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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

2011 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

The expanding aquatic-foods market requires faster growing fish with better flesh quality and longer shelf-life than currently available. However, there is limited genetic information on genes that enhance production efficiency and yield a higher quality muscle preferred by consumers. Using state-of-the-art genomic technologies, we have identified genetic markers associated with growth-rate in rainbow trout. These markers were validated on a large number of individuals and are being evaluated for marker-assisted selection for enhanced growth in the broodstock population at NCCCWA. We have also generated a comprehensive database of the rainbow trout “microRNAome”. We are currently looking for differences in microRNAs that are responsible for phenotypic variations in muscle growth yield and fillet quality traits. We have identified and characterized, for the first time, the Akt-TOR genes (known to play important roles in metabolism and muscle growth in mammals) in rainbow trout. Expression analysis of these genes suggested a role of Akt-TOR as a crucial regulator of muscle growth in rainbow trout. We have completed a study to investigate the effects of maturation on muscle growth and quality of fish on a high nutritional plane. The study indicates that improvement of nutrition and feeding protocols during sexual maturation can reduce many of the adverse effects on fish growth and fillet quality. We recently examined phenotypic variations in muscle growth yield and fillet quality traits in 100 selected families from the NCCCWA rainbow trout breeding program. Families showing extreme phenotypes will be subjected to genome scans and gene expression analysis to identify genes controlling these traits.

Egg quality in fish is highly variable and can therefore be a serious problem in the fish farming industry, especially for intensively cultured species such as rainbow trout. Genes/microRNAs specifically expressed in the oocyte play important roles in oogenesis, ovarian folliculogenesis, and early embryonic development. Identification of key oocyte-specific genes/microRNAs and understanding their roles in controlling folliculogenesis and early embryonic development may ultimately lead to the discovery of new candidate genes/microRNAs potentially associated with oocyte competence and embryonic survival in rainbow trout. To date, we have identified a number of oocyte-specific genes, including a gene encodes a new F-box protein and a group of nuclear transport proteins (importins). We have also identified proteins that interact with these oocyte-specific proteins. Using deep sequencing technology, we recently completed characterization of microRNAs in rainbow trout oocyte and identified 4 novel microRNAs predominantly expressed in eggs.

The ADODR is in frequent contact with the cooperator through phone calls, email, and site visits in addition to receipt of written reports.


Last Modified: 8/29/2014
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