Project : USDA ARS

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Research Project: Improving the Productivity and Quality of Catfish Aquaculture

Location: Warmwater Aquaculture Research Unit

2024 Annual Report

Objectives
Objective 1. Enhance selection of channel and blue catfish broodstock for economically important traits. Sub-objective 1.1. Continue selection for increased growth rate and carcass yield in channel catfish, blue catfish and channel catfish x blue catfish hybrids, and establish a selected line of blue catfish to produce improved broodstock. Sub-objective 1.2. Determine magnitude of genetic variation and evaluate potential for including additional traits in channel and blue catfish selection indices. Sub-objective 1.3. Characterize structural variation in the channel and blue catfish genomes and examine the potential for this information to improve the accuracy of estimated breeding values. Objective 2. Improve the efficiency of reproduction for purebred and hybrid catfish. Sub-objective 2.1. Identify and test reproductive pheromones in channel and blue catfish. Sub-objective 2.2. Evaluate the formulation of mammalian Luteinizing Hormone Releasing Hormone analog to improve ovulation and hatching success to improve the efficiency of hybrid catfish embryo production. Sub-objective 2.3. Determine impact of broodfish nutritional strategies on maturation and reproductive performance of channel catfish to maximize hatching success and hybrid catfish fry production. Objective 3. Increase efficiency of warmwater aquaculture by developing and improving production systems and management practices. Sub-objective 3.1. Model split-pond ecosystem dynamics to optimize design and performance. Objective 4. Improve catfish product quality by identifying and managing pre-harvest factors that affect the quality of catfish products. Sub-objective 4.1. Isolate and identify geosmin-producing species of cyanobacteria from catfish aquaculture ponds and determine the seasonal occurrences of blooms of these noxious cyanobacteria species. Sub-objective 4.2. Determine the efficacy of using sodium carbonate peroxyhydrate (SCP) in managing undesirable blooms of cyanobacteria in west Mississippi catfish ponds. Sub-objective 4.3. Determine the effects of pond culture systems on fillet flavor and texture of hybrid catfish.

Approach
In order to enhance selection of channel and blue catfish broodstock for economically important traits we will continue selection for increased growth rate and carcass yield in channel catfish, blue catfish, and channel x blue catfish hybrids, and establish a selected line of blue catfish to produce improved broodstock; determine the magnitude of genetic variation and evaluate potential for including additional traits in channel and blue catfish selection indices; and characterize structural variation in the channel and blue catfish genomes and examine its potential to improve the accuracy of estimated breeding values. In order to improve catfish reproductive efficiency, we will identify reproductive pheromones of channel and blue catfish; evaluate the formulation of mammalian Luteinizing Hormone Releasing Hormone analog to improve ovulation and hatching success to improve the efficiency of hybrid catfish embryo production; and determine the impact of broodfish nutritional strategies on maturation and reproductive performance of channel catfish to maximize hatching success and hybrid catfish fry production. In order to increase the efficiency of warmwater aquaculture by developing and improving production systems and management practices, we will model split-pond ecosystem dynamics to optimize system design and performance. In order to improve catfish product quality by identifying and managing pre-harvest factors that affect the quality of catfish products, we will isolate and identify geosmin-producing species of cyanobacteria from catfish aquaculture ponds and determine the seasonal occurrences and blooms of these noxious cyanobacteria species; determine the efficacy of using sodium carbonate peroxyhydrate (SCP) in managing undesirable blooms of cyanobacteria in west Mississippi catfish ponds; and determine the effects of pond culture system on fillet flavor and texture of hybrid catfish.

Progress Report
This is the final annual report for this project which will be replaced by new project pending the completion of the research review process. Objective 1. The Delta Select channel catfish line demonstrated improved growth and carcass yield and the Warmwater Aquaculture Research Unit hosted the initial Delta Select germplasm release to commercial fingerling producers. The release was advertised in The Catfish Journal, an industry publication, and most fingerling producers participated in the release. In subsequent years, producers reported favorably on the performance of the Delta Selects in commercial production. ARS researchers at Stoneville, Mississippi, performed two additional generations of selective breeding on the Delta Select line prior to its second germplasm release in 2024. The Delta Select line represents a large proportion of the channel catfish raised commercially in the United States. Avoidance of inbreeding was a concern as selection continued, so ARS researchers at Stoneville, Mississippi, developed a spawning system in which paired individuals spawned in tanks fed by pond water, overcoming difficulties in spawning fish in hatchery tanks fed by well water. In 2024, 70 paternal half-sibling families were produced along with 90 families from single pair matings. Tank spawning of broodstock pairs reduces potential inbreeding, provides age-matched families for comparative analyses, and avoids the effects of dominant males that can produce multiple half-sibling families in a traditional pond setting. Approximately 60% of catfish raised in the US are hybrids that are produced by manual crosses of blue catfish males with channel catfish females. In 2000, two lines of blue catfish germplasm, Rio Grande and Delta Elite, were also released to hybrid catfish fingerling producers. The blue catfish germplasm was readily received by hybrid producers. In view of limited pond resources and a limited difference between the two blue catfish lines, the Rio Grande fish were combined into the Delta Elite line. To support genomic selection efforts, ARS researchers produced high quality genome sequence assemblies for both the channel and blue catfish. These assemblies were highly complete and accurate, and currently serve as the reference genomes for these species in the National Center for Biotechnology Information (GenBank). Objective 2. The 2021 spawning season saw the initial commercial use of the catfish gonadotropin release hormone II analog (GnRH IIa) that was developed at the Warmwater Aquaculture Research Unit. The success of this new spawning aid led to its dominance in the industry in subsequent years. Researchers continued to work with commercial producers to optimize its use to improve their efficiency in producing hybird embryos. By 2022, every hybird catfish producer was using this spawning aid, and approximately 90% of hybird catfish were produce using this aid by 2023. Further research focused on reducing the amount of blue catfish sperm needed for efficient fertilization in commercial hatcheries, and at least half to one quarter the traditional amount produced sufficient fertilization rates. This can significantly reduce the number of blue catfish males required for hybird production and free broodstock holding ponds for rearing more hybird fry, thus increasing production efficiency on commercial catfish farms. Objective 3. Retirements in critical positions combined with pandemic restrictions limited research involving development and improvement of production systems and management practices. Production of catfish in earthen ponds at commercial levels requires supplemental aeration to ensure fish health and welfare, so researchers at Stoneville, Mississippi, worked with commercial aerator manufacturers to test oxygen transfer rates and inform design modifications so that the catfish industry can benefit from increased aeration efficiencies. In response to stakeholder interest, we are building a model recirculating aquaculture system to demonstrate the potential of raising catfish from fry to fingerling stage with lowered water use and reduced risk of introduced disease or predation. Objective 4. Snails are an intermediate host to parasitic worms that can degrade catfish health and filet quality. Researchers at the Warmwater Aquaculture Research Unit characterized snail ecology in commercial catfish ponds to develop strategies for the reduction or eradication of the snails. This research was complemented by the identification of selected natural compounds that can kill snails in laboratory culture. A prototype of a snail trap was created to evaluate a passive method of monitoring populations of parasite-vector snail species and better inform treatment regimes. Treatments with rotenone on phytoplankton, zooplankton, and macroinvertebrate communities suggested little disturbance, as well as rapid recovery in each group. The lethal concentrations of copper sulfate for ghost ramshorn snail eggs, juveniles, and adults were determined through lab studies. Genomic sequence was obtained from isolates of blue-green algae that are implicated in off-flavor production in catfish ponds; this research will support the development of methods to detect blue-green algal blooms as a method of early detection of potential off-flavor episodes. Scientists are using traps to monitor snail populations in catfish ponds because snails can carry parasites that will infect the catfish. Adding bait to the snail traps did not improve capture rates compared to non-baited traps, and that will reduce the labor needed for producers to monitor snail numbers in their ponds. Scientists also evaluated whether stocking larger fingerlings in ponds would reduce the risk of contracting Proliferative Gill Disease, a parasitic infection. Unfortunately, stocking larger channel catfish fingerlings did not reduce mortality or incidence of lesions in catfish exposed to the parasite. We also evaluated environmental variables that mimic daily and seasonal fluctuations in aquaculture ponds as well as conditions during transport to and within processing plants. Catfish were very resilient to stressors and filet quality was not impacted by the stressors. A new line of research involved DNA sequence analysis of entire microbial populations in catfish ponds to understand the dynamic processes of microbial species and communities and how they affect catfish production efficiency. More research was conducted to improve the production environment to realize the genetic potential of selected purebred and hybrid catfish.

Accomplishments
1. Delta Select Germplasm Release. The Delta Select line of channel catfish was initially released to producers in 2020 after 3 generations of selection. After 2 more generations of selection at the Warmwater Aquaculture ARS research at Stoneville, Mississippi, Delta Selects were 75% larger that the non-selected base population at 18 months of age. They showed the same level of feed conversion efficiency and resistance to the bacterial pathogen Edwardsiella ictaluri but had a 17% improved survival after challenge with the bacterial pathogen Edwardsiella piscicida. Considering the continued improvement in performance and positive feedback and requests from stakeholders, we released 150,000 Delta Select catfish to 8 of the 12 major catfish hatcheries in May 2024. The Delta Select line represented roughly half of the catfish fry produced at commercial hatcheries in spring 2024 so this release should increase the use of the line by United States catfish farmers.

2. Improvement in commercial hybrid catfish production. Hybrid (channel crossed with blue) catfish constitute a significant portion of United States catfish production but require manual effort to obtain and mix sperm and eggs, then efficiently culture the embryos to hatching stage. ARS researchers at Stoneville, Mississippi, worked with commercial hatcheries to demonstrate that a single-step fertilization of eggs in water that contained Fuller’s earth a clay of product used to reduce egg stickness was as efficient as fertilization in water with Fuller’s earth added afterward. This can provide a significant time savings during the short window of opportunity for hybrid production. Furthermore, reduction in sperm quantities to one-fourth the currently used amounts resulted in the same rate of fry production. This can significantly reduce the number of blue catfish males required for hybrid production and free broodstock holding ponds for rearing more hybrid fry, thus increasing production efficiency on commercial catfish farms.

3. Developing Techniques to Understand the Pond Microbial Community. Catfish aquaculture ponds are complex environments that are highly influenced by their microbial communities, which can impact dissolved oxygen and ammonia concentration, fish flavor, and catfish pathogens. ARS researchers at Stoneville, Mississippi, isolated DNA from catfish pond water samples and used new DNA sequencing technology to identify the bacterial species that were present. The team discovered 1,488 genera of bacteria in the ponds. Bacterial samples became more diverse as the catfish production season came to an end in the autumn. These data also indicated that uncovering bacteria responsible for the nitrogen cycle useful for monitoring and predicting the pond's ability to assimilate ammonia, would require differnt isolation techniques. The experiments demonstrated the feasibility of this approach to measure the distribution of catfish pond microbes so that researchers and producers can correlate the microbial populations with conditions that optimize fish production.

4. Probiotic and prebiotic feed supplementation on intestinal microbiota following antibiotic administration. Antibiotic interventions in catfish aquaculture are administered as a feed additive. These interventions can help to reduce mortality caused by bacterial infections, such as Edwardsiella ictaluri, the causative agent of enteric septicemia of catfish, but also result in disruption of the gut microbial community. This disruption may increase susceptibility of otherwise healthy fish to subsequent bacterial infections. ARS researchers at Stoneville, Mississippi, collaborating with researchers from Mississippi State University, evaluated how the antibiotic florfenicol might disrupt the gut microbe population in healthy channel catfish. Fish were fed either a basal diet, a diet fortified with probiotics, or a diet fortified with prebiotics, then the microbial species were quantified. Subsequently, fish were challenged with E. ictaluri to determine disease susceptibility. Florfenicol treatment inflated microbial diversity within the gastrointestinal tract of fish, which began to recover within a few days after treatment. Feeding probiotics also improved survival after the E. ictaluri challenge, compared to both prebiotics and the basal diet. This research demonstrated the changes in gut bacteria in response to antibiotic treatment, and the potential of probiotics to improve fish health in commercial production.

5. Understanding Catfish Performance During Hypoxia. Catfish aquaculture ponds undergo daily swings of dissolved oxygen concentration, ranging from supersaturation during the day to hypoxia (below normal oxygen levels) at night. If the dissolved oxygen concentration falls too low, catfish reduce their appetite up to 50% the following day. ARS researchers at Stoneville, Mississippi, measured key physiological responses of channel catfish during and after periods of hypoxia and discovered that even after repeated bouts of hypoxia, catfish reset their physiological parameters back to baseline values within 12 hours. We tested gene expression of two key neuropeptides for appetite reduction, but neither were changed by hypoxia, suggesting that either additional variables or different mechanisms reduce appetite. We also measured gene expression in the hypothalamus gland during and after hypoxia. The analyses revealed many genes responsible for regulating the physiological responses to hypoxia, although none of the genes known to regulate appetite in other species were significantly changed during this experiment. The research provided potential new gene targets for future analysis to determine whether genetic selection for variation in these genes can influence tolerance to low oxygen levels.

U.S. DEPARTMENT OF AGRICULTURE

Warmwater Aquaculture Research Unit: Stoneville, MS