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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

Project Number: 6066-31000-012-00-D
Project Type: In-House Appropriated

Start Date: Nov 3, 2014
End Date: Nov 2, 2019

Objective:
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.