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ARS Home » Southeast Area » Stoneville, Mississippi » Warmwater Aquaculture Research Unit » Research » Research Project #428060

Research Project: Genetics, Breeding and Reproductive Physiology to Enhance Production of Catfish

Location: Warmwater Aquaculture Research Unit

2018 Annual Report


1a. Objectives (from AD-416):
The overall goal of this project is the production of improved germplasm, genomic tools, and new reproductive methodologies to increase the production of purebred channel catfish, blue catfish, and the channel x blue F1 hybrid catfish. Incorporation of genomic selection into our breeding program has the potential to increase the rate of genetic gain by increasing accuracy and shortening the generation interval. The products of this research will contribute to improved production efficiency in the U.S. catfish industry, which provides a sustainable source of dietary protein for consumers. The objectives are to: 1) Evaluate and select for catfish germplasm with improved growth and carcass yield traits and enhanced combining ability, this includes channel catfish, blue catfish, and the hybrid. Sub-objective 1.1. Continued selection on EBVs for harvest weight and carcass yield in channel catfish. Sub-objective 1.2. Develop a selection index to select purebred blue and channel catfish that produce hybrid offspring with improved growth and carcass yield. Sub-objective 1.3: Determine whether genomic estimated breeding values improve accuracy of genetic evaluations for carcass yield and harvest weight of channel catfish. 2) Develop genomic resources and a comparative map for channel and blue catfish; and identify genomic markers for parentage determination, kinship analysis, and marker assisted selection associated with economically important traits. Sub-objective 2.1: Production of a blue catfish reference genome assembly. Sub-objective 2.2: Improve channel catfish genome assembly and produce a comparative map between the channel and blue catfish genomes. Sub-objective 2.3: Develop low density SNP genotyping assays to resolve parentage and kinship within channel and blue catfish breeding populations. Sub-objective 2.4: Production and validation of high density SNP arrays for channel and blue catfish. 3) Improve the efficiency of production of viable gametes from male and female blue and channel catfish, and improve the efficiency of production of hybrid catfish embryos. Sub-objective 3.1.: Hormonal treatment of channel catfish to improve the efficiency of hybrid catfish embryo production. Sub-objective 3.2. Characterize and improve gamete quality of channel catfish and blue catfish to improve the hatching success of hybrid catfish eggs. 4) Evaluate development of the immune system in catfish, and the effects of temperature on disease susceptibility and vaccine efficacy. 5) Evaluate genetic variation for resistance to proliferative gill disease, and identify genomic markers to enhance selection for resistance. 6) Develop ante and post mortem strategies that improve the efficiency of processing and quality and consistency of catfish products.


1b. Approach (from AD-416):
We will continue selection on estimated breeding values for harvest weight and carcass yield in channel catfish to increase average harvest weight and carcass yield in the Delta Select catfish line. We will develop a selection index to select purebred blue and channel catfish that produce hybrid offspring with improved growth and carcass yield, and determine whether genomic estimated breeding values improve accuracy of genetic evaluations for carcass yield and harvest weight of channel catfish. In order to support genomic selection in blue catfish, we will produce a blue catfish reference genome assembly that contains 95% of the assembled sequence in contigs of 1000 bp or larger, and at least 80% of the contigs will be aligned to chromosomes. We will also improve the channel catfish genome assembly and produce a comparative map between the channel and blue catfish genomes. We will use these genomic tools to develop low density single nucleutide polymorphism (SNP) genotyping assays to resolve parentage and kinship within channel and blue catfish breeding populations. We will also develop high density SNP arrays for channel and blue catfish to support genome-based selection. We will improve the efficiency of hybrid catfish embryo production by development of methods that lead to improved egg maturation, improved rate of ovulation, and improved sperm quality and quantity.


3. Progress Report:
The Delta Select population of channel catfish selected for 3 generations for improved growth and carcass yield by ARS scientists as Stoneville, Mississippi, has been compared to a randomly bred control population from the same base population, and other strains of channel catfish used by industry. These tests have demonstrated the Delta Select has superior growth and carcass yield compared to other strains. A large field trial comparing Delta Select strain catfish (n= 128,000 fingerlings) to their randomly bred control population (n = 96,000 fingerlings) is currently being conducted in earthen ponds in collaboration with Mississippi State University. Early results indicate the Delta Selects are eating more feed and presumably growing faster than the control population. Data on growth and processing yield will be collected and compared for the 2 strains at the termination of the study in the fall of 2018. Protocols are currently being developed to release the Delta Selects from this study to the industry in early winter 2019. Release of the Delta Selects will provide farmers with a faster growing fish with increased meat yield and improve production efficiency of U.S. catfish farmers and processors. Selection of blue catfish has now focused on two populations, 1) purebred Rio Grande strain due to superior performance and 2) a mixed population of Rio Grande, D7B, and Mississippi River strains to increase genetic variability. Blue catfish will be released to the catfish industry in late 2018/early 2019. A commercial broodfish diet with enhanced protein and lipid content was evaluated to improve maturation and reproductive performance under pond conditions. Higher lipid, n-3 fatty acids and n-3 long chain fatty acids from the feed were translated in oocytes, but this did not lead to improved egg quality, fecundity, or hatching success.


4. Accomplishments
1. Genomic selection for growth and carcass yield in the Delta Select strain of channel catfish. Estimation of breeding values in catfish broodstock has depended on traditional methods based only on pedigree information and phenotypic data. ARS scientists in Stoneville, Mississippi, in collaboration with scientists from the University of Georgia, have implemented selection based on genomic estimated breeding values. An array of 55,000 probes for single nucleotide polymorphic loci provided genotypes which were then incorporated into the calculation of estimated breeding values. This approach led to 30% improvement in breeding value accuracy for growth and carcass yield in 2,000 Delta Select strain catfish. The improved breeding value accuracy will result in more rapid genetic gain for growth and carcass yield in the Delta Selects which will be released to U.S. catfish farmers to improve their production efficiency.

2. Evaluation of growth and processing yield of blue catfish strains. Hybrids among blue and channel catfish now comprise approximately 75 percent of annual U.S. catfish production. Therefore, evaluation of blue catfish strains for growth and carcass yield has become an important aspect of the breeding program conducted by ARS scientists in Stoneville, Mississippi. Initially, six strains of blue catfish were obtained and evaluated, then three strains with the best growth and carcass yield were retained for further evaluations. Results indicated that the Rio Grande blue catfish strain was superior to the D&B and Mississippi River strains of blue catfish for growth and carcass yield. Accordingly, we maintain a pure Rio Grande strain because of its superior performance and also maintain a mixed population of all three strains to increase genetic diversity for future selection. Release of a superior blue catfish strain will improve production efficiency of U.S. catfish farmers and processors.

3. Calcium and magnesium hardness improve the fertility and hatching success of hybrid catfish eggs. Egg quality and water quality influence the hatching success of channel x blue hybrid catfish eggs in hatcheries. Hybrid catfish eggs are incubated in hatching waters with a recommended 60 mg/L of total hardness during embryonic development. The aquifer used for hybrid catfish hatcheries contains 10-70 mg/L of calcium hardness and 1-25 mg/L of magnesium hardness, however, the effect of magnesium hardness in combination with calcium hardness on the hatching success of hybrid catfish eggs is not known. ARS scientists at Stoneville, Mississippi, conducted two hatching trials to determine the effects of varying calcium hardness alone or in combination with magnesium hardness on fertilization and hatching success of hybrid catfish eggs. Adding graduated levels of magnesium after meeting the calcium hardness requirement had no effect on hatching success of hybrid catfish eggs. However, required water hardness for optimal hatching success of hybrid catfish eggs could be met either through calcium hardness alone or with magnesium hardness replacing up to 50% of the total hardness. The results of the study will be useful for designing treatment processes for hatchery water supplies to improve the efficiency of hybrid catfish fry production.

4. Cortisol responsiveness to stress in juvenile channel catfish influences susceptibility to Enteric Septicemia of Catfish. Disease is considered the greatest cause of reduced productivity in aquaculture production systems and culture intensifications in the catfish industry has exacerbated disease susceptibility. Cortisol is considered the principal corticosteroid in teleosts, and concentrations of cortisol increase rapidly following a stressful event. Low dissolved oxygen stressors invariably escalate susceptibility of fish to diseases in fish farms. ARS scientists at Stoneville, Mississippi, classified juvenile catfish based on their cortisol stress response to a standardized stressor and classified them either as ‘high’ or ‘low’ responders to stress. High- and low-responding channel catfish were exposed to virulent Edwardsiella ictaluri under controlled conditions. Catfish mortality rates increased with cortisol responsiveness when healthy fish were stressed prior to infection. Mitigation of stress or stress response may lead to improved survival in culture conditions.

5. Reducing variability of hybrid catfish growth during providing year-round pond harvests. Hybrid catfish constitute approximately 75 percent of U.S. farm-raised catfish production because of their superior growth, better feed conversion, higher survival, availability, and suitability of intensive production systems. However, rapid growth of hybrids, behavioral differences with channel catfish, and physical characteristics of hybrid catfish have presented some unique problems for production such as highly variable fish growth, oversized fish, and more difficulty for year-round harvest. An ARS scientist at Stoneville, Mississippi, collaborated with Auburn University researchers and catfish producers to develop a holistic approach to identify the causes and provide solutions to this problem through a two-year NIFA SRAC funded research project. Extensive field samplings were conducted at multiple farms to assess the impact of culture system, harvest technology, fingerling size and variability, grading, genetics, time and rate of stocking, and feeding rates on size variability at harvest and ability to accomplish year-round harvest. Genetics of purebred parents and stocking of multiple sizes of fingerlings in production ponds led to variability in hybrid catfish performance. However, increased aeration in production ponds and bar-grading of fingerlings prior to stocking promoted uniformity in fish size at harvest. Models based on economic analyses for specific sets of farm conditions were developed for potential adoption under field conditions to improve production and profitability of hybrid catfish production.

6. Channel catfish demonstrate low heritability for resistance to Enteric Septicemia of Catfish (ESC). Enteric Septicemia of Catfish is one of three major microbially-induced diseases in catfish, and one approach to reducing mortality and improving farm production is selection for broodstock with improved resistance. ARS scientists at Stoneville, Mississippi, challenged multiple pedigreed families of the Delta Select catfish line by exposure to virulent Edwardsiella ictaluri. Two challenges (on 2008 and 2017 year class fish) were conducted on more than 10,000 progeny in 180 full- and half-sibling families from a total of 70 sires. The results indicated a low heritability, 0.1, for this trait which pointed to a low response to selection. Improvement of ESC survival will be more likely through management rather than selective breeding.


Review Publications
Chatakondi, N.G., Peterson, B.C. 2018. Cortisol responsiveness to stress in channel catfish influences susceptibility to Edwardsiella ictaluri. Southeastern Association of Fish and Wildlife Agencies Conference. 5:53-58.

Reichley, S.R., Ware, C., Steadman, J., Gaunt, P.S., Garcia, J.C., LaFrentz, B.R., Thachil, A., Stine, C.B., Waldbieser, G.C., Arias, C.R., Lock, T., Welch, T.J., Cipriano, R.C., Greenway, T.E., Khoo, L.H., Wise, D.J., Lawrence, M.L., Griffin, M.J. 2017. Comparative phenotypic and genotypic analysis of Edwardsiella spp. isolates from different hosts and geographic origins, with an emphasis on isolates formerly classified as E. tarda and an evaluation of diagnostic methods. Journal of Clinical Microbiology. 55:3466-3491.

Bledsoe, J., Waldbieser, G.C., Swanson, K., Peterson, B.C., Small, B. 2018. Comparison of channel catfish and blue catfish gut microbiota assemblages shows minimal effects of host genetics on microbial structure and inferred function. Frontiers in Microbiology. 9:1073.

Chatakondi, N.G. 2017. Effective dose of salmon GnRha for induction of ovulation in channel catfish, Ictalurus punctatus. North American Journal of Aquaculture. 79:310-316.

Garcia, J.C., LaFrentz, B.R., Waldbieser, G.C., Wong, F., Chang, S. 2018. Characterization of atypical Flavobacterium columnare and identification of a new genomovar. Journal of Fish Diseases. 41:1159-1164.

Kumru, S., Tekedar, H., Gulsoy, N., Waldbieser, G.C., Lawrence, M.L., Karsi, A. 2017. Comparative analysis of the Flavobacterium columnare genomovar I and II genomes. Frontiers in Microbiology. 8:1375.

Li, M.H., Bosworth, B.G., Lucas, P.M. 2018. Evaluation of porcine meat and bone meal in diets for pond-raised hybrid catfish. North American Journal of Aquaculture. 80(1):69-73.

Reichley, S.R., Waldbieser, G.C., Soto, E., Lawrence, M.L., Griffin, M.J. 2017. Complete genome sequence of Edwardsiella ictaluri isolate RUSVM-1 recovered from nile tilapia (Oreochromis niloticus) in the Western Hemisphere. Genome Announcements. 5:e00390-17.

Reichley, S.R., Ware, C., Khoo, L.H., Greenway, T.E., Wise, D.J., Bosworth, B.G., Lawrence, M.L., Griffin, M.J. 2017. Comparative susceptibility of channel catfish, Ictalurus punctatus; blue catfish, Ictalurus furcatus; and channel female Blue male Hybrid catfish to Edwardsiella piscicida, Edwardsiella tarda, and Edwardsiella anguillarum. Journal of the World Aquaculture Society. 49(1):197-204.