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

ABSTRACT: 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.

ORGANISM(S): Morone saxatilis

PROVIDER: GSE42804 | GEO | 2012/12/10

SECONDARY ACCESSION(S): PRJNA183347

REPOSITORIES: GEO

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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 (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

Gene expression profiling of white bass when fed fish meal or fish meal replacement diets

Project description:White bass (Morone chrysops) are a popular sportfish throughout the southern United States, and one parent of the commercially successful hybrid striped bass (M. chrysops x M. saxatilis). Currently, white bass are cultured using diets formulated for other carnivorous fish, such as largemouth bass (Micropterus salmoides) or hybrid striped bass and contain a significant percentage of marine fish meal. Since there are no studies regarding the utilization of alternative proteins in this species, we evaluated global gene expression of white bass fed diets in which fish meal was partially or totally replaced by various combinations of soybean meal, poultry by-product meal, canola meal, soy protein concentrate, wheat gluten, or a commercial protein blend (Pro-Cision). Significant differential expressed genes and gene ontology of pairwise comparisons between control diet and each test diet are presented and discussed.

2024-02-14 | GSE220235 | GEO

Morone saxatilis

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

| PRJNA183347 | ENA

Morone saxatilis strain:NCSU 1

Project description:The striped bass, Morone saxatilis, overview

| PRJNA43383 | ENA

Gene expression profiles of white bass (Morone chrysops) and hybrid striped bass (M. chrysops x M. saxatilis) gill tissue over time following Flavobacterium covae exposure

Project description:Columnaris disease is a prevalent disease in freshwater environments worldwide caused by the ubiquitous aquatic bacterium Flavobacterium species. Adhesion to the external mucosal surfaces of fishes is the initial stage of infection, and the gills specifically have been identified as both a primary target and release site for this pathogen. Previous research has indicated that a predominant US aquaculture product, the hybrid striped bass (Morone chrysops x M. saxatilis), is more susceptible to infection with Flavobacterium columnare (covae) than the maternal white bass (M. chrysops) parental species. Therefore, to further elucidate the differences between these fish we conducted a transcriptomic profiling study examining the differences of gene expression in gill mucosal tissue over time after exposure to F. covae isolate LSU-066-04. Combined with previous work, these data provide a greater understanding of host immune response to a common pathogen in moronids.

2024-05-09 | GSE246056 | GEO

Morone saxatilis

Project description:An ovarian transcriptome for all maturational stages of a highly advanced perciform fish, the striped bass, Morone saxatilis

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Mechanism of Hyperproteinemia-Induced Damage to Female Reproduction in a Genetic Silkworm Model

Project description:Hyperproteinemia is a metabolic disorder characterized by abnormally elevated plasma protein concentrations (PPC) in humans and animals. Here, a genetic silkworm model with high PPC was employed to investigate the effect of elevated PPC on female reproduction. Transcriptomic analysis revealed that high PPC induces downregulation of the ovarian development-related genes and disrupts ovarian sugar metabolism. Biochemical and endocrinal analyses revealed that high PPC increases trehalose and glucose levels in hemolymph and glycogen content in the fat body through activation of the gluconeogenic pathway and inhibition of the IIS-AKT pathway, thus disrupting characteristic metabolic homeostasis of sugar in the ovary. These resulted in ovarian developmental delay as well as reduced number and poor quality of eggs. Insulin supplementation effectively increased egg numbers by lowering blood sugar. These collective results provide new insights into the mechanisms by which high PPC negatively affects female reproduction and support the potential therapeutic effects of insulin.

2023-09-06 | GSE242203 | GEO

Project description:Intestinal bacterial composition in hybrid striped bass

| PRJNA718291 | ENA

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

Integration of lncRNA-miRNA-mRNA reveals novel insights into reproductive regulation in honey bees

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

2017-09-14 | GSE93028 | GEO

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