Integrated Analysis of mRNA and miRNA Expression Profiles in the Ovary of Oryctolagus cuniculus in Response to Gonadotrophic Stimulation

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.

Negative effects of heat stress on ovarian tissue in female rabbit

Numerous studies have highlighted the role of miRNA in the deformation and necrosis of cells of ovarian tissue caused by heat stress (HS), which ultimately affects ovarian function. Although the role of small RNAs has been investigated in alterations in ovarian tissue functioning in response to HS, the expression profile of ovarian miRNA has been explored to a lesser extent. In this study, female rabbits were subject to HS treatment by using electrical heater. The current work demonstrated that HS could significantly change physiological performance of female rabbits including body weight, rectal temperature and relative ovary weight, and significantly reduce serum IL-2, IL-8, CAT, and GSH-Px concentrations by enzyme-linked immunosorbent assay (ELISA) technique. As a result, an increase in apoptosis in ovarian cells, as well as unhealthy follicles, were observed by Hematoxylin-eosin (HE) and TUNEL staining. Additionally, small RNA-seq revealed changes in the miRNA expression profile of rabbit ovaries under HS. Five hundred fourteen miRNAs were obtained including known miRNAs 442 and novel miRNAs 72. Among these miRNAs, 23 miRNAs were significantly expressed under HS. Eleven differentially expressed miRNAs (DE miRNAs) and 9 their predicted targets were confirmed by qPCR, which were expected miRNA-mRNA negative regulation pattern. Among the DE miRNAs and targets, miR-141-39 may target COQ6, miR-449a-5p and miR-34c-5p may control RFC5 and RTN2 together, miR-449a-5p may target ACADVL, miR-34c-5p potentially targets Bcl-2 and miR-196b-5p potentially regulates CASK and HOXB6. Thus, the current work suggested the negative effects of HS on the ovarian tissue of female rabbits, and in conclusion these changes could be caused by decreased serum IL-2, IL-8, CAT and GSH-Px levels, increased ovarian apoptosis, and changed the expression of miRNAs.

Oocyte-Specific Knockout of Histone Lysine Demethylase KDM2a Compromises Fertility by Blocking the Development of Follicles and Oocytes

The methylation status of histones plays a crucial role in many cellular processes, including follicular and oocyte development. Lysine-specific demethylase 2a (KDM2a) has been reported to be closely associated with gametogenesis and reproductive performance, but the specific function and regulatory mechanism have been poorly characterized in vivo. We found KDM2a to be highly expressed in growing follicles and oocytes of mice in this study. To elucidate the physiological role of Kdm2a, the zona pellucida 3-Cre (Zp3-Cre)/LoxP system was used to generate an oocyte Kdm2a conditional knockout (Zp3-Cre; Kdm2a^flox/flox, termed Kdm2a cKO) model. Our results showed that the number of pups was reduced by approximately 50% in adult Kdm2a cKO female mice mating with wildtype males than that of the control (Kdm2a^flox/flox) group. To analyze the potential causes, the ovaries of Kdm2a cKO mice were subjected to histological examination, and results indicated an obvious difference in follicular development between Kdm2a cKO and control female mice and partial arrest at the primary antral follicle stage. The GVBD and matured rates of oocytes were also compromised after conditional knockout Kdm2a, and the morphological abnormal oocytes increased. Furthermore, the level of 17β-estradiol of Kdm2a cKO mice was only 60% of that in the counterparts, and hormone sensitivity decreased as the total number of ovulated and matured oocytes decreased after superovulation. After deletion of Kdm2a, the patterns of H3K36me2/3 in GVBD-stage oocytes were remarkedly changed. Transcriptome sequencing showed that the mRNA expression profiles in Kdm2a cKO oocytes were significantly different, and numerous differentially expressed genes were involved in pathways regulating follicular and oocyte development. Taken together, these results indicated that the oocyte-specific knockout Kdm2a gene led to female subfertility, suggesting the crucial role of Kdm2a in epigenetic modification and follicular and oocyte development.

Dynamics of Known Long Non-Coding RNAs during the Maternal-to-Zygotic Transition in Rabbit

The control of pre-implantation development in mammals undergoes a maternal-to-zygotic transition (MZT) after fertilization. The transition involves maternal clearance and zygotic genome activation remodeling the terminal differentiated gamete to confer totipotency. In the study, we first determined the profile of long non-coding RNAs (lncRNAs) of mature rabbit oocyte, 2-cell, 4-cell, 8-cell, and morula embryos using RNA-seq. A total of 2673 known rabbit lncRNAs were identified. The lncRNAs exhibited dynamic expression patterns during pre-implantation development. Moreover, 107 differentially expressed lncRNAs (DE lncRNAs) were detected between mature oocyte and 2-cell embryo, while 419 DE lncRNAs were detected between 8-cell embryo and morula, consistent with the occurrence of minor and major zygotic genome activation (ZGA) wave of rabbit pre-implanted embryo. This study then predicted the potential target genes of DE lncRNAs based on the trans-regulation mechanism of lncRNAs. The GO and KEGG analyses showed that lncRNAs with stage-specific expression patterns promoted embryo cleavage and synchronic development by regulating gene transcription and translation, intracellular metabolism and organelle organization, and intercellular signaling transduction. The correlation analysis between mRNAs and lncRNAs identified that lncRNAs ENSOCUG00000034943 and ENSOCUG00000036338 may play a vital role in the late-period pre-implantation development by regulating ILF2 gene. This study also found that the sequential degradation of maternal lncRNAs occurred through maternal and zygotic pathways. Furthermore, the function analysis of the late-degraded lncRNAs suggested that these lncRNAs may play a role in the mRNA degradation in embryos via mRNA surveillance pathway. Therefore, this work provides a global view of known lncRNAs in rabbit pre-implantation development and highlights the role of lncRNAs in embryogenesis regulation.

The application of reduced dietary crude protein levels supplemented with additional amino acids in laying ducks

This study was aimed at studying use of reduced dietary crude protein (CP) level supplemented with additional amino acids in laying ducks. A total of 720 Jingjiang ducks (50 wk) were randomly assigned to 5 treatments and fed 5 basal diets with CP levels at 17.5, 16.5, 15.5, 14.5, or 13.5%, with additional amino acids added to each diet for 12 wk. Each treatment had 6 replicates of 24 ducks each. Dietary CP levels affected (P < 0.05) egg production and mass of laying ducks, and there was a linear and quadratic decrease with decreasing CP levels (P < 0.05). Dietary CP levels did not affect egg weight and feed conversion ratio (FCR), but egg weight decreased linearly (P < 0.05); FCR increased linearly and quadratically (P < 0.05) with decreasing CP levels. There were no significant differences in egg quality among the different CP levels (P > 0.05). Ovarian weight, total and mean weight of preovulatory follicles, and total weight of small yellow follicles (SYF) were decreased by dietary CP levels (linear, P < 0.01 and quadratic, P < 0.05). The oviductal weight decreased linearly (P < 0.05), and the number of SYF decreased linearly and quadratically with decreasing CP levels (P < 0.05). The serum estradiol content decreased linearly with dietary CP levels (P < 0.05). The serum contents of luteinizing hormone, prolactin, and progesterone decreased (P < 0.05), linearly and quadratically (both P < 0.01) with decreasing CP levels. The serum contents of creatinine (CRE), triglycerides (TG), total cholesterol (TC), and alanine aminotransferase (ALT) activity were affected (P < 0.05) by different dietary CP levels. The total protein content increased linearly (P < 0.05), TC content increased quadratically (P < 0.05), and contents of albumin, CRE, TG, and phosphorus, and activities of aspartate aminotransferase and ALT increased linearly and quadratically (both P < 0.05) with decreasing CP levels. Overall, reduced dietary CP levels with addition of amino acids affected the laying performance, the development of reproductive organs and ovarian follicles, serum hormones, and biochemical indices of laying ducks. Dietary CP levels can be reduced to 14.5% with additional amino acid supplementation for 12 wk in laying ducks without negative effect on laying performance and egg quality.

Estimation of dietary manganese requirement for laying duck breeders: effects on productive and reproductive performance, egg quality, tibial characteristics, and serum biochemical and antioxidant indices

This study was aimed at estimating the dietary manganese (Mn) requirement for laying duck breeders. A total of 504 Longyan duck breeders (body weight: 1.20 ± 0.02 kg) aged 17 wk were randomly allocated to 6 treatments. The birds were fed with a basal diet (Mn, 17.5 mg/kg) or diets supplemented with 20, 40, 80, 120, or 160 mg/kg of Mn (as MnSO₄·H₂O) for 18 wk. Each treatment had 6 replicates of 14 ducks each. As a result of this study, dietary Mn supplementation did not affect the productive performance of laying duck breeders in the early laying period (17–18 wk), but affected egg production, egg mass, and feed conversion ratio (FCR) from 19 to 34 wk (P < 0.05), and there was a linear and quadratic effect of supplement level (P < 0.05). The proportion of preovulatory ovarian follicles increased (P < 0.01) linearly and quadratically, and atretic follicles (weight and percentage) decreased (P < 0.05) quadratically with dietary Mn supplementation. The density and breaking strength of tibias increased (quadratic; P < 0.05), the calcium content of tibias decreased (linear, quadratic; P < 0.01), and Mn content increased (linear, quadratic; P < 0.001) with increase in Mn. The addition of Mn had a quadratic effect on serum contents of estradiol, prolactin, progesterone, luteinizing hormone, and follicle-stimulating hormone (P < 0.001). Dietary Mn supplementation decreased serum contents of total protein (linear, P < 0.05), glucose (quadratic, P < 0.05), total bilirubin, triglycerides, total cholesterol, low-density lipoprotein cholesterol, and calcium (linear, quadratic; P < 0.05). The serum total antioxidant capacity and total and Mn-containing superoxide dismutase activities increased (linear, quadratic; P < 0.001), and malondialdehyde content decreased (linear, quadratic; P < 0.001) in response to Mn supplemental levels. The dietary Mn requirements, in milligram per kilogram for a basal diet containing 17.5 mg/kg of Mn, for Longyan duck breeders from 19 to 34 wk of age were estimated to be 84.2 for optimizing egg production, 85.8 for egg mass, and 95.0 for FCR. Overall, dietary Mn supplementation, up to 160 mg/kg of feed, affected productive performance, tibial characteristics, and serum biochemical and antioxidant status of layer duck breeders. Supplementing this basal diet (17.5 mg/kg of Mn) with 85 to 95 mg/kg of additional Mn was adequate for laying duck breeders during the laying period.

Dynamics of the Transcriptome and Accessible Chromatin Landscapes During Early Goose Ovarian Development

In contrast to the situation in mammals, very little is known about the molecular mechanisms regulating early avian ovarian development. This study aimed to investigate the dynamic changes in the histomorphology as well as the genome-wide transcriptome and chromatin accessibility landscapes of the goose ovary during late embryonic and early post-hatching stages. Results from hematoxylin-eosin, periodic acid-Schiff, and anti-CVH immunohistochemical stainings demonstrated that programmed oocyte loss, oocyte nest breakdown and primordial follicle formation, and the primordial-to-secondary follicle transition occur during the periods from embryonic day 15 (E15) to post-hatching day 0 (P0), from P0 to P4, and from P4 to P28, respectively. RNA-seq and ATAC-seq analyses revealed dynamic changes in both the ovarian transcriptome and accessible chromatin landscapes during early ovarian development, exhibiting the most extensive changes during peri-hatching oocyte loss, and moreover, differences were also identified in the genomic distribution of the differential ATAC-seq peaks between different developmental stages, suggesting that chromatin-level regulation of gene expression is facilitated by modulating the accessibility of different functional genomic regions to transcription factors. Motif analysis of developmental stage-selective peak regions identified hundreds of potential cis-regulatory elements that contain binding sites for many transcription factors, including SF1, NR5A2, ESRRβ, NF1, and THRβ, as well as members of the GATA, SMAD, and LHX families, whose expression fluctuated throughout early goose ovarian development. Integrated ATAC-seq and RNA-seq analysis suggested that the number and genomic distribution of the newly appeared and disappeared peaks differed according to developmental stage, and in combination with qRT-PCR validation potentiated the critical actions of the DEGs enriched in cell cycle, MAPK signaling, and FoxO signaling pathways during peri-hatching oocyte loss and those in ligand-receptor interaction, tissue remodeling, lipid metabolism, and Wnt signaling during primordial follicle formation and development. In conclusion, our study provides a framework for understanding the transcriptome and accessible chromatin dynamics during early avian ovarian development and a new avenue to unravel the transcriptional regulatory mechanisms that facilitate the occurrence of relevant molecular events.