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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

2012 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:

RNA-Seq is an emerging technology that facilitates the identification of genetic markers and genes associated with traits of interest. We used this technology to identify genetic markers associated with growth traits in the NCCCWA rainbow trout broodstock population and in outbred commercial populations and determined that they are beneficial for use in selective breeding programs aimed at improving growth characteristics.

Having access to gene sequence information greatly enhances research approaches aimed at characterizing the functions of genes. To this end we employed Illumina sequencing technology to obtain sequence information on all genes expressed in 15 vital tissues, providing most comprehensive resource that is available for rainbow trout.

The nutrient and energy demand of sexual maturation in fish causes structural change to muscle proteins and affects fillet firmness. The relationship between fish maturation, measured as egg development, and chemical characteristics of fillets from fertile and sterile fish was evaluated. Thermal denaturation and viscoelastic characterization revealed changes in stability and gelling properties of muscle proteins that were related to changes in fillet texture.

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. Identification of key genes expressed in the egg and understanding their roles in early embryonic development may ultimately lead to the improved embryonic survival in rainbow trout. We have identified and characterized a number of important egg-expressed genes. We have also finished a complete survey of special RNA sequences called “microRNAs”, which may lead to the identification of factors controlling egg quality in rainbow trout.


Last Modified: 9/10/2014
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