fate of the growth-arrested primordial and primary follicles, whereas the glandular form of atresia was commonly observed in growing follicles arrested at Stages I and II. The scanning electron micrographs unveiled the follicles as hollow oval structures with a follicular lumen lined by the perivitelline membrane (glycoprotein membrane) having lacunae giving a honeycomb-like appearance.

Metagenomic reconstructions of caecal microbiome in Landes, Roman and Zhedong White geese

1. The caecal microbiota in geese play a crucial role in determining the host's health, disease status and behaviour, as evidenced by extensive epidemiological data. The present investigation conducted 10× metagenomic sequencing of caecal content samples obtained from three distinct goose species, namely Landes geese, Roman geese and Zhedong White geese (n = 5), to explore the contribution of the gut microbiome to carbohydrate metabolism.2. In total, 337GB of Illumina data were generated, which identified 1,048,575 complete genes and construction of 331 metagenomic bins, encompassing 78 species from nine phyla. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Bacteria were identified as the dominant phyla while Prevotella, Bacteroides, Streptococcus, and Subdoligranulum were the most abundant genera in the caecum of geese.3. The genes were allocated to 375 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) analysis. The most abundant classes in the caecum of geese were confirmed to be glycoside hydrolases (GHs), glycosyl transferases (GTs), as identified through the carbohydrate-active enzyme (CAZyme) database mapping. Subdoligranulum variabile and Mediterraneibacter glycyrrhizinilyticus were discovered to potentially facilitate carbohydrate digestion in geese.4. Notwithstanding, further investigation and validation are required to establish a connection between these species and CAZymes. Based on binning analysis, Mediterraneibacter glycyrrhizinilyticus and Ruminococcus sp. CAG:177 are potential species in LD geese that contribute to the production of fatty liver.

Spermidine alleviating oxidative stress and apoptosis by inducing autophagy of granulosa cells in Sichuan white geese

Spermidine have been reported a role in antioxidative, antiaging, and antiinflammatory. Oxidative stress causes granulosa cell (GC) apoptosis, follicular atresia, and impairs poultry reproductive functions. Studies have found that autophagy is the protective mechanism against antioxidant stress and apoptosis in cells. However, the relationship between spermidine-induced autophagy, oxidative stress, and apoptosis in goose GCs remains unclear. In this study, we investigated the autophagy mechanism to mediate spermidine effects on the alleviation of oxidative stress and apoptosis in goose GCs. Follicular GCs were treated with spermidine combination with 3-Nitropropanoic acid (3-NPA), rapamycin (RAPA), and chloroquine (CQ) or with hydrogen peroxide, RAPA, and CQ. Spermidine upregulated the ratio of LC3-II/I, inhibited the accumulation of p62 protein, and induced autophagy. 3-NPA treatment significantly increased ROS production, MDA content, SOD activity, cleaved CASPASE-3 protein expression, and decreased BCL-2 protein expression in follicular GCs. Spermidine inhibited oxidative stress and apoptosis induced by 3-NPA. In addition, hydrogen peroxide-induced oxidative stress was inhibited by spermidine. However, the inhibitory effect of spermidine was eliminated under chloroquine. Our results demonstrated that spermidine relieved oxidative stress and apoptosis of GCs by inducing autophagy, indicating that spermidine has a great potential to maintain proteostasis and sustain granulosa cell viability in geese.

Characterization and performance evaluation of indigenous geese of Assam

The present study aimed to phenotypically characterize the indigenous geese of Assam, in North East India. These geese were observed to have two types of plumage colour (white and cinnamon) and plumage pattern (solid and bordered); and three different bill colours (black, orange, yellow). The shank and feet colour was found to be mostly orange and sometimes yellow. The eye colour was found to be black, brown and sometimes grey and skin colour as white. The least squares means for body weight at hatching, 4, 6-8 and 12 months and above age were 0.087±0.001, 3.030±0.022, 3.480±0.055 and 3.970±0.025 kg, respectively. The average age at first egg, annual egg production, clutch size and clutch interval were 320.196±2.882 days, 19.886±0.306, 9.897±0.143 and 59.206±0.531 days. Average fertility and hatchability percentage under natural condition were found to be 87.11% and 80.53%, respectively. The study revealed that the indigenous geese of Assam are heavier birds with high potential for meat production with two colour variants, viz. White and Cinnamon in the study area covering four districts. The study generated baseline information on physical characteristics, productive and reproductive performances of indigenous geese of Assam under native field condition which would be of great help in documentation and development of breed descriptors for registration, improvement and conservation.

Whole Genome Resequencing Identifies Single-Nucleotide Polymorphism Markers of Growth and Reproduction Traits in Zhedong and Zi Crossbred Geese

The broodiness traits of domestic geese are a bottleneck that prevents the rapid development of the goose industry. To reduce the broodiness of the Zhedong goose and thus improve it, this study hybridized it with the Zi goose, which has almost no broody behavior. Genome resequencing was performed for the purebred Zhedong goose, as well as the F2 and F3 hybrids. The results showed that the F1 hybrids displayed significant heterosis in growth traits, and their body weight was significantly greater than those of the other groups. The F2 hybrids showed significant heterosis in egg-laying traits, and the number of eggs laid was significantly greater than those of the other groups. A total of 7,979,421 single-nucleotide polymorphisms (SNPs) were obtained, and three SNPs were screened. Molecular docking results showed that SNP11 located in the gene NUDT9 altered the structure and affinity of the binding pocket. The results suggested that SNP11 is an SNP related to goose broodiness. In the future, we will use the cage breeding method to sample the same half-sib families to accurately identify SNP markers of growth and reproductive traits.

Effects of Oxidative Stress on the Autophagy and Apoptosis of Granulosa Cells in Broody Geese

Broodiness is an unfavorable trait associated with the cessation of egg laying. Studies have found that excessive granulosa cell apoptosis and autophagy occur during goose broodiness. Other studies have also confirmed that oxidative stress is an important cause of apoptosis and autophagy. However, whether oxidative stress occurs during goose broodiness and whether this oxidative stress causes apoptosis and autophagy have not been fully elucidated. In this study, we investigated the effects of oxidative stress on the autophagy and apoptosis of granulosa cells in broody geese. The results showed higher mRNA expression of genes related to antioxidative stress responses (GPX, SOD-1, SOD-2, COX-2, CAT and hsp70) in pre-broody and broody geese than in laying birds. In addition, increased levels of granulosa cell apoptosis and autophagy were observed in pre-broody geese than in laying geese. Additionally, granulosa cells treated with H₂O₂ exhibited increased apoptosis and autophagy in vitro, and these effects were responsible for goose granulosa cell death. Moreover, vitamin E treatment effectively protected granulosa cells from H₂O₂-induced oxidative stress by inhibiting ROS production. Correspondingly, granulosa cell apoptosis and autophagy were greatly alleviated by vitamin E treatment. Together, our results demonstrated serious oxidative stress and granulosa cell apoptosis and autophagy in broody geese, and oxidative stress promoted apoptosis and autophagy. Vitamin E alleviated the autophagy and apoptosis of granulosa cells by inhibiting oxidative stress.

Comparative Transcriptome Analysis Provides Novel Insights into the Effect of Lipid Metabolism on Laying of Geese

Simple Summary

The importance of lipid metabolism in the egg production of poultry has been widely reported. Meanwhile, geese have lower egg production and unique lipid metabolism patterns compared with chicken and duck. It is of great significance to further improve egg laying performance to explore the differences of fat metabolism and the molecular mechanisms in geese with different egg laying performance. This study compared the phenotypic differences of liver and abdominal fat, as well as the transcriptome level differences of liver, abdominal fat, and ovarian stroma among high-, low-, and no-egg production groups. The results reveal that lipid metabolism regulated by the circadian rhythm of the liver may directly or indirectly affect ovarian function through the inflammation and hormone secretion of abdominal fat.

Abstract

The lower egg production of geese (20~60 eggs per year) compared with chicken and duck limits the development of the industry, while the yolk weight and fatty liver susceptibility of geese was higher than that of other poultry. Therefore, the relationship between lipid metabolism and the laying performance of geese remains to be explored. Phenotypically, we observed that the liver fat content of the high-, low-, and no-egg production groups decreased in turn, while the abdominal fat weight increased in turn. For transcriptional regulation, the KEGG pathways related to lipid metabolism were enriched in all pairwise comparisons of abdominal fat and liver through functional analysis. However, some KEGG pathways related to inflammation and the circadian rhythm pathway were enriched by DEGs only in abdominal fat and the liver, respectively. The DEGs in ovarian stroma among different groups enriched some KEGG pathways related to ovarian steroidogenesis and cell adhesion. Our research reveals that lipid metabolism regulated by the circadian rhythm of the liver may directly or indirectly affect ovarian function through the inflammation and hormone secretion of abdominal fat. These results offer new insights into the regulation mechanisms of goose reproductive traits.

The study of candidate genes in the improvement of egg production in ducks – a review

Duck is the second-largest poultry species aside from chicken. The rate of egg production is a major determinant of the economic income of poultry farmers. Among the reproductive organs, the ovary is a major part of the female reproductive system which is highly important for egg production. Based on the importance of this organ, several studies have been carried out to identify candidate genes at the transcriptome level, and also the expression level of these genes at different tissues or egg-laying conditions, and single nucleotide polymorphism (SNPs) of genes associated with egg production in duck. In this review, expression profile and association study analyses at SNPs level of different candidate genes with egg production traits of duck were highlighted. Furthermore, different studies on transcriptome analysis, Quantitative Trait Loci (QTL) mapping, and Genome Wide Association Study (GWAS) approach used to identify potential candidate genes for egg production in ducks were reported. This review would widen our knowledge on molecular markers that are associated or have a positive correlation to improving egg production in ducks, for the increasing world populace.

Comparative liver transcriptome analysis of duck reveals potential genes associated with egg production

BACKGROUND

Molecular studies on egg production in ducks were mostly focused on brain and ovaries as they are directly involved in egg production. Liver plays a vital role in cellular lipid metabolism. It also plays a decisive role in reproductive organ development, including yolk generation in laying ducks at sexual maturity. However, the precise molecular mechanism involved in the liver-blood-ovary axis in ducks remains elusive.

METHODS AND RESULTS

In this study, we analysed the liver transcriptome of laying (LA), immature (IM) and broody (BR) ducks using RNA sequencing to understand the role of genes expressed in the liver. The comparative transcriptome analysis revealed 82 DEGs between LA and IM ducks, 47 DEGs between LA and BR ducks and 51 DEGs between IM and BR ducks. GO analysis of DEGs, showed that DEGs were mainly involved in cellular anatomical entity, intracellular, metabolic process, and binding. Furthermore, pathway analysis indicated the important role of Wnt signaling pathway in egg formation and embryo development. Our study showed several candidate genes including vitellogenin-1, vitellogenin-2, riboflavin binding protein, G protein subunit gamma 4, and fatty acid binding protein 3 that are potentially related to egg production in ducks.

CONCLUSIONS

The study provides valuable information on the genes responsible for egg production and thus, pave the way for further investigation on the molecular mechanisms of egg production in duck.

miRNA sequencing analysis of healthy and atretic follicles of chickens revealed that miR-30a-5p inhibits granulosa cell death via targeting Beclin1

Background

The egg production performance of chickens is affected by many factors, including genetics, nutrition and environmental conditions. These factors all play a role in egg production by affecting the development of follicles. MicroRNAs (miRNAs) are important non-coding RNAs that regulate biological processes by targeting genes or other non-coding RNAs after transcription. In the animal reproduction process, miRNA is known to affect the development and atresia of follicles by regulating apoptosis and autophagy of granulosa cells (GCs).

Results

In this study, we identified potential miRNAs in the atretic follicles of broody chickens and unatretic follicles of healthy chickens. We identified gga-miR-30a-5p in 50 differentially expressed miRNAs and found that gga-miR-30a-5p played a regulatory role in the development of chicken follicles. The function of miR-30a-5p was explored through the transfection test of miR-30a-5p inhibitor and miR-30a-5p mimics. In the study, we used qPCR, western blot and flow cytometry to detect granulosa cell apoptosis, autophagy and steroid hormone synthesis. Confocal microscopy and transmission electron microscopy are used for the observation of autophagolysosomes. The levels of estradiol (E2), progesterone (P4), malondialdehyde (MDA) and superoxide dismutase (SOD) were detected by ELISA. The results showed that miR-30a-5p showed a negative effect on autophagy and apoptosis of granulosa cells, and also contributed in steroid hormones and reactive oxygen species (ROS) production. In addition, the results obtained from the biosynthesis and dual luciferase experiments showed that Beclin1 was the target gene of miR-30a-5p. The rescue experiment conducted further confirmed that Beclin1 belongs to the miR-30a-5p regulatory pathway.

Conclusions

In summary, after deep miRNA sequencing on healthy and atretic follicles, the results indicated that miR-30a-5p inhibits granulosa cell death by inhibiting Beclin1.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-022-00697-0.

Chicken ovarian follicles morphology and growth differentiation factor 9 gene expression in chicken ovarian follicles: review

Ovary follicular development is a progressive system from the beginning of small cortical follicles to the ovulation of hierarchical follicles. The review was conducted to provide information on the indigenous chickens commonly used for egg production, chicken ovarian follicles morphology and expression of growth differentiation factor 9 (GDF9) gene in ovarian follicles and its relationship with egg production. The research databases used in the study include google scholar, Science Direct, PubMed, JSTOR and Cambridge Core. Google, Yahoo and Baidu search engines were used to search the information. In this study, the papers selected for use were original research articles and reviews to ensure that the information used was from research results. Besides, only recent English papers, 2010-2021, were used. The keywords used to search for articles were chicken ovarian follicles, ovarian morphology and GDF9 gene expression. The documents showed that pre-hierarchical follicles include many small and large white follicles, which are about 2-5mm in diameter and 5 to 6 small yellow follicles (SYF) that are about 5-10mm in diameter. Preovulatory follicles are about five to six in number and above 10mm in diameter, with the sizes from F6 to F1, with F1 as the largest follicle. Further, the studies revealed that GDF9 gene mRNA is expressed in the highest concentration in small yellow follicles and other studies reported that the expression of GDF9 gene has been found in follicles of the primary to preovulatory stages in chickens. This review concludes that the GDF9 gene expression is mainly throughout follicular growth and it stimulates the proliferation of pre-hierarchical granulosa cells. The increased egg production in chickens depends on progressive developmental stages and the growth of ovarian follicles.

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.

Autophagy in farm animals: current knowledge and future challenges

Autophagy (a process of cellular self-eating) is a conserved cellular degradative process that plays important roles in maintaining homeostasis and preventing nutritional, metabolic, and infection-mediated stresses. Surprisingly, little attention has been paid to the role of this cellular function in species of agronomical interest, and the details of how autophagy functions in the development of phenotypes of agricultural interest remain largely unexplored. Here, we first provide a brief description of the main mechanisms involved in autophagy, then review our current knowledge regarding autophagy in species of agronomical interest, with particular attention to physiological functions supporting livestock animal production, and finally assess the potential of translating the acquired knowledge to improve animal development, growth and health in the context of growing social, economic and environmental challenges for agriculture.Abbreviations: AKT: AKT serine/threonine kinase; AMPK: AMP-activated protein kinase; ASC: adipose-derived stem cells; ATG: autophagy-related; BECN1: beclin 1; BNIP3: BCL2 interacting protein 3; BVDV: bovine viral diarrhea virus; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CMA: chaperone-mediated autophagy; CTSB: cathepsin B; CTSD: cathepsin D; DAP: Death-Associated Protein; ER: endoplasmic reticulum; GFP: green fluorescent protein; Gln: Glutamine; HSPA8/HSC70: heat shock protein family A (Hsp70) member 8; IF: immunofluorescence; IVP: in vitro produced; LAMP2A: lysosomal associated membrane protein 2A; LMS: lysosomal membrane stability; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MDBK: Madin-Darby bovine kidney; MSC: mesenchymal stem cells; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; NBR1: NBR1 autophagy cargo receptor; NDV: Newcastle disease virus; NECTIN4: nectin cell adhesion molecule 4; NOD1: nucleotide-binding oligomerization domain 1; OCD: osteochondritis dissecans; OEC: oviduct epithelial cells; OPTN: optineurin; PI3K: phosphoinositide-3-kinase; PPRV: peste des petits ruminants virus; RHDV: rabbit hemorrhagic disease virus; SQSTM1/p62: sequestosome 1; TEM: transmission electron microscopy.

The effects of natural mating and artificial insemination on reproductive traits of 1-and 2-year-old domestic Turkish geese

The aim of this study was to assess the sperm quality traits of 1- and 2-year-old ganders and the reproduction traits of 2-year-old domestic Turkish geese in natural mating (NM) and artificial insemination (AI) conditions. The study comprised 72 two-year-old females, 12 one-year-old, and 12 two-year-old ganders. Thirty-six female geese were mated naturally (18 with 1-year-old ganders, 18 with 2-year-old ganders); the remaining thirty-six were inseminated artificially (18 with 1-year-old ganders, 18 with 2-year-old ganders). Twenty-four ganders were separated into groups (12 for NM; 12 for AI). The male:female ratio was 1:3 for NM and AI groups. Egg production, broodiness, fertility and hatching traits were determined in female geese, sperm quality traits such as semen volume, sperm concentration, sperm quality factor (eSQF: ejaculated semen SQF; dSQF: diluted semen SQF), sperm motility, and sperm morphological traits in ganders. The insemination method and gander's age did not affect egg production, AI geese showed significantly more broodiness than NM groups as the breeding months progresses (p < 0.05). Fertility was higher in the groups containing 2-year-old ganders than in those 1-year-old ganders, and NM groups compared to AI (p < 0.05). The insemination method significantly affected semen volume, sperm concentration, eSQF, sperm motility, total live sperm, normal sperm, macro-cephalic sperm, and dead sperm percentages in ganders (p < 0.05).Managing females in the NM system with ganders was able to partially suppress the broodiness behavior, possibly due to synchronization of pair-bond behaviors. Greater fertility was achieved with 2-years-old AI ganders, which had lower dSQF compared to 1-year-old NM ganders. This is a good indication that only SQF is not sufficient to achieve sustainable-desired fertility, and sexual experience is also an important factor.

Long noncoding RNAs profiling in ovary during laying and nesting in Muscovy ducks (Cairina moschata)

There are recent reports of the important functions of long noncoding RNAs (lncRNAs) in female reproductive and ovarian development. Studies in which there was characterization of lncRNAs in the ovaries of laying compared with nesting poultry, however, are limited. In this study, RNA libraries were constructed by obtaining sequencing data of ovarian tissues from laying and nesting Muscovy ducks. In the ovarian tissues of Muscovy ducks, a total of 334 differentially abundant mRNA transcripts (DEGs) and 36 differentially abundant lncRNA transcripts were identified in the nesting period, when compared with during the laying period. These results were subsequently validated by qRT-PCR using nine randomly-selected lncRNAs and six randomly-selected DAMTs. Furthermore, the cis- and trans-regulatory target genes of differentially abundant lncRNA transcripts were identified, and lncRNA-gene interaction networks of 34 differentially abundant lncRNAs and 263 DEGs were constructed. A total of 7601 lncRNAs neighboring 10,542 protein-coding genes were identified and found to be enriched in the Wnt signaling pathway and oocyte meiosis pathways associated with follicular development. Overall, only 11 cis-targets and 57 mRNA-mRNA except trans-targets were involved in the lncRNA-gene interaction networks. Based on the interaction networks, nine DEGs were trans-regulated by differentially abundant lncRNAs and 20 differentially abundant lncRNAs were hypothesized to have important functions in the regulation of broodiness in Muscovy ducks. In this study, a predicted interaction network of differentially abundant lncRNAs and DEGs in Muscovy ducks was constructed for the first time leading to an enhanced understanding of lncRNA and gene interactions regulating broodiness.

Comparative Transcriptome Profiling of Ovary Tissue between Black Muscovy Duck and White Muscovy Duck with High- and Low-Egg Production

The egg-laying rate is an important indicator for evaluating fertility of poultry. In order to better understand the laying mechanism of Muscovy ducks, gene expression profiles and pathways of ovarian tissues in high- and low-laying black (BH and BL) and white Muscovy ducks (WH and WL) during the peak production period were performed by using RNA-seq. The total number of reads produced for each ovarian sample ranged from 44,344,070 to 47,963,328. A total of 113, 619 and 87 differentially expressed genes (DEGs) were identified in BH-vs-WH, BL-vs-BH and BL-vs-WL, respectively. Among them, 54, 356 and 49 genes were up regulated and 59, 263 and 38 genes were down regulated. In addition, there were only 10 up-regulated genes in WL-vs-WH. In the comparison of DEGs in black and white Muscovy ducks, two co-expressed DEG genes were detected between BH-vs-WH and BL-vs-WL and seven DEGs were co-expressed between BL-vs-BH and WL-vs-WH. The RNA-Seq data were confirmed to be reliable by qPCR. Numerous DEGs known to be involved in ovarian development were identified, including TGFβ2, NGFR, CEBPD, CPEB2, POSTN, SMOC1, FGF18, EFNA5 and SDC4. Gene Ontology (GO) annotations indicated that DEGs related to ovarian development were mainly enriched in biological processes of "circadian sleep/wake cycle process," "negative regulation of transforming growth factor-β secretion," "positive regulation of calcium ion transport" in BH-vs-WH and "cell surface receptor signaling pathway," "Notch signaling pathway" and "calcium ion transport" in BL-vs-BH. Besides, "steroid biosynthetic process," "granulosa cell development" and "egg coat formation" were mainly enriched in BL-vs-WL and "reproduction," "MAPK cascade" and "mitotic cell cycle" were mainly enriched in WL-vs-WH. KEGG pathway analysis showed that the PI3K-Akt signaling pathway and ovarian steroidogenesis were the most enriched in Muscovy duck ovary transcriptome data. This work highlights potential genes and pathways that may affect ovarian development in Muscovy duck.

Quantitative proteomic analysis of chicken serum reveals key proteins affecting follicle development during reproductive phase transitions

Avian reproductive behavior is regulated through the neuroendocrine system. The transition from laying to brooding is strictly controlled by the hypothalamus-pituitary-gonadal (HPG) axis. Cross talk on the HPG axis relies on the circulatory system, where the dynamics of serum proteins can be observed during different reproductive phases. Some canonical hormones, such as prolactin and luteinizing hormone, play important roles in the transition through reproductive phases. However, little is known at the whole-proteome level. To discover novel serum proteins, we employed isobaric tags for relative and absolute quantification to assay the serum proteome during different reproductive phases in chicken. We identified a total of 1,235 proteins from chicken serum; 239 of these proteins showed differential expression between the laying and brooding stages, including a low concentration of steroid metabolism-related proteins and a high concentration of calcium signaling-related proteins (fold change ≥1.5 or ≤0.66; P < 0.05). Pathway analysis and protein–protein interaction networks predicated the difference in follicle development between the brooding stage and laying stages and were related to the 14-3-3 protein family, which is associated with oocyte meiosis and maturation. Together, these results provided a proteomics foundation for investigating the dynamic changes taking place in the circulatory system during reproductive phase transition, and also uncovered new insights regarding follicle development that underlie the avian reproductive cycle.

Transcriptomic Analysis of circRNAs and mRNAs Reveals a Complex Regulatory Network That Participate in Follicular Development in Chickens

Follicular development plays a key role in poultry reproduction, affecting clutch traits and thus egg production. Follicular growth is determined by granulosa cells (GCs), theca cells (TCs), and oocyte at the transcription, translation, and secretion levels. With the development of bioinformatic and experimental techniques, non-coding RNAs have been shown to participate in many life events. In this study, we investigated the transcriptomes of GCs and TCs in three different physiological stages: small yellow follicle (SYF), smallest hierarchical follicle (F6), and largest hierarchical follicle (F1) stages. A differential expression (DE) analysis, weighted gene co-expression network analysis (WGCNA), and bioinformatic analyses were performed. A total of 18,016 novel circular RNAs (circRNAs) were detected in GCs and TCs, 8127 of which were abundantly expressed in both cell types. and more circRNAs were differentially expressed between GCs and TCs than mRNAs. Enrichment analysis showed that the DE transcripts were mainly involved in cell growth, proliferation, differentiation, and apoptosis. In the WGCNA analysis, we identified six specific modules that were related to the different cell types in different stages of development. A series of central hub genes, including MAPK1, CITED4, SOD2, STC1, MOS, GDF9, MDH1, CAPN2, and novel_circ0004730, were incorporated into a Cytoscape network. Notably, using both DE analysis and WGCNA, ESR1 was identified as a key gene during follicular development. Our results provide valuable information on the circRNAs involved in follicle development and identify potential genes for further research to determine their roles in the regulation of different biological processes during follicle growth.

Comparison of the broody behavior characteristics of different breeds of geese

A low laying performance in goose is one of the key factors preventing the industrial development, and the laying performance is related to broody behavior. However, the characteristics of broody behavior in geese remain unclear. In this study, the total 144 geese (300 day old), including Zhedong geese (Anser cygnoides), Sichuan geese (Anser cygnoides), and Carlos geese (Anser anser) were selected and assigned to 1 of 3 groups/breed (including 4♂+12♀). Laying and broody behaviors were recorded using the infrared video cameras from 2016 November 11 to 2017 June 15. The broody behavior was detected in 19.4% of Carlos geese, 33.3% of Sichuan geese, and 100% of Zhedong geese. Different goose breeds showed similar behavior characteristics. The low frequency of feeding, drinking, and low body weight were observed in the middle of broodiness. As the brooding progressed, the body temperature showed a downward trend and then recovered, whereas no difference was observed in Carlos goose. In addition, the plasma hormone concentration from different breeds and stages of broodiness were compared. The contents of FSH (follicle-stimulating hormone) and LH (luteinizing hormone) in geese were greater in the laying stage than that in the broody stage. Fewer FSH and LH were detected in Zhedong geese and Carlos geese, more in Sichuan geese. In broody goose, the PRL (prolactin) concentrations of the 3 goose breeds peaked in the middle of broodiness, and greater PRL was detected in Sichuan geese than those in Carlos geese and Zhedong geese. Finally, we compared egg production between the broody and non-broody geese in the observation period. The egg production of broody Carlos geese was 27, which was significantly higher than non-broody geese (14 eggs), while in Sichuan geese there was no significant difference between broody (24 eggs) and non-broody geese (26 eggs). Finally, the higher egg production was found with the more broody times in Zhedong geese. Taken together, although the different goose breeds showed similar broody behavior characteristics, the broody rate and hormone secretion were dissimilar, and the Zhedong geese exhibited strong broody feature.

Variations in the Expression Pattern of HSP27 and MSK1 Genes During the Development of Prehierarchical Follicles in the Zi Geese (Anser Cygnoides)

The p38MAPKs (mitogen-activated protein kinases) signaling contributes a pivotal role in mammalian ovarian follicular development; however, the knowledge regarding their expression in geese remains unresolved. The objective of the current study was to determine the spatio-temporal expression of heat shock protein 27 (HSP27) and mitogen- and stress-activated protein kinase 1 (MSK1) genes in the prehierarchical follicles during geese ovarian development. The prehierarchical follicles samples were harvested from 35- to 37-week-old healthy laying geese. HSP27 and MSK1 relative expression in various sized prehierachical follicles was detected by real-time quantitative polymerase chain reaction (RT-qPCR) and western blotting. Follicular wall localization of HSP27 and MSK1 was examined by using immunohistochemistry. Our results at mRNA level indicated that HSP27 was highly expressed in middle white follicles whereas MSK1 was predominantly expressed in small white follicles. The western blotting results for HSP27 and MSK1 were inconsistent with the RT-qPCR results in various stages of prehierachical follicular development but noticeably, HSP27 proteins were still expressed more in middle white follicles while MSK1 proteins were more abundant in primary follicles. At different stages of prehierarchical development, immunodetections in the granulosa and theca cells revealed that HSP27 was intensively localized in middle white follicles while strong detections of MSK1 were observed in large white follicles. These results indicate HSP27 and MSK1 might be associated to the key regulators of folliculogenesis in geese.

Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

BACKGROUND

De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or "pipelines," on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research.

RESULTS

New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla.

CONCLUSIONS

Given current bioinformatics approaches, there is no single "best" reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.

Hypothalamic transcriptome analysis reveals the neuroendocrine mechanisms in controlling broodiness of Muscovy duck (Cairina moschata)

Broodiness, one of the maternal behaviors and instincts for natural breeding in birds, is an interesting topic in reproductive biology. Broodiness in poultry is characterized by persistent nesting, usually associated with cessation of egg laying. The study of avian broodiness is essential for bird conservation breeding and commercial poultry industry. In this study, we examined the hypothalamus transcriptome of Muscovy duck in three reproductive stages, including egg-laying anaphase (LA), brooding prophase (BP) and brooding metaphase (BM). Differences in gene expression during the transition from egg-laying to broodiness were examined, and 155, 379, 292 differently expressed genes (DEGs) were obtained by pairwise comparisons of LA-vs-BP, LA-vs-BM and BP-vs-BM, respectively (fold change≥1.5, P < 0.05). Gene Ontology Term (GO) enrichment analysis suggested a possible role of oxidative stress in the hypothalamus might invoke reproductive costs that potentially change genes expression. KEGG analysis revealed glutamatergic synapse, dopaminergic synapse, serotonergic synapse and GABAergic synapse pathway were significantly enriched, and regulator genes were identified. Eight gene expression patterns were illustrated by trend analysis and further clustered into three clusters. Additional six hub genes were identified through combining trend analysis and protein-protein interaction (PPI) analysis. Our results suggested that the cyclical mechanisms of reproductive function conversion include effects of oxidative stress, biosynthesis of neurotransmitters or their receptors, and interactions between glucocorticoids and thyroid hormones and regulatory genes. These candidate genes and biological pathways may be used as targets for artificial manipulation and marker-assisted breeding in the reproductive behavior.

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.

Identification of Differentially Expressed Genes in Porcine Ovaries at Proestrus and Estrus Stages Using RNA-Seq Technique

Estrus is an important factor for the fecundity of sows, and it is involved in ovulation and hormone secretion in ovaries. To better understand the molecular mechanisms of porcine estrus, the expression patterns of ovarian mRNA at proestrus and estrus stages were analyzed using RNA sequencing technology. A total of 2,167 differentially expressed genes (DEGs) were identified (P ≤ 0.05, |log₂  Ratio| ≥ 1), of which 784 were upregulated and 1,383 were downregulated in the estrus compared with the proestrus group. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in the cellular process, single-organism process, cell and cell part, and binding and metabolic process. In addition, a pathway analysis showed that these DEGs were significantly enriched in 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including cell adhesion molecules, ECM-receptor interaction, and cytokine-cytokine receptor interaction. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) confirmed the differential expression of 10 selected DEGs. Many of the novel candidate genes identified in this study will be valuable for understanding the molecular mechanisms of the sow estrous cycle.

ROS activates autophagy in follicular granulosa cells via mTOR pathway to regulate broodiness in goose

Broodiness causes reduced reproductive ability in poultry, but its regulatory mechanism remains poorly understood. ROS (reactive oxygen species) and autophagy are important for follicular development, and the interaction between the two may play a role in regulating broodiness. We examined goose follicles for ROS and oxidation scavenger activities during the egg-laying and broody stages. The follicular granulosa cells were exposed to media containing H₂O₂, and the interactions between ROS and autophagy in follicular granulosa cells in vitro were analyzed using a Western blot method. We found that the activities of superoxide dismutase (SOD) and lactate dehydrogenase (LDH) were enhanced and the amount of malondialdehyde (MDA) decreased in broody goose follicles. H₂O₂ inhibited the cell viability and induced autophagy. Furthermore, it was also found that H₂O₂ regulated autophagy by reducing mTOR and increasing p53; however, H₂O₂ had no impact on Beclin1 or ATG12. It was also shown that the enhanced autophagy lessened ROS-induced damages. We conclude that ROS and autophagy both played important roles in regulating follicular development to control broodiness in geese, and ROS activated autophagy in follicular granulosa cells via the mTOR pathway.