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Transcriptome analysis reveals key gene expression changes in blue catfish sperm in response to cryopreservation

ABSTRACT: Transcriptome analysis reveals key gene expression changes in blue catfish sperm in response to cryopreservation

PROVIDER: PRJNA841962 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19374488_1.fastq.gz	Fastqsanger.gz
	SRR19374488_2.fastq.gz	Fastqsanger.gz
	SRR19374489_1.fastq.gz	Fastqsanger.gz
	SRR19374489_2.fastq.gz	Fastqsanger.gz
	SRR19374490_1.fastq.gz	Fastqsanger.gz

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Transcriptome analysis reveals key gene expression changes in blue catfish sperm in response to cryopreservation

Project description:Cryopreservation of blue catfish sperm can cause variable embryo hatch rates, which is the limiting factor for hybrid catfish breeding. In this study, we investigated gene expression changes caused by cryopreservation using transcriptome profiles of fresh sperm samples and cryopreserved sperm from the same set of blue catfish.

2022-06-26 | GSE204687 | GEO

Identification of transcriptome markers in blue catfish cryopreserved sperm to predict male reproductive performance for catfish aquaculture

Project description:Catfish is the most important species in US aquaculture, accounting for 70% of freshwater production. The production of hybrids of female channel catfish (Ictalurus punctatus) and male blue catfish (I. furcatus) constitutes over 50% of the total harvest due to their superior production traits and enhanced disease resistance. However, hybrids cannot be produced naturally, and male must be euthanized for sperm collection. An appropriate storage condition is essential to preserve the sperm’s ability to fertilize eggs during the female spawning season. Cryopreservation is a widely used method for sperm storage. However, it has been shown to affect sperm gene expression in many vertebrate species. A high degree of individual variability among cryopreserved sperm was reported, resulting in huge variations in hatch rate. Since high-quality gametes are the prerequisites for hybrid catfish reproduction, in this study, we investigate the molecular mechanisms underlying male reproductive performance, which is critical for the accurate prediction of hatching rate and offspring performance in hatchery environments.

2025-05-16 | GSE296208 | GEO

Transcriptome analysis revealed potential mechanisms of channel catfish growth advantage over blue catfish in tank culture environment

Project description:Channel catfish and blue catfish represent two economically important freshwater aquaculture species in the United States. Our study aims to investigate the gene expression differences between these two catfish species by high-throughput RNA sequencing to understand their associated phenotypic differences in growth and disease resistant. Our transcriptomic analyses provide some insights into gene function differences between the two species and the molecular basis of channel catfish growth advantage in the tank culture environment.

2023-11-20 | GSE247918 | GEO

Project description:Catfish farming is the largest aquaculture industry in the U.S., where hybrid catfish produced by channel catfish, Ictalurus punctatus ♀ × blue catfish, I. furcatus ♂, represent >50% of the harvest. Typically, older blue catfish (≥5 years) are selected for artificial fertilization. However, observations at our facilities and reports from hatcheries indicate a high degree of variation in reproductive performance among individuals. Thus, it is essential to establish links between paternal age and reproductive success, as it is apparent that advanced paternal age leads to changes in reproductive performance. Since there are no prior studies regarding the changes in testis transcriptome in blue catfish males during aging, we evaluated global gene expression of testis at age 2,4,7 and 9. Significant differential expressed genes and gene ontology of pairwise comparisons between age 2 and each test age are presented and discussed.

2025-03-17 | GSE290987 | GEO

Environmental dependent heterosis and transgressive gene expression in reciprocal hybrids between the channel catfish Ictalurus punctatus and the blue catfish Ictalurus furcatus

Project description:The hybrid between female channel catfish (Ictalurus punctatus) and male blue catfish (Ictalurus furcatus) is superior in feed conversion, disease resistance, carcass yield, and harvestability compared to both parental species. However, heterosis and heterobeltiosis only occur in pond culture, and channel catfish grow much faster than the other genetic types in small culture units. This environment-dependent heterosis is intriguing, but the underlying genetic mechanisms are not well understood. In this study, phenotypic characterization and transcriptomic analyses were performed in the channel catfish, blue catfish, and their reciprocal F1s reared in tanks. The results showed that the channel catfish is superior in growth-related morphometrics, presumably due to significantly lower innate immune function, as investigated by reduced lysozyme activity and alternative complement activity. RNA-seq analysis revealed that genes involved in fatty acid metabolism/transport are significantly upregulated in channel catfish compared to blue catfish and hybrids, which also contributes to the growth phenotype. Interestingly, hybrids have a 40-80% elevation in blood glucose than the parental species, which can be explained by a phenomenon called transgressive expression (overexpression/underexpression in F1s than the parental species). A total of 1,140 transgressive genes were identified in F1 hybrids, indicating that 8.5% of the transcriptome displayed transgressive expression. Transgressive genes upregulated in F1s are enriched for glycan degradation function, directly related to the increase in blood glucose level. This study is the first to explore molecular mechanisms of environment-dependent hetero-sis/heterobeltiosis in a vertebrate species and sheds light on the regulation and evolution of heterosis vs. hybrid incompatibility.

2022-01-05 | GSE186603 | GEO

Effect of cryopreservation on bull sperm proteins

Project description:In the present study, we evaluated the alteration of protein profile of spermatozoa during the different stages of cryopreservation i.e., freshly ejaculated sperm, equilibrated sperm, and cryopreserved sperm in crossbred bulls (Bos taurus * Bos indicus). It was found that the equilibration step of cryopreservation itself caused major changes in the proteome of spermatozoa. Therefore, cryopreservation protocols should be tailored in such a way that it minimize sperm proteome alterations.

2022-02-25 | PXD031895 | JPOST Repository

Identification of transcriptome markers in blue catfish cryopreserved sperm to predict male reproductive performance for catfish aquaculture

Project description:Identification of transcriptome markers in blue catfish cryopreserved sperm to predict male reproductive performance for catfish aquaculture

| PRJNA1258209 | ENA

Transcriptomic profiling of the livers of blue catfish (Ictalurus furcatus) after infection with Edwardsiella ictaluri

Project description:We have utilized a high-density oligonucleotide microarray for catfish in order to study the transcriptomic responses of blue catfish following infection with E. ictaluri and to identify and develop important immune-related markers for future characterization and genetic mapping. Microarray analysis of the transcriptome profile of the blue catfish liver following infection with the Gram negative bacterium led to the identification of 103 differentially expressed transcripts. Results indicated the strong upregulation of several pathways likely involved in the inflammatory immune response. A multifaceted response to infection was observed, encompassing the complement cascade, iron regulation, inflammatory cell signaling, and antigen processing and presentation. The induction of several components of the MHC class I-related pathway following infection with an intracellular bacterium is reported here for the first time in fish. Taken together, the microarray results add to our understanding of the teleost immune responses and will provide a solid foundation for future functional characterization, genetic mapping, and QTL analysis of immunity-related genes from catfish. Keywords: Disease state analysis

2007-11-22 | GSE6350 | GEO

Transcriptome Analysis Reveals Key Gene Expression Changes in Blue Catfish Sperm in Response to Cryopreservation.

Project description:The hybrids of female channel catfish (Ictalurus punctatus) and male blue catfish (I. furcatus) account for >50% of US catfish production due to superior growth, feed conversion, and disease resistance compared to both parental species. However, these hybrids can rarely be naturally spawned. Sperm collection is a lethal procedure, and sperm samples are now cryopreserved for fertilization needs. Previous studies showed that variation in sperm quality causes variable embryo hatch rates, which is the limiting factor in hybrid catfish breeding. Biomarkers as indicators for sperm quality and reproductive success are currently lacking. To address this, we investigated expression changes caused by cryopreservation using transcriptome profiles of fresh and cryopreserved sperm. Sperm quality measurements revealed that cryopreservation significantly increased oxidative stress levels and DNA fragmentation, and reduced sperm kinematic parameters. The present RNA-seq study identified 849 upregulated genes after cryopreservation, including members of all five complexes in the mitochondrial electron transport chain, suggesting a boost in oxidative phosphorylation activities, which often lead to excessive production of reactive oxygen species (ROS) associated with cell death. Interestingly, functional enrichment analyses revealed compensatory changes in gene expression after cryopreservation to offset detrimental effects of ultra-cold storage: MnSOD was induced to control ROS production; chaperones and ubiquitin ligases were upregulated to correct misfolded proteins or direct them to degradation; negative regulators of apoptosis, amide biosynthesis, and cilium-related functions were also enriched. Our study provides insight into underlying molecular mechanisms of sperm cryoinjury and lays a foundation to further explore molecular biomarkers on cryo-survival and gamete quality.

| S-EPMC9316979 | biostudies-literature

Stomach samples of blue catfish

Project description:Stomach content of blue catfish (Ictalurus furcatus)

| PRJNA509916 | ENA