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United States Department of Agriculture

Agricultural Research Service

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Research Project: FUNCTIONAL GENOMICS RESEARCH FOR RAINBOW TROUT AQUACULTURE PRODUCTION

Location: Cool and Cold Water Aquaculture Research

2010 Annual Report


1a.Objectives (from AD-416)
A major constraint to increasing the production efficiency of the Nation's cool and cold water aquaculture industry is the lack of genetically improved strains of fish for aquaculture. There is only limited genetic information on traits that will enhance production efficiency and yield a better quality fish. Identification and characterization of genes affecting aquaculture production traits will facilitate the development of genetically improved strains to increase aquaculture production efficiency. The objectives of the research outlined in this agreement focus on the identification of genes affecting oocyte maturation and embryogenesis in rainbow trout. Characterization of these genes will result in more in-depth understanding of the biology of reproduction and embryonic development and will impact strategies for improving developmental characteristics in broodstock.


1b.Approach (from AD-416)
Collaborators at the USDA/ARS/NCCCWA and West Virginia University have worked to develop resources for conducting functional genomic research in rainbow trout. Resources which specifically target studies on embryogenesis include large volumes of expressed sequence tag data from oocyte and embryonic developmental stages and a cDNA panel representing oocytes thru day 50 post fertilization for gene expression analyses. Strategies will include analyses of gene expression and proteomic data in NCCCWA Broodstock to identify and characterize novel-oocyte specific genes, similar strategies will be employed to characterize gene expression throughout embryonic development.


3.Progress Report

The objectives of the research outlined in this agreement focus on the identification of genes affecting oocyte maturation and embryogenesis in rainbow trout. Characterization of these genes will result in more in-depth understanding of the biology of reproduction and embryonic development and will impact strategies for improving developmental characteristics in broodstock. To this end multiple oocyte-expressed genes important for folliculogenesis and early embryonic development have been identified and characterized. F-box proteins are components of ubiquitin-ligase complexes, which bind substrates for uiquitin-mediated proteolysis. Using yeast two-hybrid screen system, a number of proteins that interact with the novel F-box protein (Fbos) were indentified.

Three MuRF genes were cloned and characterized and their expression in association with starvation- and spawning-induced muscle atrophy in rainbow trout was determined. All three genes are predominantly expressed in muscle and heart tissues and are up-regulated in starvation- and spawning-induced muscle atrophy in rainbow trout, suggesting an important role of these genes in muscle protein degradation in fish.

Deep sequencing of a rainbow trout double-haploid transcriptome using 454 pyrosequencing technology resulted in about 1.3 million reads with an average length of 344 bp (447 million bases). Gene Ontology analysis of the combination assembly showed similarity to transcriptomes of other fish species with known genome sequences, suggesting a genome-wide representation of the rainbow trout transcriptome.

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: 7/23/2014
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