Supplying high-quality sperm from blue catfish, Ictalurus furcatus is a requirement for channel catfish, I. punctatus female x blue catfish male hybrid production. Storing sperm at low temperatures (4 degrees C) is a simple and inexpensive method to facilitate hatchery production. Our study objective was to determine the effect of short-term storage on sperm quality and microbiome dynamics in blue catfish. Mature males (n = 8) were selected, testes dissected, milt extracted and stored at 4 degrees C. Sperm swimming kinematics [motility, curvilinear velocity (VCL), average path velocity (VAP), straight-line velocity (VSL)], viability, and lipid peroxidation were quantified in conjunction with microbial community composition at 0, 24, 48, and 72 h post-storage. Sperm kinematics and viability declined during short-term storage, while malondialdehyde (MDA), an indicator of lipid peroxidation, significantly increased within the first 24 h. Time-specific microbiome changes were observed in sperm during short-term storage. Amplicon sequence variant (ASV) richness was significantly decreased at 72 h. Evenness and Shannon index of bacterial communities significantly decreased at 24 h and remained unchanged from 48 to 72 h. The ASVs belonging to potentially harmful bacterial species, Pseudomonas fluorescens and Aeromonas hydrophila, showed significantly higher abundances following 48 and 72 h. Our results demonstrate changes in sperm quality and microbial communities during short-term storage. These findings can be used to improve sperm storage techniques for hybrid catfish hatchery facilities.

Production traits such as growth, disease resistance, and fatty acid content in engineered animals are anticipated to be enhanced via transgenesis (TG) or genome editing (GE). It is, however, unclear whether this expectation is upheld when making global comparisons across taxa. In this study, we performed a meta-analysis of 154 research papers covering 72 species and 55 genes, with the aim of quantifying and comparing the effects of TG and GE on animal production traits through overexpressing or disrupting key genes. Although TG is more commonly used for trait enhancement, GE has more pronounced and widespread effects, particularly on growth and disease resistance traits. This is reflected in larger effect sizes and broader impacts across trait responses. Yet, we observe differences in patterns of trait enhancement that are specific to taxon and parameter. For instance, TG reduces pathogen load in chickens and cattle, but not in pigs; conversely, GE lowers virus RNA levels in pigs, but is less successful in chickens and cattle. In contrast, both TG and GE significantly increase growth rates in ray-finned fish. It is notable that, although transgenes or edited genes remain highly expressed or repressed in Filial 1 (F1) offspring, the magnitude of trait improvement is diminished compared to the founder generations. This study provides evidence-based insights to assist researchers in refining their methods and directing future investigations into trait enhancement in genetically engineered animals, while also informing policymaking.

Blue catfish (Ictalurus furcatus) is an important aquaculture species because the F1 hybrid produced from mating female channel catfish with male blue catfish exhibits strong heterosis with a number of important performance and production traits. While the mechanism of sex determination has been well studied in channel catfish, only limited work has been conducted with sex determination in blue catfish. As a first step toward understanding of sex determination in blue catfish, in this study, we conducted whole genome re-sequencing using pooled DNA of 64 male and 64 female blue catfish. Genomic variations were identified between the males and females, with a focus on the sex chromosome. We focused our work on insertions and deletions because the size differences caused by indels are amenable to PCR analysis. Here we report the identification of two Y chromosome-specific insertions. The two insertions are nearby and, therefore, a single PCR allowed amplification of the locus containing both the insertions. Upon PCR amplification, two bands were produced from males whereas only one band was produced from females, making this locus a marker suitable for genetic sex identification at any stage of blue catfish. This marker will be very useful for stock management for hybrid production and will facilitate studies to identify the sex determination gene of blue catfish.

This study evaluated the texture, flavor, and color of commercially available frozen catfish fillets, including channel catfish (Ictalurus punctatus), hybrid catfish, and swai (Pangasianodon hypophthalmus), with and without sodium phosphate treatment. Genetic testing confirmed the species' identity. Untreated fillets were redder, while phosphate-treated fillets were softer and less firm. Control swai exhibited the firmest and toughest texture, whereas phosphate-treated fillets were mushiest, as confirmed by mechanical and sensory analyses. Sensory panels noted phosphate-treated fillets as significantly softer than untreated counterparts. This study highlights texture differences between Ictalurus and Pangasianodon catfish, with swai demonstrating a chewier, firmer texture overall.

Transgenic technologies have been used for genetic improvement of catfish performance with notable success. However, these developments are useless from a commercialization standpoint without extremely efficient confinement. Transgenic sterilization has the potential to accomplish 100

There is a lack of biomarkers that can be used to predict fresh and frozen-thawed sperm quality for the commercially important blue catfish, Ictalurus furcatus. Sperm membranes are composed of various fatty acids (FAs) that have been linked to reproductive success across other animal and fish taxa, making it a potential biomarker. The objectives of this study were to (i) compare sperm FA percentages between fresh and cryopreserved male groups; and (ii) use sperm kinematics of fresh and cryopreserved males to create "good" (i.e. fast swimming sperm kinematics) and "bad" (i.e. slow swimming sperm kinematics) quality groups, then compare FA percentages of the groups to pinpoint physiological biomarkers of fresh and frozen-thawed sperm quality and cryotolerance. We found significant differences between fresh and cryopreserved sperm where fresh sperm had significantly higher ratios of n-3:n-6 and EPA:ARA as well as n-3 PUFAs and MUFAs, while cryopreserved sperm had higher concentrations of saturates. Cryopreserved sperm from good and bad males also had differences, such as a significantly higher concentration of saturates in good males and significantly higher concentrations of MUFAs, n-6 PUFAs, n-3 PUFAs, and total PUFAs in bad males. Lastly, low levels of MUFAs and n-6 PUFAs in fresh sperm resulted in higher post-thaw sperm kinematics. This knowledge can now be used to create additional biomarkers of sperm quality and to formulate the FA profile of catfish diets to improve sperm quality, thereby, improving their ability to handle the stressors of the cryopreservation process.

With the rising global demand for seafood and the challenges posed by overfishing and climate change, the aquaculture sector has become increasingly important in providing high-quality protein for human consumption. Although traditional selection breeding programs have made great strides in genetic improvement of aquaculture species over the past decades, faster and more precise breeding tools, such as genome manipulation, are needed for performance enhancement of aquaculture stock. This review presents a comprehensive overview of the current status of three major genome manipulation tools, including RNA interference (RNAi), gene transfer, and genome editing in aquaculture species, and discusses the advances made, challenges faced, and potential future directions of this fast-developing field. Taking catfish as an example, this paper reviews the specific applications of these techniques to improve traits such as growth, disease resistance, reproduction, and nutritional profiles in various commercially important fishes and crustaceans, highlighting successful applications and ongoing research efforts. We also propose CRISPR/Cas9-mediated multiplex genome editing for the knockout or replacement of multiple genes in parallel to improve multiple traits in fish. Collectively, this review provides insights into the evolving landscape of genome manipulation in aquaculture and sheds light on its implications for sustainable practices and responsible innovation.

AbstractDespite catfish being the dominant freshwater aquaculture product in the United States, catfish texture and sensory evaluation are understudied compared with other aquaculture species, and very few studies have been conducted to evaluate these traits in catfish. Texture, sensory, carcass yield, flavor, visceral fat deposition, gonadal development, and fillet color analyses were conducted on four size classes, small (<0.68 kg), medium (0.68–0.92 kg), large (0.93–1.75 kg), and extra‐large (>1.75 kg), for channel catfish (n = 456) (Ictalurus punctatus), blue catfish (n = 78) (I. furcatus), and hybrid catfish (n = 195) (channel catfish ♀ × blue catfish ♂). Within genetic type comparisons indicated that the texture traits, hardness, and chewiness and the sensory trait toughness increased with increasing size in hybrid catfish and channel catfish but were the most pronounced in channel catfish. Overall, channel catfish had the firmest fillets based on several attributes. Blue catfish were found to have differences among texture traits between the extra‐large size class and the three remaining size classes, but overall size had less of an effect compared with the channel catfish and hybrid catfish. A trend of paternal predominance was observed as the hybrid catfish was more similar to the blue catfish than the channel catfish. Hybrid catfish had the highest fillet percentage. This study is the first large‐scale analysis of texture and sensory traits within two catfish species and their interspecific hybrid at different sizes and highlights the differences in commercially important texture and sensory traits.

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

The innovations of the “Omics Era” have ushered in significant advancements in genetic improvement of agriculturally important animal species through transforming genetics, genomics and breeding strategies. These advancements were often coordinated, in part, by support provided over 30 years through the 1993–2023 National Research Support Project 8 (NRSP8, National Animal Genome Research Program, NAGRP) and affiliate projects focused on enabling genomic discoveries in livestock, poultry, and aquaculture species. These significant and parallel advances demand strategic planning of future research priorities. This paper, as an output from the May 2023 Aquaculture Genomics, Genetics, and Breeding Workshop, provides an updated status of genomic resources for United States aquaculture species, highlighting major achievements and emerging priorities. Finfish and shellfish genome and omics resources enhance our understanding of genetic architecture and heritability of performance and production traits. The 2023 Workshop identified present aims for aquaculture genomics/omics research to build on this progress: (1) advancing reference genome assembly quality; (2) integrating multi-omics data to enhance analysis of production and performance traits; (3) developing resources for the collection and integration of phenomics data; (4) creating pathways for applying and integrating genomics information across animal industries; and (5) providing training, extension, and outreach to support the application of genome to phenome. Research focuses should emphasize phenomics data collection, artificial intelligence, identifying causative relationships between genotypes and phenotypes, establishing pathways to apply genomic information and tools across aquaculture industries, and an expansion of training programs for the next-generation workforce to facilitate integration of genomic sciences into aquaculture operations to enhance productivity, competitiveness, and sustainability. This collective vision of applying genomics to aquaculture breeding with focus on the highlighted priorities is intended to facilitate the continued advancement of the United States aquaculture genomics, genetics and breeding research community and industries. Critical challenges ahead include the practical application of genomic tools and analytical frameworks beyond academic and research communities that require collaborative partnerships between academia, government, and industry. The scope of this review encompasses the use of omics tools and applications in the study of aquatic animals cultivated for human consumption in aquaculture settings throughout their life-cycle.

Optimization of xenogenesis for hybrid catfish (♀ channel catfish, Ictalurus punctatus × ♂ blue catfish, I. furcatus) embryo production was the goal. The effect of density of unsorted gonadal cells (80,000, 100,000, or 120,000 cells/fry) from blue catfish (BGCs) injected into triploid channel catfish surrogates, and BGCs or channel catfish (CGCs) into triploid white catfish (Ameiurus catus) surrogates on proliferation and colonization rates in surrogates injected at 4-, 5-, or 6-days post-hatch (DPH) was evaluated. At 45 and 90 DPH, survival and size of surrogates, and colonization/proliferation of donor cells (cell area < 150 μm2 and cluster area > 150 μm2) were evaluated. Survival and size of all surrogate species were not impacted by cell density or donor. All surrogate species injected with 100,000 cells/fry had larger cluster cell areas than those injected with 80,000 cells/fry. White catfish surrogates with BGCs and CGCs had larger cell areas when injected with 100,000 cells/fry than those injected with 80,000 cells/fry. Both cell and cluster area increased by 90 DPH for all surrogates. PCR and PKH26 red fluorescence analysis confirmed that > 89% and > 86% of surrogates were positive xenogens at 45 and 90 DPH, respectively. No surrogate type or donor was superior to the others regarding colonization and proliferation, survival or growth, thus, channel catfish or white catfish were equally effective surrogates. Potential advantages of white catfish are small size, early sexual maturity, and spawning early in the season. These findings enhance the efficiency of germ cell transplantation for commercial hybrid catfish production.

Our objectives were to investigate how permeating cryoprotectant agents (CPAs; dimethyl sulfoxide, methanol), non-permeating CPAs (trehalose at 100 and 300 mmol/L; lactose at 5 and 10 %), and freezing rates (-1.0, -5.0, -10, -20 °C/min) impact post-thaw sperm motility and velocity (VCL) in blue catfish (Ictalurus furcatus) using 2.5 mL straws. Sperm frozen with methanol at -20 °C/min had the highest kinematics (VCL = 141.8 ± 18.5 μm/s, motility = 30.5 ± 12.2 %), and showed similar results to fresh sperm (VCL = 162.7 ± 5.4 μm/s, motility = 50.2 ± 15.1 %). Adding non-permeating CPAs did not improve VCL, and sperm motility was inhibited by lactose 5-10 % and trehalose 300 mmol/L. However, trehalose 100 mmol/L increased motility by 41.2 %, relative to straws without the addition of non-permeating CPAs. Development of this new freezing technology has merit for selective breeding, large research projects, and commercial-scale production for an economically important farm animal.

Catfish accounts for ∼70 % of U.S. finfish aquaculture production with the channel catfish (Ictalurus punctatus) female by blue catfish (I. furcatus) male hybrid constituting the majority of the harvest. Issues in hatcheries persist with blue catfish due to late sexual maturity, lethal sperm collection procedures, and variable sperm quality. Our objectives were to (i) relate male morphometrics, hormones, and sperm parameters to offspring traits (i.e., hatch, survival, weight, morphometrics), and (ii) examine parental contributions to offspring traits using cryopreserved sperm. Sperm were collected from 44 males and quality indices quantified post-cryopreservation. Collected sperm were used to fertilize 3 channel catfish females, creating 44 families. Fifty offspring were reared in triplicate tanks per family from 0 to 40 days post-hatching (DPH) and offspring traits quantified. Larger males produced larger offspring at 40 DPH (R2 ≥ 0.32, P ≤ 0.03) with higher survival (R2 ≥ 0.23, P ≤ 0.05), while males with a higher gonadosomatic index produced significantly smaller offspring expressing lower hatch and survival (R2 ≥ 0.26). Sperm quality significantly correlated to offspring performance, where higher lipid peroxidation created offspring with lower survival (R2 = 0.34). Sperm kinematics were positively correlated to hatch (R2 ≥ 0.26) and significant maternal (VC = 23.2 %) and paternal(maternal) (VC = 32.1 %) variance components (VC) were detected for hatch. Maternity significantly impacted most morphometric traits (VC ≥ 20.8 %), while paternal effects increased (VC = 2.7-3.4 %) throughout early development. To conclude, paternal body measurements and sperm traits can be used to predict hatch and offspring performance. Hatcheries should account for maternal/paternal variation to select the best broodstock for reproduction.

Channel catfish (Ictalurus punctatus) is the most important aquaculture species in the United States. An interspecific hybrid made from female channel catfish and male blue catfish is increasingly becoming the predominant genotypes in the catfish industry. However, artificial hybridization is required because of reproductive isolation. While sex determination and its epigenetic regulation is well studied for channel catfish, no work has been done in blue catfish concerning its sex determination. In this study, as a first step in understanding reproductive isolation and the molecular basis of sex determination and differentiation in blue catfish, we conducted comparative transcriptome analyses of channel catfish and blue catfish, using RNA-Seq analysis of the gonad tissues. Blue catfish sex determination was speculated to be similar to that of channel catfish because they are closely related, and because its sex determination locus was also mapped to chromosome 4. However, RNA-Seq analysis revealed that hydin, the candidate master sex determination (MSD) gene of channel catfish, is not differentially expressed between males and females in blue catfish. The expression profiles of the genes within the channel catfish sex determination region (SDR) are drastically differentially expressed in blue catfish. Among the genes within the SDR, a total of 90 genes were differentially expressed in channel catfish, while only 52 were differentially expressed in blue catfish. It is important to note that of the differentially expressed genes in channel catfish, 19 are non-coding RNAs, while only one non-coding RNA was annotated in blue catfish in this region. This difference in annotation was caused by the shortage of transcriptome datasets from blue catfish. However, there are still 71 differentially expressed protein-coding genes in channel catfish but only 51 differentially expressed protein-coding genes in blue catfish. Global gene expression profiles of channel catfish and blue catfish, especially in terms of differentially expressed genes between males and females, are also highly different between the two species, suggesting that blue catfish may have different sex determination mechanisms, and explaining, at least partially, the molecular basis of reproductive isolation. Future studies are warranted to identify the MSD in blue catfish.

The confinement of transgenic fish is essential to prevent their escape and reproduction in natural ecosystems. Reversible transgenic sterilization is a promising approach to control the reproduction of transgenic fish. Therefore, the present study was conducted to develop a reversibly sterile channel catfish (Ictalurus punctatus) via the transgenic overexpression of the goldfish (Carassius auratus) glutamic acid decarboxylase (GAD) gene driven by the common carp (Cyprinus carpio) β-actin promoter to disrupt normal gamma-aminobutyric acid (GABA) regulation. Three generations of GAD-transgenic fish were produced. All studied generations showed repressed reproductive performance; however, this was not always statistically significant. In F1, 5.4% of the transgenic fish showed a sexual maturity score ≥ 4 (maximum = 5) at five years of age, which was lower (p = 0.07) than that of the control group (16.8%). In the spawning experiments conducted on F1 transgenic fish at six and nine years of age, 45.5% and 20.0% of fish spawned naturally, representing lower values (p = 0.09 and 0.12, respectively) than the percentages in the sibling control fish of the same age (83.3% and 66.7%, respectively). Four of six pairs of the putative infertile six-year-old fish spawned successfully after luteinizing hormone-releasing hormone analog (LHRHa) therapy. Similar outcomes were noted in the three-year-old F2 fish, with a lower spawning percentage in transgenic fish (20.0%) than in the control (66.7%). In one-year-old F2-generation transgenic fish, the observed mean serum gonadotropin-releasing hormone (GnRH) levels were 9.23 ± 2.49 and 8.14 ± 2.21 ng/mL for the females and males, respectively. In the control fish, the mean levels of GnRH were 11.04 ± 4.06 and 9.03 ± 2.36 ng/mL for the females and males, respectively, which did not differ significantly from the control (p = 0.15 and 0.27 for females and males, respectively). There was no significant difference in the estradiol levels of the female transgenic and non-transgenic fish in the one- and four-year-old F2-generation fish. The four-year-old F2-generation male transgenic fish exhibited significantly (p < 0.05) lower levels of GnRH and testosterone than the control fish. In conclusion, while overexpressing GAD repressed the reproductive abilities of channel catfish, it did not completely sterilize transgenic fish. The sterilization rate might be improved through selection in future generations.

Xenogenesis has been recognized as a prospective method for producing channel catfish, Ictalurus punctatus ♀ × blue catfish, I. furcatus ♂ hybrids. The xenogenesis procedure can be achieved by transplanting undifferentiated stem cells derived from a donor fish into a sterile recipient. Xenogenesis for hybrid catfish embryo production has been accomplished using triploid channel catfish as a surrogate. However, having a surrogate species with a shorter maturation period, like white catfish (Ameiurus catus), would result in reduced feed costs, labor costs, and smaller body size requirements, making it a more suitable species for commercial applications where space is limited, and as a model species. Hence, the present study was conducted to assess the effectiveness of triploid white catfish as a surrogate species to transplant blue catfish stem cells (BSCs) and channel catfish stem cells (CSCs). Triploid white catfish fry were injected with either BSCs or CSCs labeled with PKH 26 fluorescence dye from 0 to 12 days post hatch (DPH). No significant differences in weight and length of fry were detected among BSCs and CSCs injection times (0 to 12 DPH) when fry were sampled at 45 and 90 DPH (P > 0.05). The highest survival was reported when fry were injected between 4.0 to 5.5 DPH (≥ 81.2%). At 45 and 90 DPH, cell and cluster area increased for recipients injected from 0 to 5.2 DPH, and the highest cluster area values were reported between 4.0 to 5.2 DPH. Thereafter, fluorescent cell and cluster area in the host declined with no further decrease after 10 DPH. At 45 DPH, the highest percentage of xenogens were detected when fry were injected with BSCs between 4.0 to 5.0 and CSCs between 3.0 to 5.0 DPH. At 90 DPH, the highest number of xenogens were detected from 4.0 to 6.0 DPH when injected with either BSCs or CSCs. The current study demonstrated the suitability of white catfish as a surrogate species when BSCs and CSCs were transplanted into triploid white catfish between 4.0 to 6.0 DPH (27.4 ± 0.4°C). Overall, these findings allow enhanced efficiency of commercializing xenogenic catfish carrying gametes of either blue catfish or channel catfish.

CRISPR/Cas9-mediated multiplex genome editing (MGE) conventionally uses multiple single-guide RNAs (sgRNAs) for gene-targeted mutagenesis via the non-homologous end joining (NHEJ) pathway. MGE has been proven to be highly efficient for functional gene disruption/knockout (KO) at multiple loci in mammalian cells or organisms. However, in the absence of a DNA donor, this approach is limited to small indels without transgene integration. Here, we establish the linear double-stranded DNA (dsDNA) and double-cut plasmid (dcPlasmid) combination-assisted MGE in channel catfish (Ictalurus punctatus), allowing combinational deletion mutagenesis and transgene knock-in (KI) at multiple sites through NHEJ/homology-directed repair (HDR) pathway in parallel. In this study, we used single-sgRNA-based genome editing (ssGE) and multi-sgRNA-based MGE (msMGE) to replace the luteinizing hormone (lh) and melanocortin-4 receptor (mc4r) genes with the cathelicidin (As-Cath) transgene and the myostatin (two target sites: mstn1, mstn2) gene with the cecropin (Cec) transgene, respectively. A total of 9000 embryos were microinjected from three families, and 1004 live fingerlings were generated and analyzed. There was no significant difference in hatchability (all P > 0.05) and fry survival (all P > 0.05) between ssGE and msMGE. Compared to ssGE, CRISPR/Cas9-mediated msMGE assisted by the mixture of dsDNA and dcPlasmid donors yielded a higher knock-in (KI) efficiency of As-Cath (19.93 %, [59/296] vs. 12.96 %, [45/ 347]; P = 0.018) and Cec (22.97 %, [68/296] vs. 10.80 %, [39/361]; P = 0.003) transgenes, respectively. The msMGE strategy can be used to generate transgenic fish carrying two transgenes at multiple loci. In addition, double and quadruple mutant individuals can be produced with high efficiency (36.3 % similar to 71.1 %) in one-step microinjection. In conclusion, we demonstrated that the CRISPR/Cas9-mediated msMGE allows the one-step generation of simultaneous insertion of the As-Cath and Cec transgenes at four sites, and the simultaneous disruption of the lh, mc4r, mstn1 and mstn2 alleles. This msMGE system, aided by the mixture donors, promises to pioneer a new dimension in the drive and selection of multiple designated traits in other non-model organisms.

Intraspecies variability in sperm quality is common among aquaculture species, thus necessitating an urgent need to establish reliable molecular biomarkers to screen for males with high-quality sperm. The channel catfish (Ictalurus punctatus) female x blue catfish (I. furcatus) male hybrid accounts for >50% of United States catfish production. Blue catfish sperm cannot be collected using non-lethal methods, and thus, males must be sacrificed to determine reproductive quality. To establish gene expression biomarkers of sperm quality, we characterized important sperm traits, ranked blue catfish males based on the curvilinear velocity of their sperm, and sequenced testicular tissue for mRNAs and sRNAs. Of the 43 males characterized, testicular tissue from 4 individuals with low-velocity (155.70 mm/s +/- 1.49 SD) and 4 with high-velocity (205.01 mm/s +/- 4.63 SD) were chosen for sequencing. No differentially expressed sRNAs were detected between the two sperm performance groups. However, we identified two differentially expressed mRNA transcripts between the low-velocity and high-velocity groups, aqp3a and ly97.3, both upregulated in the high-velocity group compared to the low-velocity group. These molecular biomarkers of sperm quality in testicular tissue are linked to gamete quality and may be applied for more efficient catfish aquaculture.

The hybrid between the female channel catfish (Ictalurus punctatus) and the male blue catfish (I. furcatus) is the best genetic type currently available for commercial catfish farming due to their superior traits. However, further genetic improvements can be achieved by selecting parents with increased combining abilities. Twenty female channel catfish and twelve male blue catfish were crossed in a partial factorial mating design, resulting in forty hybrid families. These families were evaluated for early growth in three different rearing systems, including ponds and aquaria. The early growth performance of hybrid catfish was significantly (p < 0.05) affected by the additive gene action of the female parent and the male parent. There were genotype–environment or genotype–age interactions affecting the combining abilities, both the amount and the type of genetic variation. Dam GCA was significant in all environments/ages; however, sire GCA was variable, and SCA was not significant. These findings suggest that reciprocal recurrent selection for growth could potentially improve the performance of F1 hybrid catfish.

Channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus) are two economically important freshwater aquaculture species in the United States, with channel catfish contributing to nearly half of the country’s aquaculture production. While differences in economic traits such as growth rate and disease resistance have been noted, the extent of transcriptomic variance across various tissues between these species remains largely unexplored. The hybridization of female channel catfish with male blue catfish has led to the development of superior hybrid catfish breeds that exhibit enhanced growth rates and improved disease resistance, which dominate more than half of the total US catfish production. While hybrid catfish have significant growth advantages in earthen ponds, channel catfish were reported to grow faster in tank culture environments. In this study, we confirmed channel fish’s superiority in growth over blue catfish in 60-L tanks at 10.8 months of age (30.3 g and 11.6 g in this study, respectively; p < 0.001). In addition, we conducted RNA sequencing experiments and established transcriptomic resources for the heart, liver, intestine, mucus, and muscle of both species. The number of expressed genes varied across tissues, ranging from 5,036 in the muscle to over 20,000 in the mucus. Gene Ontology analysis has revealed the functional specificity of differentially expressed genes within their respective tissues, with significant pathway enrichment in metabolic pathways, immune activity, and stress responses. Noteworthy tissue-specific marker genes, including lrrc10, fabp2, myog, pth1a, hspa9, cyp21a2, agt, and ngtb, have been identified. This transcriptome resource is poised to support future investigations into the molecular mechanisms underlying environment-dependent heterosis and advance genetic breeding efforts of hybrid catfish.