iTRAQ-based quantitative proteomic analysis provides insights into strong broodiness in Muscovy duck (Cairina moschata) combined with metabolomics analysis

Synergistic transcriptomic and metabolomic analyses in Zi geese ovaries with different clutch lengths

The clutch is defined as consecutive days of oviposition. Clutch length is an index that reflects ovulation persistence, and is highly correlated with egg production in birds. To identify the genetic markers associated with clutch length in geese, two consecutive experiments were conducted. In the first experiment, 200 Zi geese were selected, all 230 days old, were selected from the same batch and raised individually in the same environment. Data of egg-laying and clutch traits were recorded. After the laying period, three geese with the longest clutch lengths were selected to form the length clutch group (LCG) and three geese with the shortest clutch lengths were formed the short clutch group (SCG). In the second experiment, the ovaries of six geese were collected for transcriptomic and metabolomic analyses. The results showed that large clutch length (LCL) and average clutch length (ACL) were positively correlated with egg number (EN) (P < 0.01; r = 0.63 and 0.60, respectively). Large clutch number (LCN) was significantly correlated with the peak egg number (PEN) (r = 0.58, P < 0.01) and EN (r = 0.60, P < 0.01). EN, LCN, LCL, and ACL showed significant differences (P < 0.01) between the two clutch length groups. Transcriptomic analysis identified 424 differentially expressed genes (DEGs). Functional enrichment analysis revealed that these DEGs were mainly involved in neuroactive ligand-receptor interactions, ovarian steroidogenesis, and calcium signaling pathways. Further, AVPR1A, FGF14, and LHCGR were predicted as the key genes regulating LCL. Metabolomic analysis identified 349 differential metabolites (DMs) in both the positive and negative ion modes. Pyruvate, isocitric acid, D/L‑serine, 3-phospho-d-glycerate, succinate, glycine, and glutamic acid were identified as the key metabolites mainly enriched in the signaling pathways of the TCA cycle. Integration of transcriptomic and metabolomic data revealed critical gene-metabolite pairs, including ACSL4-phosphoenolpyruvate, implicated in LCL regulation. In summary, this study provides new insights into the genes and molecular markers affecting LCL in Zi geese.

Ovarian Transcriptome Profile from Egg-Laying Period to Incubation Period of Changshun Green-Shell Laying Hens

Background/Objectives: The Changshun green-shell laying hen with a strong broodiness is a Chinese indigenous chicken breed. Little is known about the mechanisms responsible for the ovary development of Changshun green-shell laying hens from the egg-laying period (LP) to the incubation period (BP). Methods: A total of six hens were selected from LP (n = three) and BP (n = three) at 28 weeks old. The RNA sequencing (RNA-seq) of ovaries from hens in LP and BP groups was performed to identify candidate genes and pathways associated with broodiness. Results: We identified 1650 differently expressed genes (DEGs), including 429 up-regulated and 1221 down-regulated DEGs, in chicken ovaries between LP and BP groups. Gene ontology term (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these DEGs were mainly involved in the pathways related to follicle development in chicken ovaries, including focal adhesion, the MAPK signaling pathway, and the FoxO signaling pathway, and vascular smooth muscle contraction, ECM-receptor interaction, and the GnRH signaling pathway were down-regulated in incubating ovaries. Eight candidate genes (EGFR, VEGFRKDRL, FLT1, KDR, PDGFRA, TEK, KIT and FGFR3) related to angiogenesis, folliculogenesis, steroidogenesis and oogenesis in ovaries were suggested to play important roles in the ovarian development of Changshun hens during the transition from LP to BP. Conclusions: This study identified a range of genes and several pathways that may be involved in regulating the broodiness of Changshun green-shell laying hens. These data are helpful to further enrich our understanding of the mechanism of incubation behaviour in chickens.

Proteomic analysis of egg production peak and senescence in the ovaries of Taihe black-boned silky fowl (Gallus gallus domesticus Brisson)

BACKGROUND

The Taihe black-boned silky fowl, a distinguished indigenous breed of chicken, is renowned for its dual utility in both traditional medicinal and culinary applications. However, the breed faces significant challenges due to its suboptimal reproductive capabilities and a notably brief egg-laying period, which have impeded its broader development and cultivation. In this research endeavor, we employed an advanced, rapid DIA (Data independent acquisition) quantitative proteomics method on the Astral platform to meticulously analyze the ovarian proteome of these chickens. By analyzing the ovarian proteomic information of Taihe black-boned silky fowl during peak and decline egg-laying periods, we aim to identify potential reproductive candidate proteins and the molecular mechanisms underlying egg-laying decline. This could enable us to implement interventions to improve the reproductive efficiency of this valuable breed.

RESULT

In this study, a total of 8,281 proteins were identified within the ovarian proteome of the Taihe black-boned silky fowl. Among these, 303 proteins exhibited significant differential expression, with 98 proteins significantly up-regulated and 205 proteins significantly down-regulated. The functional annotation of these proteins illuminated their crucial roles in the steroid hormone synthesis pathways, which are pivotal during the peak of egg production. Furthermore, during the later stages of laying, there was a noticeable upregulation of proteins associated with inflammatory senescence and oxidative stress. This change suggests an increase in reproductive stress within the ovary, highlighting the physiological shifts that affect productivity as the chickens age.

CONCLUSION

This study identified key candidate protein markers in the Taihe black-boned silky fowl during critical phases of their reproductive cycle, specifically peak and late egg-laying periods. These findings contribute valuable new scientific insights that can be utilized for the breeding optimization and effective management of this unique breed. By elucidating the protein dynamics during different laying phases, the research offers potential strategies aimed at enhancing reproductive performance and extending the reproductive lifespan of the Taihe black-boned silky fowl. This could lead to significant improvements in both the sustainability and profitability of farming this indigenous breed.

Variations in gut microbiota composition and reproductive hormone levels between laying and broody Muscovy ducks

High broodiness in Muscovy ducks impedes animal husbandry growth. The interaction between endocrine hormones and gut microbiota has been proven to play a crucial role in reproductive performance, and whether it can regulate the broody behavior of Muscovy ducks requires further research. Nine laying ducks (Laying group) and nine broody ducks (Broodiness group) were selected. Corresponding serum, ileum, and cecum chyme were collected for further research. The results showed that, compared to the laying group, the serum concentration of prolactin decreased, while the levels of Mullerian inhibiting substance, follicle-stimulating hormone, and follistatin increased in the broodiness group (P < 0.05). 16S rDNA sequencing showed that, the broodiness group exhibited lower abundance levels of Rothia, Streptococcus, and Lactobacillus, whereas the abundance of Turicibacter, Aliicoccus, and Facklamia was higher in the ileum compared to the laying group (P < 0.05). In the cecum, the broodiness group exhibits a significant reduction in the abundance of Butyricicoccus and unclassified_f_Rikenellaceae, while the abundance of Christensenellaceae_R-7_group, Ruminococcus_torques_group, Parabacteroides, norank_f_Oscillospiraceae, Cloacibacillus, Sellimonas, Shuttleworthia, norank_f_UCG-010, unclassified_f_Lachnospiraceae, Oscillospira, Synergistes, Family_XIII_AD3011_group and Eubacterium_nodatum_group is higher compared to the laying group. A Spearman correlation analysis reveals that both in the ileum and cecum, serum hormones exhibit significant correlations with the top 20 abundant intestinal microbial genera. Among these, serum follistatin has most entries of significant correlations with the detected microbial genera (P < 0.05). In conclusion, the broody behavior of Muscovy ducks can be modulated by the interaction between hormones and gut microbiota. Notably, the relationship between Follistatin and the composition of gut microbiota, specifically Firmicutes, is the most prominent.

Growth differentiation factor 9 activates the TGF-β pathway in follicle atresia of Muscovy ducks

Muscovy ducks' high broodiness hinders industry growth. Studying broodiness regulation contributes to the theoretical foundation for enhancing reproductive performance in Muscovy ducks. Experiment 1, a total of 18 Muscovy ducks were divided into 2 groups: Laying group (LO) and Broody group (BO). To collect ovaries for morphological and transcriptome analysis. Experiment 2, Primary Muscovy ducks granulosa cells (GC) were isolated and treated with or without GDF9 at appropriate concentrations as indicated. Experiment 3, GC were treated with or without GDF9 in the presence or absence of a receptor inhibitor. The cell viability, cell apoptosis rate and levels of TGF-β pathway were determined. In vivo, there was a gradual disappearance of follicles in the ovaries and accompanied by follicle atrophy and a concentration of cytoplasm in BO group. The transcriptome expression profile revealed a total of 1,185 up-regulated differentially expressed transcripts (DEs) and 1,258 down-regulated DEs in the BO group compared to the LO group. The up-regulated differentially expressed GDF9 is involved in regulating the TGF-β pathway, which is among the top 10 pathways identified through the KEGG pathway analysis (P < 0.05). Additionally, the fluorescence intensity of apoptosis is primarily observed in the granulosa layers of the ovary. Compared to the LO group, the mRNA level of TGF-β pathway and the protein of GDF9 and p-Smad2/3 were increased in ovary of the BO group (P < 0.05). In vitro, GDF9 supplementation demonstrated does-related promotion of GC (P < 0.01). Compared to CTRL group, 12 ng/mL GDF9 supplementation to GC increased the rate of cell apoptosis, the mRNA and protein expression of TGF-β pathway and the apoptosis-related genes. Pretreatment of GC with GDF9-receptor inhibitor largely abrogated the negative function of GDF9 treatment (P < 0.05). In summary, granulosa cell apoptosis leading to follicle atresia in broodiness of Muscovy ducks is associated with GDF9 activation of the TGF-β pathway. This discovery lays a solid foundation for understanding duck follicular development and enhancing egg production in Muscovy ducks.

ACE Inhibitory Peptides Derived from Muscovy Duck (Cairina moschata) Plasma

In this study, angiotensin-converting enzyme inhibitory peptides (ACE-IPs) derived from Muscovy duck (Cairina moschata) plasma hydrolysate (MDPH) were investigated. According to the general research protocol for bioactive peptides, the crude ACE-IPs of Muscovy duck plasma were separated and purified by ultrafiltration, gel chromatography and reversed-phase high-performance liquid chromatography (RP-HPLC). Then the components with the highest ACE inhibition potential were selected for identification. Finally, the inhibition mechanism was explored by molecular docking and in silico simulated digestion. A total of 121 peptides was detected, and five were screened for synthesis verification and molecular docking. The peptide VALSSLRP revealed high ACE inhibitory activity (91.67 ± 0.73%) because this peptide bound tightly to the S1' pocket and formed 3 hydrogen bonds. Meaningfully, this work provides some new information about the generation of ACE-IPs derived from duck blood plasma.

Transcriptomics and Metabolomics Analysis of the Ovaries of High and Low Egg Production Chickens

Simple Summary

The ovarian tissues of different breeds of hens during egg production were investigated through transcriptomics and metabolomics to provide a more comprehensive understanding of the molecular mechanisms of the ovary during egg production. Four genes involved in egg production were predicted by the transcriptome, including P2RX1, INHBB, VIPR2, and FABP3, and several close metabolites associated with reproduction were identified in the metabolome, including 17α-hydroxyprogesterone, iloprost, spermidine and adenosine. Correlation analysis of specific differential genes and differential metabolites identified important gene-metabolite pairs VIPR2–Spermidine and P2RX1–Spermidine in the reproductive process.

Abstract

Egg production is a pivotal indicator for evaluating the fertility of poultry, and the ovary is an essential organ for egg production and plays an indispensable role in poultry production and reproduction. In order to investigate different aspects of egg production mechanisms in different poultry, in this study we performed a metabolomic analysis of the transcriptomic combination of the ovaries of two chicken breeds, the high-production Ninghai indigenous chickens and the low-production Wuliangshan black-boned chickens, to analyze the biosynthesis and potential key genes and metabolic pathways in the ovaries during egg production. We predicted four genes in the transcriptomic that are associated with egg production, namely P2RX1, INHBB, VIPR2, and FABP3, and identified three important pathways during egg production, “Calcium signaling pathway”, “Neuroactive ligand–receptor interaction” and “Cytokine–cytokine receptor interaction”, respectively. In the metabolomic 149 significantly differential metabolites were identified, 99 in the negative model and 50 in the positive model, of which 17α-hydroxyprogesterone, iloprost, spermidine, and adenosine are important metabolites involved in reproduction. By integrating transcriptomics and metabolomics, the correlation between specific differential genes and differential metabolites identified important gene-metabolite pairs “VIPR2-Spermidine” and “P2RX1-Spermidine” in egg production. In conclusion, these data provide a better understanding of the molecular differences between the ovaries of low- and high-production hens and provide a theoretical basis for further studies on the mechanics of poultry egg production.

Dietary Bacitracin Methylene Disalicylate Improves Growth Performance by Mediating the Gut Microbiota in Broilers

The growth performance of livestock and poultry has always been a concern. However, much work is currently focused on the selection of breeds and diets to improve the growth performance of livestock and poultry. Furthermore, numerous studies have shown that the gut microbiota is closely related to the growth performance of livestock and poultry. At present, there are many reports on the impact of antibiotic intervention on the structure of gut microbiota. However, there are few reports on the influence of antibiotic intervention on the structure of intestinal microbes and the effect of this change on growth performance. Bacitracin methylene disalicylate (BMD) intervention changes the microbial structure in the caecum of broilers at different growth stages, as shown in this study. To further reveal the potential relationship between gut microbiota changes and growth performance caused by BMD intervention, correlation analysis was used for analysis. A total of 144 1-day-old male Cobb-Vantress were randomly divided into two groups. In addition to antibiotic-free starter mash diets, starter mash diets supplemented with 55 mg/kg BMD were also used, called the CON group and the BMD group, and lasted 28 days. (1) These study results showed that adding BMD to the diet had a significant effect on the growth performance of broilers. Compared with the CON group, the body weight of the BMD group increased significantly by 11.08% and 20.13% on Days 14 and 28, respectively (p < 0.05). Similarly, at 0−14, 14−28 and 0−28 days of age, the average daily gain of the BMD group increased significantly by 12.28%, 24.49% and 20.80%, respectively. The average daily feed intake of the BMD group increased significantly by 18.28%, 27.39% and 24.97% (p < 0.05). In addition, at 0−28 days of age, the feed conversion ratio increased significantly by 5.5% (p < 0.05). (2) Alpha diversity results show that BMD intervention has an impact on gut microbiota at different growth stages. (3) The early intervention significantly affected 7 taxa by Day 14, followed by 22 taxa by Day 28, which is similar to the results in the caecal flora. Compared with the CON group, the Christensenellaceae R-7 group had the highest linear discriminant analysis (LDA) score on Day 28. In addition, Pearson’s correlation analysis showed that the Lachnospiraceae FCS020 group was significantly negatively correlated with growth performance. In general, these results indicate that dietary supplementation of BMD has an effect on broiler gut microbiota structure and growth performance. However, changes in growth performance may be caused by the gut microbiota structure.

Ileal Microbiota Alters the Immunity Statues to Affect Body Weight in Muscovy Ducks

The ileum is mainly responsible for food absorption and nutrients transportation. The microbes in its intestinal lumen play an essential role in the growth and health of the host. However, it is still unknown how the ileal microbes affect the body weight of the host. In this study, we used Muscovy ducks as an animal model to investigate the relationship between the ileal microbes and body weight and further explore the potential mechanism. The ileum tissue and ileal contents of 200 Muscovy ducks were collected for mRNA extraction and real-time quantitative PCR, as well as DNA separation and 16S rRNA gene sequencing. With body weight being ranked, the bottom 20% (n = 40) and top 20% (n = 40) were set as the low and high groups, respectively. Our results showed that in the ileum of Muscovy ducks, the Bacteroides, Firmicutes, and Proteobacteria were the predominant phyla with the 10 most abundant genera, namely Candidatus Arthromitus, Bacteroides, Streptococcus, Vibrio, Romboutsia, Cetobacterium, Clostridium sensu stricto 1, Terrisporobacter, Escherichia-Shigella, and Lactobacillus. We identified Streptococcus, Escherichia-Shigella, Candidatus Arthromitus, Bacteroides, Faecalibacterium, and Oscillospira were closely correlated to the growth of Muscovy ducks. Streptococcus and Escherichia-Shigella were negatively related to body weight (BW), while Candidatus Arthromitus, Bacteroides, Faecalibacterium, and Oscillospira were positively associated with BW. In addition, we found that the relative expression levels of tight junction proteins (Claudin 1, Claudin 2, ZO-1 and ZO-2) in the high group showed an upward trend, although this trend was not significant (P > 0.05). The expression of pro-inflammatory factors (IL-1β, IL-2 and TNF-α) decreased in the high group, while the anti-inflammatory factor IL-10 increased. Of course, except IL-2, these differences were not significant (P > 0.05). Finally, the correlation analysis showed that Escherichia-Shigella was significantly positively correlated with IL-1β (P < 0.05). These findings may provide fundamental data for the development of next-generation probiotics and assist the development of strategies for changing the gut microbiota to promote the growth performance in the duck industry.

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.

Human follicular fluid shows diverse metabolic profiles at different follicle developmental stages

BACKGROUND

To investigate the metabolic profiles in the follicular fluid (FF) samples from patients undergoing in vitro fertilization (IVF) and to analyze the correlations with follicular development.

METHODS

The FF samples were obtained from participants (N = 26) who were receiving IVF under the gonadotropin-releasing hormone agonist (GnRH-a) long protocol stimulation and were collected separately from small (8-13 mm) and large (17-22 mm) follicles at the time of oocyte retrieval. Metabolomic analysis of the FF samples was performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS).

RESULTS

The results demonstrated that the size of the follicle influences the metabolic signature of the FF according to the profile and differential metabolites. Dehydroepiandrosterone (DHEA), which is enriched in steroid hormone biosynthesis, correlated negatively with the oocyte maturation rate and the high-quality embryo rate, and thus could be used to estimate the predictive diagnostic potential of follicular development.

CONCLUSION

The FF has different metabolic characteristics in different stages of follicular development. Exploring meaningful metabolites could predict follicular development, and modifications of these metabolites could influence follicular development.

Proteomics analysis of serum protein patterns in duck during aflatoxin B1 exposure

Background and Aim:

Unlike the already well-documented human serum proteome, there are still limitations regarding analyzing and interpreting the various physiological changes and disease states of the serum proteomes found in duck. Serum proteome in duck under the condition of mycotoxin contamination in feed has not yet been examined. This study aimed to introduce the characterization of the circulating proteomes in duck serum during exposure to aflatoxin B1 (AFB1).

Materials and Methods:

Duck serum samples were collected from four experimental groups, gel-based mass spectrometry was then applied, and finally, 445 proteins were identified in pulled serum sample.

Results:

Among these 445 proteins, 377 were present in at least one group from all. There were 35 proteins which were expressed when the duck was exposed to AFB1. The protein library that allows the identification of a large number of different proteins in duck serum will be enhanced by the addition of these peptide spectral data. It is noteworthy that chromodomain-helicase-DNA-binding protein 7 (CHD7) [Gallus gallus] was up-regulated in the group with the highest AFB1 contamination.

Conclusion:

CHD7 protein might be somehow relative to aflatoxicosis in the duck that causes poor performance and economic loss. Moreover, other proteins present in duck serum were also added in the protein library.