Location: Warmwater Aquaculture Research Unit
2015 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.
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
A genome sequence assembly was produced for the channel catfish and was one of the most complete fish genome assemblies to date. The 29 channel catfish chromosomes were defined for the first time based on the physical sizes of assembled scaffolds that were anchored to the linkage groups on the genetic map. Alignment of genomic sequence from 48 founders of the Delta Select line to the genome assembly revealed 1.6 million single nucleotide variants in these fish, and these variants will be used to produce a genotyping array that supports genomic selection within the Delta Select line. Initial data from analyses of purebred and hybrid catfish performance indicate that selection of purebreds with superior performance will lead to improved performance in their hybrid offspring. Researchers have made progress in the Delta Select catfish line for growth rate and have begun a parallel selection program for blue catfish. Warmwater Aquaculture Research Unit scientists continued to investigate physiological pathways involved in growth, reproduction, and immunity in order to identify biomarkers and phenotypes useful in selection indices. Researchers continued to improve protocols for efficient production of high quality gametes from channel and blue catfish and improve management of embryos for hybrid fry production. Technology transfer to the catfish industry contributed to the increased commercial production of hybrid catfish, and producers estimated production of 200 million hybrid fry in 2014, an increase of 25 million from 2013. Commercial processors estimated that hybrids comprised more than 50% of the catfish processed in 2013.
Accomplishments
1. Production of the channel catfish genome sequence assembly. Analysis of genomic contributions to production phenotypes, and efficient selection of catfish that contain positive genomic variation requires a reference genome sequence assembly. ARS scientists at the Warmwater Aquaculture Research Unit and the Genomics and Bioinformatics Research Unit in Stoneville, MS, and the Animal Genomics and Improvement Laboratory in Beltsville, MD, collaborated with scientists at Auburn University, the Department of Homeland Security, and the University of Maryland to produce a whole genome sequence assembly for the channel catfish. Genomic Deoxyribonucleic acid (DNA) was utilized from “Coco”, a doubled haploid (homozygous) catfish, to produce 1.3 billion DNA sequences with next-generation DNA sequencing technologies. The sequences were filtered and assembled using the MaSuRCA assembly software, and a novel method was used to fill gaps within scaffolded sequences. The team produced the most complete and continuous fish genome sequence to be assembled from next-generation technology to date. Assembly accuracy was validated using a variety of genomic resources such as sequences from DNA libraries and alignment to the catfish genetic map. The team demonstrated that the vast majority of DNA sequences from other channel catfish can be aligned to this assembly. The catfish genome assembly contained more predicted genes than any fish genome assembly - 26,381 gene predictions could be validated from experimental gene expression data. The genome assembly will be key to the identification of sequence variation that is linked to improved performance for traits such as growth rate and carcass yield, and will permit selection of broodstock based on high resolution relationships with fish that exhibit superior performance.
2. Egg quality and method of incubation influence hatching success in catfish hatcheries. Commercial production of hybrid catfish has been steadily increasing as hybrids can demonstrate superior production in ponds compared to channel catfish. However, production of hybrid catfish fry has been inconsistent and unpredictable in commercial hatcheries, and egg quality can be affected by variations in maturity levels, dosage of ovulatory peptide, age and the physical stripping process. ARS scientists at the Warmwater Aquaculture Research Unit in Stoneville, Mississippi, compared the hatching success of manually stripped, fertilized catfish eggs of varying quality in either troughs or McDonald jars. Eqq quality was determined based on pH of ovarian fluid where pH of 7.5 or greater provided higher quality eggs. Batches of eggs considered high quality hatched at a higher rate (60.9%) than batches considered low quality (41.4%). The hatching success of the low quality batch was higher in troughs (46.7%) than in jars (36.1%). Method of incubation did not affect the hatching success of the high quality batch. The findings of the study point to the importance of obtaining high quality eggs to maximize the production of hybrid catfish fry in commercial hatcheries regardless of the incubation method.
3. A potent peptide to induce ovulation in catfish. Hybrid catfish produced by manual mating of channel catfish females with blue catfish males demonstrate superior production in ponds compared to purebred channel catfish. Induced spawning of channel catfish is the only reliable method for production of hybrid catfish embryos in hatcheries, but the type and dose of peptides used to induce ovulation in catfish could be optimized to improve the efficiency of hybrid fry production. ARS scientists at the Warmwater Aquaculture Research Unit in Stoneville, Mississippi, evaluated the efficacy of salmon gonadotropin releasing hormone analog (sGnRHa) to induce ovulation in channel catfish. The results suggested 10 ug sGnRHa per kg of body weight was the minimum effective dose to induce ovulation in channel catfish, and this dose is ten times lower than the widely used mammalian peptide currently used in catfish hatcheries. The dosage was validated in 5 commercial hatcheries. The recommended dose of this synthetic peptide halved the cost of the peptide thus lowering the cost of hybrid embryo production.
4. Production of genome sequence assemblies for microbial pathogens. Bacterial species within the Edwardsiella (E.) genus have been historically implicated in fish disease outbreaks worldwide, including channel and blue catfish. Until recently, Edwardsiella tarda was considered pathogenic to fish, but recent molecular genetic research has led to the division of this clade into E. tarda and E. piscicida, with the latter species pathogenic to fish. Several published genomes initially categorized as E. tarda are actually E. piscicida. ARS scientists at the Warmwater Aquaculture Research Unit in Stoneville, Mississippi, in collaboration with scientists at Mississippi State University, have used new Deoxyribonucleic acid (DNA) sequencing technologies and new sequence assembly software to produce a complete reference genome sequence assembly of the FL95-01 strain of E. tarda, and this is the only E. tarda sequence currently available. The genome sequence permits comparative genomic analyses with E. piscicida isolates that are implicated in fish disease outbreaks, with the goal of understanding virulence and environmental adaptations of Edwardsiella species in order to develop diagnostics and therapeutants to reduce catfish production losses.
5. Evaluation of processing yield in catfish from nutrition studies. Changes in the composition of catfish diets and feeding regimes can alter fillet yield and composition, but researchers and producers are constantly testing new diets to determine whether less expensive ingredients can be used without affecting catfish yield. ARS scientists at the Warmwater Aquaculture Research Unit in Stoneville, MS, in cooperation with scientists at Mississippi State University raised catfish on diets in which soybean meal was partially replaced with cottonseed meal, corn gluten, or corn germ. Approximately half the soybean meal could be replaced with these less expensive alternatives without negatively affecting meat yield or meat quality. This research demonstrated that partial replacement of soybean meal with alternative protein sources can lower the feed cost without negatively affecting product quality.
Review Publications
Gaunt, P.S., Chatakondi, N.G., Gao, D., Endris, R. 2015. Efficacy of florfenicol for control of mortality associated with Edwardsiella ictaluri in three species of catfish. Journal of Aquatic Animal Health. 27:45-49.
Kobayashi, Y., Peterson, B.C., Waldbieser, G.C. 2015. Identification of Two Distinct Uncoupling Protein 2 (UCP2) Messenger RNAs and the Relationship between Expression, Food Intake, and Growth in Channel Catfish. Domestic Animal Endocrinology. 51:56-64.
Li, M.H., Robinson, E.H., Lucas, P.M., Bosworth, B.G. 2015. Evaluation of low-protein alternative diets for pond-raised hybrid catfish, Ictalurus puncatus X Ictalurus furcatus. Journal of the World Aquaculture Society. 46:228-234.
Peterson, B.C., Peatman, E., Ourth, D.D., Waldbieser, G.C. 2015. Effects of a phytogenic feed additive on susceptibility of channel catfish to Edwardsiella ictaluri and levels of mannose binding lectin. Fish and Shellfish Immunology. 44:21-25.
Tekedar, H., Karsi, A., Akgul, A., Kalindamar, S., Waldbieser, G.C., Sonstegard, T.S., Schroeder, S.G., Lawrence, M. 2015. Complete genome sequence of Aeromonas hydrophila AL06-06. Genome Announcements. 3(2):e00368-15.
Straus, D.L., Farmer, B.D., Beck, B.H., Bosworth, B.G., Torrans, E.L., Tucker, C.S. 2014. Water hardness influences Flavobacterium columnare pathogenesis in channel catfish. Aquaculture. 435:252-256.
