Location: Warmwater Aquaculture Research Unit
2019 Annual Report
Objectives
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.
Approach
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.
Progress Report
This is the final report for this project which was designed to improve genomic resources for catfish, select genetically superior channel and blue catfish broodstock, and develop and transfer methodologies that improved the quality and quantity of gametes to improve production of hybrid catfish. Over the lifetime of this project, we continued genetic selection for growth and carcass yield in the Delta Select strain of channel catfish and increased growth rate by 30% and carcass yield up to 0.8%. We produced whole genome DNA sequence assemblies from individual channel and blue catfish. Whole-genome sequence from additional channel and blue catfish was aligned to the reference genomes to identify DNA sequence variation in populations under selection, and the DNA sequence variants were used to produce high-density genotyping arrays for each species. Approximately 2,000 Delta Select catfish broodstock were genotyped at 55,000 genomic locations to facilitate whole genome selection for growth and carcass yield. Genomic breeding values were 28% more accurate for harvest weight and 36% more accurate for carcass yield than traditional estimated breeding values. During this project, commercial production of channel x blue hybrid catfish steadily increased from 50 to 75% of US catfish production. Hybrid production requires manual stripping of eggs from channel catfish females and terminal collection of sperm from blue catfish males. We have collected a variety of blue catfish strains and created a collection of cryopreserved sperm from several hundred individuals. Performance testing has shown the Rio Grande strain to have superior production traits, therefore we have begun a breeding program for this strain. We have also identified new reproductive peptides that can improve maturation and ovulation of channel catfish eggs, demonstrated the use of modified McDonald-style hatching jars to increase hatching rate of hybrid eggs, and developed methods that reduce handling stress for broodfish. We have hosted several technical workshops for educating hatchery managers on improved methods for hybrid catfish production and followed up with on-farm visits to help producers improve facilities and increase hybrid production efficiency. This project produced 63 peer-reviewed publications.
Accomplishments
1. Comparison of growth and carcass yield of Delta Select and Delta Control strains of channel catfish. Improved catfish germplasm will allow United States (U.S.) catfish farmers to reduce production costs and remain competitive in the global seafood market. Agriculture Research Service (ARS) scientists in Stoneville, Mississippi, initiated a selective breeding program to develop a strain of channel catfish (Delta Select) with superior growth rate and meat yield, traits important to catfish producers and processors. A series of performance trials were conducted to compare the growth and meat yield of the Delta Select strain to the Delta Control strain, an unselected strain representative of channel catfish currently being grown by U.S. farmers. The Delta Select strain of channel catfish grew 30 percent (%) faster and had 0.25 to 0.80% higher meat yield than the Delta Control strain, demonstrating that selection has improved both traits in the Delta Select strain. Approximately 150,000 two-year-old Delta Select strain channel catfish will be available for release to famers during fiscal 2020 to allow U.S. catfish farmers to be more efficient and profitable.
2. Evaluation and development of blue catfish germplasm for release to U.S. catfish farmers. Over the last 15 years, U.S. catfish production has shifted from predominant use of purebred channel catfish to the production of F1 hybrids between channel catfish and blue catfish. Therefore, evaluation and development of improved blue catfish germplasm is warranted to develop improved catfish germplasm for release to U.S. catfish farmers. ARS scientists in Stoneville, Mississippi, established the most diverse collection of blue catfish in existence and initiated evaluations of these strains for purebred blue catfish and hybrid catfish performance. Initial research revealed that purebred and hybrid progeny of the Rio Grande strain of blue catfish showed superior growth and meat yield relative to other blue catfish strains. Approximately 10,000 four to six-year-old Rio Grande fish, 20,000 2 year-old Rio Grandes, and 100,000 Rio Grande fingerlings will be made available for release to farmers during fiscal 2020, allowing U.S. catfish farmers to be more efficient and profitable.
3. Development of a blue catfish cryopreserved sperm collection. The F1 hybrid between the blue and channel catfish represents 75% of current U.S. farm-raised catfish production. However, the blue male catfish must be sacrificed to obtain sperm for use in hybrid production. ARS scientists in Stoneville, Mississippi, in cooperation with scientists at the ARS National Animal Germplasm Repository and Louisiana State University, have established the largest collection of cryopreserved blue catfish sperm in existence. This collection is a crucial component of the Warmwater Aquaculture Research Unit (WARU) effort to produce improved blue catfish germplasm for release to U.S. catfish farmers. Currently sperm from approximately 300 blue catfish males has been cryopreserved and is used in the WARU catfish breeding program. Development and release of improved blue catfish germplasm will benefit U.S. catfish producers.
4. Identification of the sex-determining locus in channel catfish. Channel catfish utilize an XY sex determination system in which XY fish are male and XX fish are female, but the gene controlling sexual differentiation is unknown. ARS scientists in Stoneville, Mississippi, and scientists at Auburn University utilized testosterone to sex-reverse catfish to females, identified XY females using molecular markers, and mated them with normal XY males. The YY male offspring were identified using molecular markers and progeny testing. We then produced a genome assembly from a YY male to obtain the Y chromosome sequence. Comparison with the reference genome X chromosome showed no difference in gene content. However, RNA sequence analysis revealed a transcript from the BCAR1 gene was differentially expressed in males during the critical time of differentiation of gonadal tissues. A gene editing experiment provided functional evidence that disruption of the BCAR1 gene in genetic males led to a female phenotype. These results will be used to develop accurate markers to identify genetic sex at an early age and provide a target for identification of the sex determining gene in blue catfish. Culture of only blue catfish males would increase the efficiency of hybrid catfish production.
5. Effects of catfish diets on meat yield. Meat yield, the percentage of whole fish weight comprised on saleable meat, is an important trait in farm-raised catfish and diet composition and feeding regimes can affect meat yield. Lysine is an important amino acid in catfish diets, and ARS scientists in Stoneville, Mississippi, worked in cooperation with Mississippi State University fish nutritionists to determine that catfish diets supplemented to 1.43% available lysine improved meat yield in channel catfish relative to lower rates of lysine supplementation. Ongoing research is designed to determine effects of dietary restrictions on growth and meat yield of hybrid catfish. These results have been provided to catfish producers, processors and feed manufacturers and allow the catfish farming industry to develop feeds and feeding strategies to minimize production costs and maximize profits.
6. Anesthetization using a portable electrosedation unit reduces catfish handling stress and improves post-spawning survival. Channel x blue hybrid catfish are increasingly raised in commercial catfish ponds in Southeastern USA because of superior production traits. In order to obtain eggs for hybrid production, handling stress on channel catfish is unavoidable and can contribute to high losses of broodfish after spawning. Only one FDA approved chemical sedative, Tricaine Methanesulfonate (MS222) is used to reduce physical damage and handling stress for routine procedures. Under farm conditions, broodfish are often exposed to higher concentrations and held for a longer duration in sedative solution than required. ARS scientists at Stoneville, Mississippi, collaborated with scientists at the University of Arkansas, at Pine Bluff, to identify effective parameters for electrosedation of catfish broodstock. The scientists found that electrosedation of mature channel catfish was as effective as MS222 sedation but avoided bioaccumulation of MS222 and provided a more controlled exposure than MS222. Field testing showed that catfish producers preferred using electrosedation. This method could improve broodstock survival to reduce losses due to handling stress.
7. Novel ghrelin receptor in catfish. The peptide ghrelin is a hormone that regulates feed intake and energy use in animals. Its role in feed intake and its actions on growth hormone are important to researchers working to enhance channel catfish growth and feed efficiency. Agriculture Research Service (ARS) scientists in Stoneville, Mississippi, in collaboration with scientists at the University of Idaho, identified a ghrelin receptor, GHS-R3a, that is unique in fish. Tissue expression and regulation differ from two previously known ghrelin receptor genes. The GHS-R3a receptor preferentially binds to catfish ghrelin and may be a key regulator of growth and feed intake in catfish. As such, GHS-R3a is being looked at as a possible marker in a selective breeding program for growth and fillet yield.
8. Cytotoxic T-cell action in a catfish cell line. Cytotoxic T cells are critical elements of the immune response to pathogens or cancers. They function by recognizing and killing abnormal cells, such as malignant cells or those invaded by pathogens. Agriculture Research Service (ARS) scientists in Stoneville, Mississippi, in collaboration with scientists at the University of Mississippi Medical Center, characterized the reaction of cytotoxic T cell from cell line TS32.15 when exposed to abnormal cells. The small cytotoxic T cells multiplied and changed morphology to become large, granular and able to kill abnormal cell targets. Once the abnormal cells were killed, the cytotoxic cells lost the ability to kill and then died. These experiments added to the understanding of how the catfish immune system eliminates pathogens, the mechanisms involved in disease resistance in fish, and provided clues for the design of better vaccines to protect fish.
Review Publications
Bao, L., Tian, C., Liu, S., Zhang, Y., Elaswad, A., Khalil, K., Sun, F., Yung, Y., Zhou, T., Li, N., Tan, S., Zeng, Q., Liu, Y., Li, Y., Goa, D., Dunham, R., Davis, K., Waldbieser, G.C., Liu, Z. 2019. The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish. BMC Biology. 17:6.
Garcia, A., Bosworth, B.G., Waldbieser, G.C., Tsuruta, S., Misztal, I., Lourenco, D. 2018. Development of genomic predictions for harvest and carcass weight in channel catfish. Genetics Selection Evolution. 50:66.
Small, B., Quiniou, S., Hiroyuki, K., Bledsoe, J.W., Musungu, B.M. 2019. Characterization of a third ghrelin receptor, GHS-R3a, in channel catfish reveals novel expression patterns and a high affinity for homologous ligand. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology. 229:1-9.
Spencer, D.A., Quiniou, S., Crider, J., Musungu, B.M., Benten, E., Wilson, M. 2019. Insights into the dynamics of memory, effector and apoptotic cytotoxic T Lymphocytes in channel catfish, Ictalurus punctatus. Developmental and Comparative Immunology. 92:116-128.
Abdelhamed, H., Lawrence, M.L., Waldbieser, G.C. 2019. Complete genome sequence of multidrug-resistant Aeromonas veronii strain MS-18-37. Genome Announcements. 23:103689.
S, A., Griffin, M.J., Mischke, C.M., Bosworth, B.G., Waldbieser, G.C., Wise, D.J., Marsh, T.L., Scribner, K.T. 2019. Biotic and abiotic factors influencing channel catfish eggs and gut microbiome dynamics durning early life stages. Aquaculture. 498:556-567.
Lange, M.D., Waldbieser, G.C., Lobb, C.J. 2019. The proliferation and clonal migration of B cells in the systemic and mucosal tissues of channel catfish suggests there is an interconnected mucosal immune system. Fish and Shellfish Immunology. 84:1134-1144. https://doi.org/10.1016/j.fsi.2018.11.014.
Mischke, C., Filbrun, J., Li, M., Chatakondi, N.G. 2019. Quantifying the contribution of zooplankton to channel catfish and hybrid catfish growth in nursery ponds. Aquaculture. 510:51-55.
Peterson, B.C., Chatakondi, N.G., Small, B.C. 2019. Ontogeny of the cortisol stress response and glucocorticoid receptor expression during early development in channel catfish (Ictalurus punctatus). Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology. 231:119-123.
Peterson, B.C., Peatman, E., Ourth, D., Waldbieser, G.C. 2018. Phytogenic feed-additive effects on channel catfish rhamnose binding lectin levels and susceptibility to Edwardsiella ictaluri. Diseases of Aquatic Organisms. 129:99-106.
Shappell, N.W., Duke, S.E., Bartholomay, K.A. 2019. In vitro subcellular characterization of flunixin liver metabolism in heifers, steers, and cows. Research in Veterinary Science. 123:118-123. https://doi.org/10.1016/j.rvsc.2018.12.012.
