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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

2016 Annual Report

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.

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
Hybrid catfish currently comprise over 50% of total U.S. catfish production. There is a demand for hybrid catfish fingerlings from food fish producers and hence the existing hatcheries has increased their production capacity, and commercial production is projected to exceed 200 million hybrid fry in 2016. This year, three new hatcheries are devoted to produce hybrid fry. Adoption of hybrid catfish by the industry is largely due to the active involvement of ARS scientists at Stoneville, Mississippi, and we continue to consult with producers to develop and refine hybrid production technologies. As we focus on genetic improvement of blue catfish to provide to the industry, we have produced blue x channel hybrid and crossbred blue catfish from the same blue catfish males to measure the correlation between growth and carcass yield in purebred blues versus hybrids. This information will inform our selection process for genetically improved blue catfish. We also continue to develop methods for improving quality and quantity of sperm and eggs, improving fertilization rate, and improving embryo development and fry survival. Molecular research involves production of long nucleotide sequences for a blue catfish genome assembly and a new genotyping system for more efficient identification of hybrid catfish families. We also continue selection of the Delta Select strain of channel catfish and will utilize our new genotyping array to perform genomic selection to increase the rate of improvement in carcass yield while maximizing genetic diversity within this strain. The new genotyping array, containing probes for 670,000 loci, was produced based on single nucleotide polymorphic loci that were segregating in the Delta Select population. After screening the loci in individual channel and blue catfish, we will select approximately 50,000 probes for a smaller array to be used in genomic selection.

1. Evaluation of processing yield in catfish from nutrition studies. Diet composition and feeding regimes can affect fillet yield in farm-raised catfish. Soybean meal represents the main source of dietary protein in traditional catfish diets, but increased pricing of soybean meal dramatically increases feed costs. ARS and Mississippi State University scientists in Stoneville, Mississippi, examined the effects of substituting soybean meal with other, less expensive dietary protein sources (cotton seed meal, corn distillers dried grains with solubles, corn germ meal, peanut meal, and porcine meat and bone meal) on growth and fillet yield of farm-raised catfish. The results demonstrated soybean meal could be completely replaced with cheaper sources of dietary protein with no effect on growth or fillet yield of channel catfish. This information was provided to catfish feed producers who altered diet compositions and thus lower feed costs for catfish farmers.

2. Cryopreservation of catfish sperm. Use of cryopreserved sperm is critical to development of improved catfish germplasm and preservation of genetic material from catfish breeding populations. ARS scientists in Stoneville, Mississippi, continue to improve sperm cryopreservation techniques in collaboration with scientists at Louisiana State University and Cryogenetics Inc. To date we have preserved sperm from 260 blue catfish from four strains to maintain the genetic diversity of blue catfish populations. Spawning trials demonstrated that cryopreservation reduced blue catfish sperm motility by 50% compared to fresh sperm. However, cryopreserved and fresh sperm did not differ in the percentage of viable embryos observed 48 hours after fertilization. Availability of cryopreserved blue catfish sperm can also improve the efficiency of hybrid catfish production.

3. Fertilizing sperm from multiple blue catfish males with channel catfish eggs reduces potency, progeny proportion and performance. Channel x blue hybrid catfish fry are produced by fertilizing channel catfish eggs with blue catfish sperm. Commercial producers commonly pool sperm from multiple males for spawning efficiency, but effects of pooled sperm on hatching success and progeny performance are not known. ARS researchers in Stoneville, Mississippi, conducted spawning trials to determine the effects of fertilizing sperm solutions from individual and pooled sperm on hatching success, potency and progeny performance. Five pooled hybrid families were each produced by fertilizing eggs from one channel catfish female with pooled sperm from 4 blue catfish male, and the offspring were identified using molecular genetic markers. Hatching success did not differ between individual or pooled sperm groups. Each male contributed from 13.4 to 38.9% of the family’s progeny. However, average weight of hybrid catfish fingerlings from spawns fertilized by sperm from individual males was higher than the average weight of hybrid catfish sired by pooled sperm (23.0 vs 14.1 grams). The results suggest that catfish farmers should use caution when pooling blue catfish sperm for hybrid catfish production.

4. Sire strain affects blue x channel catfish progeny performance in commercial setting. Channel x blue hybrid catfish is presently the desired aquaculture species in US farm-raised catfish industry and the D&B strain and Rio Grande strain of blue catfish are the only domesticated strains used in commercial catfish hatcheries. ARS scientists in Stoneville, Mississippi, examined the influence of sire strain on hybrid catfish embryo production and fingerling performance under commercial hatchery conditions. Average testis weight was higher in Rio Grande (1.98 grams per kilogram body weight) compared to D&B (1.02 grams per kilogram body weight) strain. However, mean survival (99.3%), production (8875 kg/hectare), and feed conversion (1.14) of D&B hybrids were higher (P <0.05) to Rio Grande hybrid catfish fingerlings compared in replicated earthen ponds. This research demonstrated the potential of genetic differences between strains to increase production on commercial farms.

5. Acclimating pH of stripped catfish eggs to hatchery water facilitate hatching success of hybrid catfish. Variable egg quality is one of the most important constrains to the development of US farm-raised catfish aquaculture. The quality of stripped channel catfish eggs are affected by variation in parental genetics, maturity, ovulating peptides, stress, and sub-optimal hatching conditions. ARS scientists in Stoneville, Mississippi, conducted hatching trials to evaluate progressive periodic exposure of pH waters from fertilization to incubation in hatching waters. Stripped eggs from 12 channel catfish females with varying egg quality (determined with the correlated measurement of pH level of ovarian fluid) were mixed with blue catfish sperm and activated with water at pH 7.0, 7.5, 8.0 or 9.0, then incubated in hatchery water. The results of the study suggest that stripped eggs of lower quality incubated initially in water at higher pH levels did not improve hatching success. Thus, future research will continue to improve genetics, nutrition, and induction of ovulation to improve egg quality and consistency to maximize the hatching success of hybrid catfish eggs.

The 2013 USDA Census of Aquaculture identified 695 catfish farms, reduced from 1,160 farms in 2005, but an increase in average sales per farm from $398,000 to $541,000. The USDA Census of Aquaculture conducted in 2000 classified 84% of catfish farms as small businesses, with annual sales of less than $500,000. Increased foreign competition and higher feed and fuel prices have reduced the profit margins for these small businesses. Development of catfish with superior performance for commercially important traits, utilization of these lines in commercial culture, and utilization of production technologies originating from the Warmwater Aquaculture Research Unit in Stoneville, Mississippi, will help solve production problems, increase efficiency and profitability for both small and large catfish farmers, and provide a quality product for consumers. Most catfish producers with limited acreage buy fingerlings from large breeders that are very likely to utilize improved brood stocks, and the development and use of improved catfish lines can quickly affect the profits of small producers. Because small farms do not enjoy the same economies of scale experienced by larger operations, breeding fish with improved production traits will be highly beneficial to small farmers. Average consumers also benefit from the increased availability of higher-quality, safer domestic products at a reduced price.

Review Publications
Li, M.H., Robinson, E.H., Bosworth, B.G., Torrans, E.L. 2014. Growth and feed conversion of pond-raised hybrid catfish harvested at different sizes. North American Journal of Aquaculture. 76:261-264.
Torrans, E.L., Ott, B.D., Bosworth, B.G. 2015. Impact of minimum daily dissolved oxygen concentration on production performance of hybrid female channel catfish x male blue catfish. North American Journal of Aquaculture. 77(4):485-490.
Liu, Z., Liu, S., Yao, J., Bao, L., Jiang, C., Want, R., Sun, L., Li, Y., Zhang, Y., Zhang, J., Zhou, T., Zeng, Q., Fu, Q., Gao, S., Li, N., Koren, S., Jiang, Y., Zimim, A., Xu, P., Phillippy, A., Geng, X., Song, L., Sun, F., Li, C., Want, X., Chen, A., Jin, Y., Yuan, Z., Yang, Y., Tan, S., Peatman, E., Lu, J., Qin, Z., Dunham, R., Li, Z., Sonstegard, T.S., Feng, J., Danzmann, R.G., Schroeder, S.G., Scheffler, B.E., Duke, M.V., Ballard, L.L., Kucuktas, H., Kaltenboeck, L., Liu, H., Armbruster, J., Xie, Y., Kirby, M.A., Tian, Y., Moore Flanagan, M.E., Mu, W., Waldbieser, G.C. 2016. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nature Communications. 7:11757.
Bosworth, B.G., Ott, B.D., Torrans, E.L. 2015. Effects of stocking density on production traits of channel catfish Ictalurus punctatus x blue catfish Ictalurus furcatus hybrids. North American Journal of Aquaculture. 77:437-443.
Peterson, B.C., Flora, C.L., Wood, M.L., Bosworth, B.G., Quiniou, S., Greenway, T.E., Byers, T.S., Wise, D.J. 2016. Vaccination of full-sib channel catfish families against enteric septicemia of catfish with an oral live attenuated Edwardsiella ictaluri vaccine. Journal of the World Aquaculture Society. 47:207-211.
Reichley, S.R., Waldbieser, G.C., Lawrence, M.L., Griffin, M.J. 2015. Complete genome sequence of an Edwardsiella piscicida-like species recovered from tilapia in the United States. Genome Announcements. 3:e01004-15.
Kumru, S., Tekedar, H., Waldbieser, G.C., Lawrence, M.L., Karsi, A. 2016. Genome sequence of the fish pathogen Flavobacterium columnare genomovar II strain 94-081. Genome Announcements. 4:e00430-16.
Tekedar, H., Kumru, S., Karsi, A., Waldbieser, G.C., Sonstegard, T., Schroeder, S.G., Liles, M., Griffin, M., Lawrence, M. 2016. Draft genome sequence of Aeromonas hydrophila TN97-08. Genome Announcements. 4:e00436-16.