Research Project: Improving the Productivity and Quality of Catfish Aquaculture

Location: Warmwater Aquaculture Research Unit

2023 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
Warmwater Aquaculture Research Unit (WARU) researchers and staff continued selective breeding of the Delta Select line of channel catfish. In addition to growth rate and carcass yield phenotypes, feed conversion rate and resistance to two bacterial pathogens were also tested for inclusion in the selection index. Catfish producers have requested another germplasm release of this line, so approximately 1 million fry were produced from 180 matings in the 2023 spawning season for a planned release in winter 2024. The Rio Grande line of blue catfish was combined with the Delta Elite line of blue catfish to increase the genetic variability of that blue catfish line. High quality genome assemblies were produced for each species and deposited in GenBank to serve as the reference genomes for each species. The catfish gonadotropin releasing hormone analogue developed at WARU was responsible for producing approximately 90% of the commercial hybrid catfish fry in the U.S. in 2023. New research included metagenomic analysis of microbial populations in catfish ponds to begin 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. Furthermore, we expanded research in pre-harvest product quality to reduce the negative effects on health and filet quality due to parasite infection.

Accomplishments
1. Effects of selection for increased growth and carcass yield on feed conversion efficiency and disease resistance in the Delta Select line of channel catfish. ARS researchers at Stoneville, Mississippi, developed the Delta Select line channel catfish with superior growth and carcass yield, and the industry’s response to its performance upon release in spring 2020 has been favorable. However, it is also important to determine the effects of selection for growth and carcass yield on other important performance traits in the Delta Select line. ARS researchers in Stoneville, Mississippi, along with researchers from Mississippi State University, compared selectively bred catfish (Delta Select line) with randomly selected catfish (Delta Control line) from the same base population for feed conversion efficiency and resistance to two important bacterial pathogens of catfish, Edwardsiella ictaluri and Edwardsiella piscicidia. The Delta Select line catfish grew faster than the Delta Control line, but both lines demonstrated similar feed conversion efficiencies indicating the faster growth of the Delta Selects was due to greater feed consumption. In experimental challenges the Delta Control and Delta Select line survived Edwardsiella ictaluri challenge similarly, but the Delta Select had higher survival rates after Edwardsiella piscicidia challenge. The results suggest selection for increased growth and carcass yield has not had a negative impact on feed conversion efficiency or resistance to Edwardsiella ictaluri and may have improved resistance to Edwardsiella piscicidia in the Delta Select line channel catfish. This information supports the continued use of the Delta Selects line in the United States catfish industry.

2. Reference genomes for channel and blue catfish. Channel and blue catfish are native to North America and are key to United States aquaculture. To efficiently implement genomic selection in these species, require accurate, complete genome assemblies. ARS researchers in Stoneville, Mississippi, and collaborators utilized state-of-the-art molecular technologies and bioinformatics to produce highly complete DNA sequence assemblies that accurately represent the channel and blue catfish genomes. The new channel catfish genome assembly is a marked improvement over the previous reference assembly, while the blue catfish genome assembly is novel. Three chromosomes contained large structural changes which likely lead to the lowered fertility observed in channel x blue hybrid F1 offspring. The research also revealed sets of genes that are unique within each species, also genes unique to both species but different from other fish. The new genome assemblies serve as the reference genomes for these species in the GenBank database and will support genomic selection and selective breeding in both species toward improvement of United States catfish production.

3. Development of a vacuum degasser to decrease gas supersaturation of well water. Most of the commercial catfish operations utilize water that comes from deep aquafers. Often, this water is supersaturated with nitrogen gas that is harmful to fish. ARS researchers in Stoneville, Mississippi, developed a vacuum degasser that eliminates nitrogen supersaturation from well water without changing other water quality parameters. This degasser eliminated gas supersaturation and facilitated research on hypoxia using water sources that mimicked commercial conditions, and this research will help researchers and producers develop best practices for improved production in commercial ponds.

4. Identifying sources of catfish size variation. Harvesting over- or undersized catfish reduces profitability of commercial catfish farming, but some size variation can be mitigated through extensive size grading when fingerlings are stocked in ponds. ARS researchers in Stoneville, Mississippi, investigated the amount of size variation within and among channel catfish spawns from different aged brooders. We measured 16,000 catfish fry over two different spawning seasons from 2-, 3-, 4-, and 5-year old broodstock, and determined that older brooders produced significantly larger fry than younger brooders. However, size variation within spawns was not impacted by age. These data led to both popular and peer-reviewed publications that highlighted the importance of broodstock management in reducing size variation in catfish culture.

5. Effect of rotenone on catfish ponds. Rotenone is a common chemical therapeutic used to rid ponds of undesirable and/or hold-over fish in catfish ponds prior to restocking, but prior research in natural water systems showed recovery of phytoplankton and zooplankton communities could take months, or even years, following rotenone treatment. ARS researchers in Stoneville, Mississippi, collaborating with researchers from Mississippi State University’s Delta Research and Extension Center, evaluated rotenone use on various aspects of the catfish pond environment. Treatment with rotenone showed no effects on water quality or macroinvertebrate communities. Phytoplankton and zooplankton populations recovered within 14 days, nearly the same timeframe as the typical wait time for normal management operations. This research demonstrated rotenone is an effective therapeutic with no significant long-term effects on key catfish pond ecology. The research was highlighted in the Fish Culture Section of the American Fisheries Society Winter/Spring 2023 newsletter.

6. Characterizing microbial communities with long read DNA sequencing. Microbes serve many crucial roles in aquatic systems such as nutrient cycling, competition, and photosynthesis, but little is known of the microbial communities in catfish ponds – both in their make-up and their impact on production. ARS researchers in Stoneville, Mississippi, collaborating with researchers from Mississippi State University’s Delta Research and Extension Center, evaluated the utility of nanopore sequencing technology to characterize microbial communities in water samples collected from catfish ponds. The analysis revealed the dynamic nature of these ponds, as well as the limitations of available DNA sequence databases to accurately quantify novel species. The research also revealed issues of sequencing depth, taxonomic availability within databases, and high variability between ponds, but nanopore technology showed strong utility for rapid characterization of the microbial communities in catfish ponds that can allow producers to monitor the pond environment.

7. Snail trap prototype. Two species of aquatic snails serve as intermediate hosts for the trematode parasite Bolbophorus damnificus that can infect pond cultured catfish. Management strategies for the parasite are severely limited, and snail control is the most advantageous option for catfish farmers. However, copper sulfate pond treatments are largely arbitrary, relying on the farmer’s perceived snail density in each pond. ARS researchers in Stoneville, Mississippi, collaborating with researchers from Mississippi State University’s Delta Research and Extension Center, developed a simple, low-cost snail trap prototype. The prototype used readily available materials including a cricket cage, PVC pipe, and zip ties. The trap can be deployed into individual ponds for rapid assessment of snail populations, allowing farmers to make more informed management decisions in their efforts to control B. damnificus host snails.

Review Publications
Mischke, C.C., Richardson, B.M., Wise, D.J., Tiwari, A. 2023. Rotenone has little effect on water quality, phytoplankton, zooplankton or macroinvertebrates in aquaculture nursery ponds. North American Journal of Aquaculture. https://doi.org/10.1002/naaq.10276.
Malone, R.F., Alt, D., Pfeiffer, T.J. 2022. Food-based sizing criteria of bead filters with floating media in serial treatment with moving bed bioreactors. Journal of Aquaculture Engineering. 100:1-9. https://doi.org/10.1016/j.aquaeng.2022.102298.
Gunn, M.A., Griffin, M.J., Ott, B.D., Rosser, G.T., Wise, D.J., Allen, P.J. 2022. Physiological response of channel (Ictalurus punctatus) and hybrid (I. punctatus x I. furcatus) catfish following Bolbophorus damnificus infection. Aquaculture. 563(2). https://doi.org/10.1016/j.aquaculture.2022.739016.
Mischke, C.C., Richardson, B.M., Tiwari, A., Griffin, M.J., Wise, D.J., Rehman, J.U., Ashfaq, M.K., Nanayakkara, P., Khan, I.A. 2022. Copper toxicity to the ghost rams-horn snail Biomphalaria havanensis. North American Journal of Aquaculture. https://doi.org/10.1002/naaq.10279.
Richardson, B.M., Reifers, J.G., Walker, C.M., Byars, T.S., Mischke, C.C., Griffin, M.J., Wise, D.J. 2023. Evaluation of snail trap prototype for monitoring the intermediate gastropod hosts of Bolbophorus spp. in commercial catfish ponds in the southeastern United States. Journal of the World Aquaculture Society. 54(5):1247-1259. https://doi.org/10.1111/jwas.12962.
Johnston, A.E., Shavalier, M.A., Scribner, K., Soto, E., Griffin, M.J., Waldbieser, G.C., Richardson, B.M., Winters, A.D., Yun, S., Baker, E.A., Larson, D.L., Kiupel, M., Loch, T.A. 2022. First Isolation of a Herpesvirus (Family Alloherpesviridae) from Great Lakes Lake Sturgeon (Acipenser fulvescens). Animals. https://doi.org/10.3390/ani12233230.
Ott, B.D., Bosworth, B.G., Torrans, E.L., Waldbieser, G.C. 2023. Effect of brooder age and size on fry size variation in channel catfish. North American Journal of Aquaculture. https://doi.org/10.1002/naaq.10280.
Waldbieser, G.C., Liu, S., Yuan, Z., Older, C.E., Gao, D., Shi, C., Bosworth, B.G., Li, N., Boa, L., Kirby, M.A., Jin, Y., Wood, M.L., Scheffler, B.E., Simpson, S.A., Youngblood, R.C., Duke, M.V., Ballard, L.L., Phillipy, A., Koren, S., Liu, Z. 2023. Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. BMC Biology. 21:67. https://doi.org/10.1186/s12915-023-01556-8.
Schrader, K. 2023. Flavor wheel for sensory analysis of fish raised in recirculating aquaculture systems. North American Journal of Aquaculture. 85:87-91. https://doi.org/10.1002/naaq.10275.
Pfeiffer, T.J., Ott, B.D. 2023. Biofiltration reactivation kinetics of a Cyclobio fluidized sand filter in a warmwater recirculating aquaculture system. North American Journal of Aquaculture. 85(2):166-173. https://doi.org/10.1002/naaq.10282.
Crider, J., Wilson, M., Felch, K.L., Dupre, R.A., Quiniou, S., Bengten, E. 2023. A subset of leukocyte immune-type receptors (LITR) regulates phagocytosis in channel catfish (Ictalurus punctatus) leukocytes. Molecular Immunology. 154:33-44. https://doi.org/10.1016/j.molimm.2022.12.009.