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United States Department of Agriculture

Agricultural Research Service

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Research Project: UTILIZATION OF GENOMICS FOR IMPROVING PRODUCTION TRAITS IN COOL AND COLD WATER AQUACULTURE

Location: Cool and Cold Water Aquaculture Research

2013 Annual Report


1a.Objectives (from AD-416):
The application of genomic technologies towards the genetic improvement of aquaculture species is expected to facilitate selective breeding and provide basic information on the biochemical mechanisms controlling traits of interest. In the previous project, a suite of genome tools and reagents for rainbow trout was developed to identify and characterize genes affecting aquaculture production traits. This included genetic markers, genetic maps, and comparative maps with the genome sequences of model aquatic organisms, expressed sequence tags, and microarrays for functional genomic research. This proposed project not only continues the development of resources that will facilitate biological research for this species, but aims to use the existing complement of tools to identify genes affecting production traits including disease resistance and stress tolerance, in the process providing information for selectively breeding these traits in commercial populations.


1b.Approach (from AD-416):
Rainbow trout (Oncorhynchus mykiss) are the most widely farmed cold freshwater species and the second most valuable finfish aquaculture product in the United States. The application of genomic technologies towards the genetic improvement of aquaculture species is expected to facilitate selective breeding and provide basic information on the biochemical mechanisms controlling traits of interest. In the previous project, a suite of genome tools and reagents for rainbow trout was developed to identify and characterize genes affecting aquaculture production traits. Projects concurrent with the previous project characterized the genetic variation of the National Center for Cool and Cold Water Aquaculture (NCCCWA) broodstock with respect to resistance to Bacterial Cold Water Disease (BCWD) and response to crowding stress. Specific crosses were identified that will facilitate the identification of chromosome regions and genes affecting these traits through genetic mapping and functional genomic approaches. The current project will continue the genome scans of these crosses with new sets of markers to identify positional candidate genes affecting these traits. In addition, possibilities for developing informative crosses and functional genomic approaches which target the identification of genes affecting carcass quality traits will be determined. We will also continue to identify and characterize genes in the oocyte which impact embryonic development and egg quality traits important to breeders. This information is important to gain a better understanding of the genetics of production traits and for transferring genetic information and improved germplasm from the NCCCWA selective breeding program to customers and stakeholders.


3.Progress Report:

Four studies were conducted to identify genes responsible for differences in fillet quality and changes in energy metabolism during sexual maturation. In the first study, effects of feeding level and chromosome set number on fatty acid composition and metabolism of energy stores were considered. This study showed that ploidy (sets of chromosomes) had greater impacts on fatty acid metabolism and composition of energy stores than moderately restricted diets at sexual maturation. A second study investigated changes in fatty acid metabolism of diploid (2 sets of chromosomes) and triploid (3 sets of chromosomes) female trout throughout sexual maturation (16-24 months). These data showed that there are no physiological differences between diploid and triploid females prior to 18 months of age; however, there are dramatic differences in energy store compositions and gene expression beginning at 20 months. A subsequent study examined differences in fatty acid composition and gene expression between immature male and female rainbow trout. Females had higher muscle omega-3 content; albeit, no differences were observed for other fatty acids measured. Lastly, to evaluate the specific effects of genetic selection; fillet yield, and fat content, fillet fatty acid composition and gene expression of 20 families selected for improved growth were assessed. This study indicated that high-yield/low-fat fish produced the highest quality fillets as measured by instrumental texture and composition.

A study on the effects of sexual maturation on muscle showed that fish fed on a high plane of nutrition did not exhibit the muscle deterioration signs that are typically associated with the nutrient demands of reproduction. Instead, fish carry eggs exhibited reduced intramuscular crude fat that is lower in saturated and monounsaturated fatty acids and higher in polyunsaturated fatty acids compared to sterile fish. Studies of gene expression point out that nutrition affects the molecular signals that underlie adverse effects of sexual maturation on fish muscle growth and fillet quality.

Variations in muscle crude fat (%) were measured in 100 families from the USDA breeding program. Variations in fat content were correlated to transcriptome-wide SNP allele frequencies and to global patterns of gene expression in families showing extreme phenotypes (4 high-muscle fat families [10.20%± 0.32] versus 4 low-muscle fat families [5.15% +/- 0.86]). Thousands of presumptive genetic markers were identified, and 30 of them were specific to the “high-muscle fat” group and 18 were specific to the “low-muscle fat” group. A subset of the markers specific to each group are currently being evaluated for association with muscle yield in about a 500-fish panel from 97 families.

High volume sequencing of tissue samples to identify 4830 tissue-specific genes.


Last Modified: 7/30/2014
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