2011 Annual Report
1a.Objectives (from AD-416)
1) Identify mechanisms and develop tools and methods to improve growth efficiency of catfish..
2)Determine mechanisms of host-pathogen interactions and sources of variation in catfish immune function to improve catfish health and survival. .
3)Improve efficiency of channel and blue catfish reproduction and channel x blue hybrid production..
4)Identify genomic regions affecting variation in traits of economic importance through quantitative trait locus (QTL) discovery and fine mapping strategies..
5)Develop, and transfer to commercial producers, channel catfish and blue catfish germplasm improved for growth, yield, and disease resistance for improved production of channel, blue and hybrid catfish.
1b.Approach (from AD-416)
To attain the first objective, we will correlate mitochondrial functional variation with catfish feed efficiency and identify and determine the role of specific genes and gene products (peptides and proteins) involved in controlling growth in catfish. For the second objective, we will construct a catfish microarray targeted toward immune function, characterize functional genetic variation in resistant vs. susceptible channel catfish, and characterize the effect of prebiotic administration on catfish immune function. For the third objective we will induce early maturation in channel catfish and blue catfish through compressed annual temperature cycles, increase ovulation and fertilization efficiency for production of blue X channel F1 hybrid catfish, and establish a technique for spematogonial transplantation between blue and channel catfish. For the fourth objective we will enhance and integrate genetic and physical maps, and identify quantitative trait loci associated with superior production traits, especially carcass traits and survivability to E. ictaluri infection. For the fifth objective, we will produce a line of select channel catfish based on multi-trait selection within a commercial composite population, produce a line of select blue catfish based on males that produce hybrid offspring with superior growth and carcass yield, and produce male channel and blue catfish which have a YY sex chromosome complement for all male catfish production.
Commercial production of hybrid catfish fry has increased to an estimated 110 million in 2011. Part of the increase has been due to technology developed and refined by ARS researchers at the Catfish Genetics Research Unit (CGRU), such as more efficient broodstock preparation, gamete collection, and embryo culture. The technology has been transferred to commercial producers through workshops and on-farm consultation.
Low doses of salmon luteinizing hormone releasing hormone (LHRHa) were as efficacious as the currently used mammalian LHRHa to induce channel catfish ovulation. The research was validated in three field trials in commercial hatcheries. Salmon LHRHa would provide significant cost savings to hybrid catfish producers.
One of the largest catfish fingerling producers in Alabama, Mississippi, and Arkansas has begun incorporating essential oils into the diets of their juvenile channel catfish as a direct result of cooperative research conducted by ARS and Mississippi State University researchers at the National Warmwater Aquaculture Center in Stoneville, MS.
Catfish Genetics Research Unit research showed that macrophages from fish of “Enteric Septicemia of Catfish (ESC) resistant” families had an enhanced ability to kill intracellular pathogens and inhibit the replication of bacteria within the macrophage. This research provides a novel tool for the investigation of the variation in immune responses between catfish and the identification of selection markers for catfish selective breeding.
Development of gene expression assays for a full set of catfish Toll-like receptor genes permits investigation into the role of these receptors in catfish resistance or susceptibility to pathogens, and whether these receptors can serve as selection markers for catfish selective breeding.
Deep sequencing of catfish genomic DNA and sequence assembly led to the production of approximately 250,000 unique sequences that were greater than 400 nucleotides and averaged 2,500 nucleotides in length. These sequences were shared with cooperating scientists and permitted efficient identification of several genes related to catfish immunity that had previously been difficult to clone.
Evaluation of prebiotics and essential oils for improving catfish production. Losses to disease lead to significant losses in catfish production so practical approaches are needed to improve catfish immunity. Studies conducted by ARS scientists at Stoneville, MS, showed that up to 80% of fish meal in catfish diets could be replaced with a yeast-derived prebiotic without negatively affecting weight gain or feed efficiency. In addition, this prebiotic did not appear to negatively affect disease susceptibility of catfish challenged with Edwardsiella (E.) ictaluri. A second study with essential oils showed that treated fish gained approximately 40% more weight compared to control fish. Future studies using essential oils will be conducted and studies will examine whether these additives improve immune function in fish challenged with E. ictaluri.
Evaluation of processing yield in fish from nutrition studies. Diet composition can affect fillet yield and composition, traits that influence profit and product quality. In cooperation with Mississippi State University and the University of Arkansas Pine Bluff, ARS researchers at the Catfish Genetics Research Unit (CGRU) in Stoneville, Mississippi, analyzed fish from multiple studies for processing yield at the CGRU processing facility. Data was provided to cooperators who utilized it to determine impact of altering diet composition on processing yield. Multiple studies indicated dietary protein levels of 28 to 32% were optimal for growth and fillet yield of farm-raised catfish. Dietary protein levels lower than 28% led to reduced fillet yield while protein levels higher than 32% did not provide sufficient improvements in growth and fillet yield to be economically justifiable. Currently nearly all catfish producers feed either 28 or 32% protein diets.
Effects of stocking density on production traits of channel catfish x blue catfish hybrid foodfish. Hybrid catfish are more commonly grown in commercial ponds but more information is needed to determine optimal production strategies. ARS scientists at the Catfish Genetics Research Unit in Stoneville, Mississippi, performed pond growth trials of hybrid catfish fingerlines at varying stocking densities, then measured growth, survival, feed conversion, and meat yield. Net production (lbs of fish produced per acre) increased as stocking density increased but stocking density did not affect survival, feed conversion ratio, or meat yield from 3,000 to 9,000 fish per acre. However, ponds stocked at 11,000 fish per acre resulted in smaller fish and fewer fish of marketable size, therefore the production cycle would be longer and production costs would increase at this density. The experiments provided producers with information on efficient stocking parameters for hybrid catfish growth.
Estimation of genetic parameters for growth and Enteric Septicemia of Catfish (ESC) resistance in channel catfish. Information on heritabilities for economically important traits is required for efficient improvement of these traits in channel catfish. ARS scientists at the Catfish Genetics Research Unit in Stoneville, Mississippi, evaluated channel catfish growth, fillet yield and resistance to ESC as part of an integrated breeding program. Heritability for growth and fillet yield were moderately high (0.35 and 0.38, respectively) while heritability for survival to ESC challenge was not different from zero. Breeding values were estimated and fish were selected for improved growth and fillet yield based on a selection index with equal weighting for growth and fillet yield. The selected catfish formed the foundation of a genetically improved population for ultimate release to the industry.
Production and evaluation of hybrid catfish from various strains of blue catfish. Little information is available on the effects of blue catfish germplasm on production traits of channel x blue hybrid catfish offspring. ARS scientists at the Catfish Genetics Research Unit in Stoneville, Mississippi, have obtained blue catfish from several geographic sources (strains) and have initiated a program to determine the effects of blue catfish strain and individual within strain on hybrid offspring growth and fillet yield. Blue catfish sperm was cryopreserved in conjunction with these evaluations to maintain a repository of germplasm for future use. This population will be useful in a genetic selection program to identify blue catfish males that sire hybrid offspring with superior performance.
Commercial production of channel x blue hybrid catfish fry. Production of channel catfish x blue catfish hybrids has increased substantially over the last 3 years. Hybrids will comprise about 20% of food fish harvested in 2011 and interest in producing hybrids continues to increase. The hybrid generally has better growth, survival and meat yield than channel catfish, which most producers currently grow. However, production of hybrid fry involves hormone induced ovulation and manual (or strip) spawning of females. Few farmers are familiar with the techniques for hormone induced spawning required to produce hybrids. ARS scientists at the Catfish Genetics Research Unit (CGRU) in Stoneville, Mississippi, in conjunction with Mississippi State University scientists, offered a 2 day workshop demonstrating techniques for production of hybrid catfish fry. Eighteen catfish produces attended the workshop and provided very positive feedback. Additionally, CGRU scientists provided frequent on-site consultation to the 6 hatcheries that currently produce hybrid catfish fry. Hybrid fry production for the spring of 2011 was estimated to be 110 million, an increase of 20% from 2010. Three additional hatcheries have contacted unit scientists indicating intent to produce hybrid fry in 2012 and requesting advice and assistance of unit scientists.
Jar hatching of hybrid catfish fry. Fertilization rates obtained from hormone induced spawning of catfish are generally lower than those obtained from pond-spawning. The lower fertility of eggs from hormone-induced spawns results in increased bacterial and fungal infections and reduced hatch compared to pond-spawned egg masses which typically have higher fertility. ARS scientists at the Catfish Genetics Research Unit in Stoneville, Mississippi, developed techniques for jar hatching of hybrid catfish embryos. Although jar hatching is used to hatch eggs from various fish species, unit scientists designed jars that would allow hatching of the large volume of eggs required at commercial catfish hatcheries and developed strategies to eliminate the adhesiveness of catfish eggs necessary for jar hatching. Research and commercial trials have indicated jar hatching increases hatch by 5 to 15%, and substantially decreases labor compared to traditional trough hatching of hybrid egg-masses. Two of the six commercial hatcheries producing hybrids used the jar hatching technology for all hybrid fry production in 2011, two others tested the technique and indicated they would increase use of the technology in spring 2012, and the other two expressed interest in trying the technology in 2012.
Hormone implants improved channel catfish spawning: Synchronizing ovulation of channel catfish females and subsequent production of good quality eggs has been a major obstacle in producing commercial quantities of channel X blue F1 hybrid fry. ARS scientists at the Catfish Genetics Research Unit in Stoneville, Mississippi, showed that carbopol- and cholesterol-sustained-release luteinizing hormone releasing hormone (LHRHa) implants synchronized maturation and improved ovulation of channel catfish compared to LHRHa in liquid suspension. Improved maturation of ovulated eggs also resulted in higher hatching success of hybrid embryos. Future studies will address the endocrinological response of implants on egg quality.
Supplemental catfish oil dietary lipid improves maturation and reproductive readiness for hormone induced spawning of channel catfish. Hybrid catfish production requires large quantities of mature brood fish with potential to produce high quality eggs through manual stripping. Lipids and fatty acids have been reported to play a major role in broodstock nutrition and influence the quality of developing eggs. Pond trials conducted by ARS scientists at the Catfish Genetics Research Unit in Stoneville, MS, showed that catfish oil incorporated as a dietary lipid supplement improved the oocyte fatty acid profile and subsequent reproductive performance of channel catfish. At 5% catfish oil supplementation to the brood fish diet, a higher percent of catfish females attained a threshold level of maturity suitable for hormone induced spawning, ovulating response, fecundity and hybrid embryo production. This project addresses the need to develop brood fish diets for improving the reproductive efficiency of channel catfish.
Hybrid catfish embryos need higher levels of calcium hardness than channel catfish embryos during hatching. Hatching success of hybrid catfish embryos is lower than the naturally pond spawned channel catfish embryos in catfish hatcheries. Apart from reduced egg quality, hatchery water with suboptimal calcium levels (hardness) also lowers hatchability of hybrid embryos. ARS scientists at the Catfish Genetics Research Unit in Stoneville, Mississippi, evaluated the effect of dissolved calcium on hatching success to develop a practical criterion for desired calcium level in hatching waters for hybrid embryo. Water with 50 parts per million (ppm) of calcium hardness was optimal for hatching hybrid embryos, and was higher than the recommended 10 ppm of calcium hardness to hatch channel catfish embryos. The results also showed that hatching hybrid embryos at suboptimal levels of calcium hardness significantly reduced the hatching success of hybrid embryos.
Efficacy of salmon luteinizing hormone releasing hormone (LHRHa) to induce channel catfish spawning for hybrid embryo production. Exogenous hormone treatments are successfully used in channel x blue hybrid embryo production in catfish hatcheries but there is a need for an effective hormone that can be applied at reduced rates to lower production costs. ARS scientists at the Catfish Genetics Research Unit in Stoneville, MS, demonstrated that low doses of salmon LHRHa were as efficacious as the currently used mammalian LHRHa to induce channel catfish ovulation. The results of this research were field tested in three commercial hatcheries. Low dosage salmon LHRHa can reduce the hormone costs associated with strip spawning of channel catfish in hybrid embryo production.
Determining the role of macrophages in resistance and susceptibility to disease in catfish. Developing strategies for encouraging disease resistance through selective breeding requires an understanding of the biological and genetic basis of resistance to disease. ARS scientists at the Catfish Genetics Research Unit in Stoneville, Mississippi, have cultured macrophages from catfish that demonstrate a highly resistant (>80% survival) or a highly susceptible phenotype following experimental challenge with relevant pathogens. Results of experiments show that macrophages from resistant families have an enhanced ability to kill intracellular pathogens and are able to inhibit intracellular replication, despite the fact that there is no difference in initial uptake rates by either “resistant” or “susceptible” cells. The results from these studies will be applied to vaccine development, husbandry methods, and development of food additives that will enhance innate immunity in catfish.
Identification of catfish T-lymphocyte surface markers. T lymphocytes are critical cells in the immune response. Research to determine the role of T cells in catfish immunity have been hampered by the lack of subgroup cell surface markers. ARS scientists at the Catfish Genetics Research Unit in Stoneville, Mississippi, in cooperation with the University of Mississippi Medical Center, used molecular approaches to identify three CD3 molecules, which are surface markers in all T cells, and two CD8 molecules, which are cytotoxic T cell surface markers. These cell markers facilitate studies of the specific cellular responses to pathogen infection or vaccination in catfish.
Identification of all catfish Toll-like receptor molecules. Recognition of microbial products by Toll-like receptor (TLR) molecules results in the induction of innate immunity mechanisms and development of antigen-specific adaptive immune responses. Toll-like receptors are the front line of the immune system against bacteria, virus or parasites and dysfunction can result in an impaired response to pathogens. In order to determine the role of TLRs in catfish immune responses, 15 TLR types were identified in catfish using molecular genetic techniques. This represents the most complete set of TLRs in any bony fish. Quantitative real-time polymerase chain reaction (PCR) assays were validated for each TLR gene. These assays enable measurement of variation in TLR gene activity in catfish that are resistant or susceptible to specific pathogens and can serve as potential selection markers for catfish improvement.
Regulators of feed efficiency in catfish. Factors that control feed efficiency are not well understood in catfish. Therefore ARS scientists in Stoneville, MS, conducted research to investigate the role mitochondrial respiratory chain enzyme activities on low and high Feed Efficient (FE) families of catfish. Mitochondrial complex enzyme activities showed that the activities of the liver mitochondrial complexes (I, II, III, IV) were all lower in the low FE family compared to the high FE family. Enzyme activities of the muscle and gene expression from the liver and muscle are currently being evaluated. Understanding how the mitochondrial respiratory chain controls FE will help researchers develop strategies to improve FE in catfish.
Li, M.H., Robinson, E.H., Oberle, D.F., Lucus, P.M., Peterson, B.C., Bates, T.D. 2011. Clearance of yellow pigments lutein and zeathanxin in channel catfish reared at different water temperatures. Journal of the World Aquaculture Society. 41:105-110.
Davis Jr, K.B., Gaylord, T.G. 2011. Effect of fasting on body composition and responses to stress in sunshine bass. Comparative Biochemistry and Physiology. 158A:20-36.
Booth, N.J., Bourgeois, A.L. 2009. Proteomic analysis of head kidney tissue from high and low susceptibility families of channel catfish following challenge with Edwardsiella ictaluri. Fish and Shellfish Immunology. 26:193-196.
Davis Jr, K.B., Mcentire, M.E. 2011. Influence of reproductive status, sex hormones and temperature on plasma IGF-I concentrations in sunshine bass (Morone Chrysops X Morone Saxatilis). Comparative Biochemistry and Physiology. 158A:13-16.
Lakeh, A.B., Farahmand, H., Mirvaghefi, A., Kloas, W., Peterson, B.C., Wuertz, S. 2011. GH and IGF-I induction by passive immunization of rainbow trout Oncorhynchus mykiss Walbaum using a somatostatin 14 antibody. Aquaculture. 316(1-4):99-103.
Li, M.H., Robinson, E.H., Bosworth, B.G., Oberle, D.F., Lucas, P.M. 2011. Use of corn gluten feed and cottonseed meal to replace soybean meal in diets for pond raised channel catfish. North American Journal of Aquaculture. 73:153-158.
Liu, H., Peatman, E., Wang, W., Abernathy, J., Liu, S., Kucuktas, H., Lu, J., Xu, D., Klesius, P.H., Waldbieser, G.C., Liu, Z. 2010. Molecular responses of calreticulin genes to iron overload and bacterial challenge in channel catfish Ictalurus punctatus. Developmental and Comparative Immunology. 35:267-272.
Niu, D., Peatman, E., Liu, H., Lu, J., Kucuktas, H., Liu, S., Sun, F., Zhang, H., Feng, T., Zhou, Z., Terhune, J., Waldbieser, G.C., Li, J., Liu, Z. 2011. Microfibrillar associated protein 4 mfap4 genes in catfish play a novel role in innate immune responses. Developmental and Comparative Immunology. 35:568-579.
Peterson, B.C., Booth, N.J. 2010. Validation of a whole-body cortisol extraction procedure for channel catfish (Ictalurus punctatus) fry. Fish Physiology and Biochemistry Journal. 36:661-665.
Peterson, B.C., Bosworth, B.G., Small, B.C. 2010. Comparison of growth, body composition, and stress response of USDA 103 USDA 403 industry and fast growing lines of channel catfish. Journal of the World Aquaculture Society. 41:156-162.
Peterson, B.C., Bramble, T.C., Manning, B.B. 2010. Effects of Bio-Mos on growth and survival of channel catfish challenged with Edwardsiella ictaluri. Journal of the World Aquaculture Society. 41:149-155.
Quiniou, S., Sahoo, M., Edholm, E., Bengten, E., Wilson, M. 2011. Channel catfish CD8a and CD8ß co-receptors characterization expression and polymorphism. Fish and Shellfish Immunology. 30(3):894-901.
Quiniou, S., Wilson, M., Boudinot, P. 2011. Processing of fish lg heavy chain transcripts: Diverse splicing patterns and unusual nonsense mediated decay. Developmental and Comparative Immunology. 35:949-958.
Small, B.C., Quiniou, S., Kaiya, H. 2009. Sequence, genomic organization and expression of two channel catfish, Ictalurus punctatus, Ghrelin receptors. Comparative Biochemistry and Physiology. 154(4):451-464.
Taylor, J.D., Cooper, A.L., Barras, S.C., Chatakondi, N.G., Jackson, J.R., Riffell, S.K., West, B.C. 2010. Feeding behavior and diet of free ranging black crowned night herons on a catfish aquaculture facility in Mississippi. Southeastern Association of Fish and Wildlife Agencies Conference. 64:118-124.
Waldbieser, G.C. 2011. SNP discovery through de novo deep sequencing using the next generation of DNA sequencers. Whole Genome-based Selection for Aquaculture: Principles and Protocols. p. 69-90.
Carrias, A., Welch, T.J., Waldbieser, G.C., Mead, D.A., Terhune, J.S., Liles, M.R. 2011. Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri. Virology Journal. 8:6. DOI: 10.1186/1743-422X-8-6.
Quiniou, S., Waldbieser, G.C. 2011. Mapping of the toll like receptor family in channel catfish, Ictalurus punctatus. Animal Genetics. 42:567-568.