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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

2017 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.

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 line of channel catfish has been selected for increased growth and carcass yield for three generations. Evaluations at ARS facilities have demonstrated significant increases in performance of the Delta Select compared to a randomly mated line developed from the same base population (Delta Control). Evaluation of performance on commercial farms will be a critical step prior to release of the Delta Select line of channel catfish to the U.S. catfish industry. Commercial farm testing requires large numbers of fish and we have stocked approximately 1 million Delta Select fry and 400,000 Delta control fry in ponds this spring. Agreements are being developed with commercial farmers to evaluate growth and carcass yield of these two populations on commercial farms. The successful adoption of protocols for broodstock management, gamete production, and embryo production has increased the commercial availability of channel x hybrid catfish. Hybrid catfish have also proven superior in higher intensity production systems. Hybrid catfish fry production in 2016 was estimated to produce 225 million hybrid catfish fry from 10 hatcheries. Three hatcheries have expanded their production capacity and three new hatcheries have started hybrid fry production this year. Thus our research continues to focus on improvements in spawning protocols, fertilization protocols, production of high quality gametes, and improved survival of embryos and fry. Experimental broodstock diets with increased levels of lipids or protein were fed for six months after spawning. However, these diets did not improve growth, percentage of females ovulating, relative number of eggs produced, or embryo hatching success. Higher levels of protein and lipid in diets led to higher (P<0.05) levels of n-3 fatty acids and lower (P<0.05) levels of n-6 fatty acids in oocytes. However, this translation of fatty acids in oocytes result in neither improved maturation nor reproductive performance. Evaluation of six strains of blue catfish has shown the Rio Grande strain produced hybrid offspring with superior growth and carcass yield. We have stocked 200,000 Rio Grande fry for potential release as fingerlings to U.S. catfish farmers in the winter of 2018. Whole transcriptome data were generated from fry collected at 8, 15, or 23 days post-hatch. The transcriptome assemblies have been produced and are currently under analysis to determine the timing of the development of the specific immune system. This will direct efforts to determine the age at which fry can be efficiently vaccinated.

4. Accomplishments
1. Production of high-throughput channel catfish genotyping platform. Efficient selection of genetically superior broodstock depends on identification of DNA sequence variants that are correlated with superior trait performance. In order to identify genome-wide DNA sequence variants in channel catfish, ARS scientists in Stoneville, Mississippi, sequenced genomic DNA from Delta Select strain catfish and aligned those sequences to the catfish reference genome assembly. Using computer algorithms, the scientists identified 6 million sequence variants in this population and developed a genotyping platform that contained 660,000 probes for potential sequence variants. Subsequent genotyping demonstrated that 75% of the probes detected DNA sequence variants in other channel catfish. This research produced a platform for interrogating DNA sequence variation throughout the genome to support more efficient genetic selection in the Delta Select catfish population.

2. Genomic selection for growth and carcass yield. Estimation of breeding values in catfish broodstock has depended on progeny testing and the resulting breeding values had a lowered accuracy of predicting the true breeding values. Therefore ARS scientists in Stoneville, Mississippi, used a new array of 50,000 genotyping probes to detect DNA sequence variants in more than 2000 Delta Select strain catfish. This genetic data, combined with trait measurements from more than 20,000 fish from current and prior generations, was analyzed in cooperation with scientists at the University of Georgia to produce genome-based breeding values. The analysis demonstrated a 7% increase in breeding value accuracy compared to traditional estimates of breeding values. This is the first use of genomic breeding values in a catfish selection program, and progeny from parents selected for increased growth and carcass yield based on genomic breeding values were produced in the spring of 2017.

3. Testis development in blue catfish. Testes from blue male catfish are used to obtain sperm to fertilize eggs from channel catfish females for production of hybrid catfish fry. Testis development in blue catfish varies greatly between individuals and understanding the sources of this variation will be useful for improving the efficiency of hybrid catfish fry production. ARS scientists at Stoneville, Mississippi, found that blue catfish strain, fish size, and time of the year (early vs. late spring) all affected testis development. The D&B strain of blue catfish had the largest, best quality testes of the strains tested; larger fish tended to have larger, better quality testes; and testis size and quality were better early in the spring than later in the spring. These results were presented to hybrid catfish producers through workshop presentations and one-on-one meetings to inform their blue catfish broodstock management practices.

4. 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 higher pricing of soybean meal dramatically increases feed costs. ARS and Mississippi State University scientists in Stoneville, Mississippi, continued to examine 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.

5. Alternate feeding regimes for hybrid catfish. Rapidly growing hybrid catfish can often exceed the size range preferred by processors when grown under management practices developed for channel catfish. ARS and Mississippi State University scientists in Stoneville, Mississippi, investigated the effects of reduced feeding on growth and carcass yield of hybrid catfish. The results indicated that feeding to satiation once per week was the best strategy to prevent weight loss and maintain carcass yield in market-size hybrid catfish. This information was provided to catfish feed producers who altered diet compositions and thus lowered feed costs for catfish farmers.

6. Combinations of reproductive peptides improve maturation and ovulation of channel catfish eggs. Induced spawning through injection of natural or synthetic peptides is the only reliable method to produce channel catfish eggs for the production of channel x blue catfish hybrids in hatcheries. Currently, catfish fry producers use two timed injections of a single peptide but it is unknown whether combinations of peptides would improve egg production. ARS scientists at Stoneville, Mississippi, tested five combinations of natural and synthetic ovulating hormones in a spawning trial. A combination of a natural peptide as a priming dose followed by a synthetic hormone as a resolving dose improved egg production by 11.1% and fry production by 477 fry per kilogram female body weight compared to traditional, single peptide methods. Incidence of females that ovulated and hatching rate did not differ from traditional methods. This research demonstrated the potential of a combination of ovulating peptides to increase fry production and thus increase the efficiency of hybrid catfish production.

7. Incubation temperature and paternal species affects the hatching success and progeny performance of catfish. Channel x blue hybrid catfish are exclusively produced in hatcheries by fertilizing the stripped eggs of induced spawn channel catfish with pooled blue catfish sperm. Variations in season and parental species influence the progeny production in hatcheries. Hybrid catfish fry production is inconsistent and variable, hence the need for consistent and increased embryo production is desired to meet the needs of U.S. catfish producers. ARS scientists at Stoneville, Mississippi, evaluated the influence of incubating temperature (to mimic optimum and extreme temperatures in a spawning season) on hatching success and progeny performance. Fertilized eggs were incubated either at 80°F or 90°F and the time to hatch and percent hatching success were lower at the higher water temperature. However, incubation temperature did not affect the survival and progeny performance. This research contradicted an impression by some producers that late-season fry were less viable than early- and mid-season fry.

8. Identification of genomic variation linked to resistance to Proliferative Gill Disease. There is no vaccine against Henneguya ictaluri, the organism that causes Proliferative Gill Disease (PGD) in catfish. Because blue catfish are more resistant than channel catfish to PGD, ARS scientists at Stoneville, Mississippi, evaluated genetic variation in PGD resistance in a backcross family produced by mating a channel x blue catfish F1 hybrid female to a channel catfish male. Fish were challenged with Henneguya ictaluri in a pond. Variation in PGD resistance among the offspring was correlated with their genotype. The analysis revealed two Quantitative Trait Loci associated with PGD resistance that explained 20% of the resistance trait variation. Refinement of these loci will provide targets for marker-assisted selection.

Review Publications
Reichley, S.R., Waldbieser, G.C., Tekedar, H.C., Lawrence, M.L., Griffin, M.J. 2016. Complete genome sequence of Edwardsiella piscicida isolate S11-285 recovered from channel catfish (Ictalurus punctatus) in Mississippi, USA. Genome Announcements. 4(6):e01259-16. doi:10.1128/genomeA.01259-16.

Bickhart, D.M., Rosen, B.D., Koren, S., Sayre, B.L., Hastie, A.R., Chan, S., Lee, J., Lam, E.T., Liachko, I., Sullivan, S.T., Burton, J., Huson, H.J., Kelley, C.M., Hutchison, J.L., Zhou, Y., Sun, J., Crisa, A., Ponce De Leon, F.A., Schwartz, J.C., Hammond, J.A., Waldbieser, G.C., Schroeder, S.G., Liu, G., Dunham, M., Shendure, J., Sonstegard, T.S., Phillippy, A.M., Van Tassell, C.P., Smith, T.P. 2017. Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes. Nature Genetics. 49(4):643-650.

Bosworth, B.G., Quiniou, S., Chatakondi, N.G. 2017. Effects of Season, Strain and Body Weight on Testes Development and Quality in Three Strains of Blue Catfish, Ictalurus furcatus. Journal of the World Aquaculture Society. 49(1):175-182.

Chatakondi, N.G., Yant, R.D., Dunham, R.A. 2016. Effect of paternal blue catfish strain effects on hatchery fry production and performance of channel catfish X blue catfish F1 hybrid fry production and fingerling performance under commercial conditions. North American Journal of Aquaculture. 78:301-306.

Griffin, M.J., Reichley, S.R., Greenway, T.E., Quiniou, S., Ware, C., Gao, D.X., Gaunt, P.S., Yanoung, R.E., Pouder, D.B., Hawke, J.P., Soto, E. 2016. Comparison of Edwardsiella ictaluri isolates from different hosts and geographic origins. Journal of Fish Diseases. 39:947-969.

Hu, E., Bosworth, B.G., Baxter, J., Tiersch, T.R. 2014. On-site evaluation of commercial-scale hybrid catfish production using cryopreserved blue catfish sperm. Aquaculture. 426-437:88-95.

Menghe, L.H., Lucas, P.M., Kingery, K., Bosworth, B.G. 2016. Efficacy of crystalline lysine in alternative diets for pond-raised hybrid catfish, female Ictalurus punctatus X male Ictalurus furcatus. North American Journal of Aquaculture. 47(4):519-525.

Menghe, L.H., Lucas, P.M., Bosworth, B.G. 2017. Evaluation of various combinations of alternative protein feedstuffs to replace soybean meal in diets for pond-raised channel catfish. North American Journal of Aquaculture. 79(2):163-167.

Reichley, S.R., Waldbieser, G.C., Lawrence, M.L., Griffin, M.J. 2016. Complete genome sequence of Edwardsiella hoshinae ATCC 35051. Genome Announcements. doi:10.1128/genomeA.01605-16.

Rosser, T.G., Griffin, M.J., Quiniou, S., Alberson, N.R., Woodyard, E.T., Mischke, C.C., Greenway, T.E., Wise, D.J., Pote, L.M. 2016. Myxobolus ictiobus n. sp. and Myxobolus minutus n. sp. (Cnidaria: Myxobolidae) from the gills of the smallmouth buffalo Ictiobus bubalus Rafinesque (Cypriniformes: Castostomidae). Systematic Parasitology. 93(6):565-574.

Stewart, H.A., Bosworth, B.G., Petrie-Hanson, L., Martin, J., Allen, P.J. 2015. Effects of chronic upper temperature regimes on growth of two geographic strains of channel and hybrid catfish. Aquaculture Research. 46:2407-2417.

Tekedar, H., Kumru, S., Karsi, A., Waldbieser, G.C., Sonstegard, T.S., Schroeder, S.G., Liles, M., Griffin, M., Lawrence, M. 2016. Draft genome sequences of four virulent aeromonas hydrophila strains from catfish aquaculture. Genome Announcements. 4:e00860-16.

Tekedar, H.C., Kumru, S., Kalindamar, S., Karsi, A., Waldbieser, G.C., Sonstegard, T.S., Schroeder, S.G., Liles, M.R., Griffin, M.J., Lawrence, M.L. 2017. Draft genome sequences of three Aeromonas hybrophila isolates from catfish and tilapia. Genome Announcements. 5:e01509-e01516.

Zeng, Q., Fu, Q., Li, Y., Waldbieser, G.C., Bosworth, B.G., Liu, S., Yang, Y., Bao, L., Yuan, Z., Li, N., Liu, Z. 2017. Development of a 690K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence. Scientific Reports. 7:40347.