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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

2006 Annual Report


1.What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? Why does it matter?
Aquaculture is the most rapidly growing segment of US agriculture and the only sustainable option for satisfying the globally increasing demand for seafood products. Although demands in domestic and international markets remain high, the growth of the US rainbow trout aquaculture industry has leveled off. In order to compete, US trout farmers must improve the growth characteristics of this species.

This project utilizes a functional genomics approach to characterize the growth and survivability of rainbow trout during embryonic development. Early embryonic development is a complex process that requires the interaction of large groups of genes and is accompanied by changes in gene expression. The identities of the majority of genes involved in the process and their interactions and functions remain unknown. Part of the difficulty has been that studies in the past have focused on the identification and characterization of a few individual genes, while embryogenesis involves many genes and their dynamic interactions over time. With the advent of microarray technologies, it is now feasible to identify and characterize the patterns of gene expression of the entire population of genes that control embryogenesis. Genes expressed in similar complex patterns often participate in a common pathway and such synexpression groups can lead to the discovery of novel components of known pathways. Furthermore, the ability to analyze the expression patterns of numerous novel genes facilitates the identification of new genes that are developmentally active. In rainbow trout, expression profiles of a number of well-characterized genes during embryonic development have been documented. However, no systematic studies have been conducted to specifically determine the gene expression profiles in early embryos at different stages of development using the powerful microarray approach. Our objectives will be to construct a microarray for studying embryonic development in rainbow trout and to use it in identifying key genes regulating this process.

Activities primarily fall within the scope of the Genetic Improvement component (#3) of the Aquaculture National Program Action Plan (106). Section c (Genomic resources, goals 1-3) applies as genetic mapping, physical mapping, and functional genomics will be the major focus of this project.


2.List by year the currently approved milestones (indicators of research progress)
2005 2E Complete EST sequencing including oocyte and embryonic libraries.

2006 2E Analysis of EST data for construction of a rainbow trout microarray.

2007 2E Construction of a high-density oligonucleotide microarray and determine suitability of the microarrays to identify genes differentially expressed during embryonic development.

2008 2E Analysis and validation of microarray data, molecular characterization of cDNAs for candidate genes.

2009 2E Genomic characterization of candidate genes identified through microarray experiments.

2F Isolate and map markers associated with candidate genes identified in microarray experiments.


4a.List the single most significant research accomplishment during FY 2006.
None.


4b.List other significant research accomplishment(s), if any.
None.


4c.List significant activities that support special target populations.
None.


4d.Progress report.
This report serves to document research conducted under a Specific Cooperative Agreement between ARS and West Virginia University. Additional details of research can be found in the report for the parent CRIS 1930-31000-008-00D, Identification and Characterization of Genes Affecting Cool and Cold Water Aquaculture.

Significant progress has been made in the identification of genes which may affect aquaculture production traits. With respect to identifying and characterizing genes important in embryonic development, a novel oocyte-specific gene (OORP-T) encoding a protein with a conserved oxysterol binding protein domain has been identified. Also, a molecular characterization of caspase-9 was conducted including expression patterns in spawning-associated muscle atrophy. Finally, the anabolic effects of feeding beta2-adrenergic agonists (clenbuterol and ractopamine) on rainbow trout muscle proteases and proteins were determined.


5.Describe the major accomplishments to date and their predicted or actual impact.
None.


6.What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end-user (industry, farmer, other scientists)? What are the constraints, if known, to the adoption and durability of the technology products?
None.


7.List your most important publications in the popular press and presentations to organizations and articles written about your work. (NOTE: List your peer reviewed publications below).
Scientific Publications:

Salem, M., Levesque, H., Moon, T.W., Rexroad, C.E. and Yao, J. 2006. Anabolic effects of feeding ¿2-adrenergic agonists on rainbow trout muscle proteases and proteins. Comparative Biochemistry and Physiology 144: 145-154.

Salem, M., Kenney, P.B., Rexroad, C.E. and Yao, J. 2006. Molecular characterization of muscle atrophy and proteolysis associated with spawning in rainbow trout. Comparative Biochemistry and Physiology 1: 227-237.

Abstracts:

Ramachandra, R. and Yao, J. Transcription factor profiling during early embryonic development in rainbow trout (Oncorhynchus mykiss). 39th Annual Meeting Society for the Study of Reproduction, Omaha, Nebraska. July 29-August 1, 2006.

Salem, M., Kenney, B., Rexroad, C. E., and Yao, J. Microarray gene expression analysis in atrophying rainbow trout muscle. 2nd International Symposium on Animal Functional Genomics, East Lansing, Michigan, May 16-19, 2006.


Last Modified: 9/10/2014
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