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Transcriptome-wide m6A methylation of Wuhua yellow-feathered chicken ovary revealed potential molecular mechanisms underlying the low egg performance

ABSTRACT: Transcriptome-wide m6A methylation of Wuhua yellow-feathered chicken ovary revealed potential molecular mechanisms underlying the low egg performance

PROVIDER: PRJNA1000480 | ENA |

REPOSITORIES: ENA

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Transcriptome-wide m6A methylation of Wuhua yellow-feathered chicken ovary revealed potential molecular mechanisms underlying the low egg performance

Project description:RNA N6-melthyladenosine has been suggested to play important roles in various biological processes. Chicken ovary development is a process controlled by complex gene regulations. In this study, transcriptome-wide m6A methylation of the Wuhua yellow-feathered chicken ovaries before and after sexual maturation was profiled to identify potential molecular mechanisms underlying chicken ovary development. The results showed that m6A levels of mRNAs changed dramatically during sexual maturity. A total of 1476 differential m6A peaks were found between these two stages with 662 significantly up-regulated methylation peaks and 814 down-regulated methylation peaks after sexual maturation. A positive correlation was found between the m6A peaks and gene expression levels. Functional enrichment analysis indicated that apoptosis related pathways might be the key molecular regulatory pathway underlying the poor reproductive performance of Wuhua yellow-feathered chicken. The fine expressional regulation of genes related to follicles development and follicle atresia controlled by m6A during the maturity results in the poor reproductive performance in the Wuhua yellow-feathered chicken. However, the regulatory mechanisms are still unclear, thus more further studies are required. The pathways and corresponding candidate genes found here may be useful for molecular design breeding for improving egg production performance in Chinese local chicken breed, and it will also benefit for the genetic resource protection of valuable avian species.

2023-11-01 | GSE239644 | GEO

Comparative Transcriptome Profiling of mRNA and lncRNA of Ovaries in High and Low Egg Production Performance in Domestic Pigeons (Columba livia)

Project description:To evaluate the lncRNAs and mRNAs in ovaries associated with egg production performance in domestic pigeons, high-throughput RNA sequencing of ovaries between high and low egg production performance groups were performed and analyzed in this study.

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Ovary transcriptome profiling via application of artificial intelligence predicts egg quality in striped bass

Project description:We modeled profiles of ovary gene expression and their relationship to egg quality, evaluated as production of viable mid-blastula stage embryos, in striped bass (Morone saxatilis) using artificial neural networks and supervised machine learning. Collective changes in expression of a limited suite of genes (233) representing only 2% of the queried ovary transcriptome explained >90% of the eventual variance in embryo survival. Egg quality related to minor changes in expression (≤0.2-fold), with most gene transcripts making minor contribution (<1%) to the overall prediction of egg quality. Correlation analyses of this suite of candidate genes indicated that collective dysfunction of the ubiquitin-26S proteasome, COP9 signalosome, and subsequent control of the cell cycle engenders embryonic developmental incompetence in striped bass. Our results show that the transcriptomic signature evidencing this dysfunction is of, and therefore likely to influence, egg quality, a biologically complex trait that is crucial to reproductive fitness.

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Association of egg mass and egg sex in chicken

Project description:Association of egg mass and egg sex: gene expression analysis from maternal RNA in the germinal disc region of layer hens (Gallus gallus)

2015-01-29 | GSE59041 | GEO

Ovary transcriptome profiling via application of artificial intelligence predicts egg quality in striped bass

Project description:We modeled profiles of ovary gene expression and their relationship to egg quality, evaluated as production of viable mid-blastula stage embryos, in striped bass (Morone saxatilis) using artificial neural networks and supervised machine learning. Collective changes in expression of a limited suite of genes (233) representing only 2% of the queried ovary transcriptome explained >90% of the eventual variance in embryo survival. Egg quality related to minor changes in expression (M-bM-^IM-$0.2-fold), with most gene transcripts making minor contribution (<1%) to the overall prediction of egg quality. Correlation analyses of this suite of candidate genes indicated that collective dysfunction of the ubiquitin-26S proteasome, COP9 signalosome, and subsequent control of the cell cycle engenders embryonic developmental incompetence in striped bass. Our results show that the transcriptomic signature evidencing this dysfunction is of, and therefore likely to influence, egg quality, a biologically complex trait that is crucial to reproductive fitness. Female striped bass were sorted into groups (N=8 each) producing M-bM-^@M-^Xhigh qualityM-bM-^@M-^Y or M-bM-^@M-^Xlow qualityM-bM-^@M-^Y eggs (spawns) based upon the percentage of eggs bearing viable 4 h embryos. Spawns with >50% of eggs producing 4 h embryos were considered to be of high quality and spawns with <30% of eggs producing 4 h embryos were considered to be of low quality.

2012-12-10 | E-GEOD-42804 | biostudies-arrayexpress

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

Project description:Purpose: To identify the key regulatory genes and pathways involved in chicken high egg productivon in HPG axis. Methods: A total of 856 Chinese Luhua chicken was raised in poultry breeding farm of Sichuan Agricultural University, 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, integrated with RNA-seq sequencing of samples of HPG axis (hypothalamus, pituitary gland and ovary) from three HEP and three LEP chickens at 300 days of age. Results: A total 86.7 Gb RNA-seq sequences were generated, and with each library averaged 5.1 Gb. Conclusions: These important data might improve our understanding of reproductive biology of Luhua chicken by providing comprehensive gene expression information at transcriptional level. We indicate that our approach will contribute to the isolation of effective molecular markers that can be used in genetic breeding programs in Chinese domestic Luhua chicken.

2019-12-07 | GSE141588 | GEO

Differential circular RNAs expression in ovary during oviposition in honey bees

Project description:The present study is the first study to identify the involvement of circRNAs in the ovary activation and oviposition regulation processes in honey-bee queens.CircRNAs expresion profiles were examined in ovaries of virgin queens, egg-laying queens, egg-laying inhibited queens and egg-laying recovery queens.

2018-06-07 | GSE103860 | GEO

Protein composition of the chicken egg tooth.

Project description:The egg teeth of chicken of the developmental stage 36 according to Hamburger and Hamilton (about 10 days of egg incubation at 37 °C) were sampled to investigate the protein composition of the egg tooth.

2024-05-21 | PXD048875 | Pride

Comparative transcriptome analysis reveals critical genes/pathways related yolk precursor synthesis in livers of Guangxi Ma chicken with different egg laying rate

Project description:Liver tissues of Guangxi Ma chicken from 32-week old with m performance, 50-week old with high and low laying performance, and 72-week old with high and low laying performance were collected and sequenced in quadruplicate using RNA-seq. The sequences were double-ended sequenced on the DNBSEQ sequencing platform. The sequence reads were quality controlled and then aligned with genomic sequences using HISAT2 program, quantified by featureCounts program, and gene expression levels were verified by qRT-PCR with SYBR Green detection. The results will be helpful to explore the factors that affecting laying performance from the perspective of yolk synthesis and provide a theoretical basis for improving the egg production of Guangxi Ma chicken.

2022-10-08 | GSE193655 | GEO

Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum

Project description:Overfeeding reduces laying performance in broiler breeder hens (Gallus gallus domesticus). To unravel the effect of feeding regimes on energy metabolism and egg production, high-throughput RNA sequencing was utilized to identify differentially expressed genes (DEGs) in ovary, liver and adipose tissues of broiler chickens under ad libitum and restricted feeding. The transcriptome analysis showed that 289, 388 and 204 DEGs were identified in the adipose tissue, liver and ovary, respectively, between ad libitum and restricted feeding groups. Bioinformatics analysis by STRING further revealed DEGs were significantly enriched in phagosome pathway, lipid transport and location biological process, and the molecular function of lipid transporter activity and nutrient reservoir activity in ovary; the pathways of “steroid hormone biosynthesis” and “metabolism of xenobiotics by cytochrome P450”, and the molecular function of nutrient reservoir activity in adipose tissue; the metabolic pathways, Jak-STAT signaling pathway and PPAR signaling pathway in liver.

2019-05-08 | GSE113722 | GEO

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