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United States Department of Agriculture

Agricultural Research Service

Research Project: IDENTIFICATION AND CHARACTERIZATION OF GENES AFFECTING COOL AND COLD WATER AQUACULTURE PRODUCTION

Location: Cool and Cold Water Aquaculture Research

Title: Development of a High-density oligo-nucleotide microarray for rainbow trout

Authors
item Salem, Mohaned - WEST VIRGINIA UNIVERSITY
item Kenney, Brett - WEST VIRGINIA UNIVERSITY
item Rexroad, Caird
item Yao, Jianbo - WEST VIRGINIA UNIVERSITY

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: August 3, 2007
Publication Date: February 9, 2008
Citation: Salem, M., Kenney, B., Rexroad III, C.E., Yao, J. 2008. Development of a High-density oligo-nucleotide microarray for rainbow trout. Meeting Abstract.

Technical Abstract: Progress in aquaculture is hindered by a lack of knowledge about the biochemical processes affecting fish production efficiency and quality. Rainbow trout is the most cultivated cold freshwater fish in the US and one of the most intensively studied due to interest as a research model organism for carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. The increasing interest using genomic tools for salmonid research and development is reflected in the considerable accumulation of genomic resources for salmonids in the last several years. DNA microarray chip technology allows us to monitor global gene expression profiles in a single assay. This technology has generated tremendous information regarding the molecular consequences of gene expression associated with genetic, pharmacological, and nutritional models. The field of gene profiling is still relatively new in fish. Few microarray platforms are available for salmonid species research and none of them uses the high-throughout genome-wide, high-density approach. The availability of these whole transcriptome expression profiling studies can identify novel candidate genes and physiological pathways to target in hypothesis-driven studies. To address this need, we have constructed a rainbow trout-specific high-density oligonucleotide microarray by using all the available tentative consensus (TC) sequences from the Rainbow Trout Gene Index database (The Computational Biology and Functional Genomics Lab., Dana Farber Cancer Institute and Harvard School of Public Health). The Rainbow Trout Gene Index integrates research data from all available international rainbow trout gene research projects. The newly designed microarray incorporates 37,394 unique transcript-specific oligonucleotide probes, 60-mer long each. The microarray was printed according to our design by Agilent Technologies using the 4 X 44 design format and contains 1417 Agilent control spots. The performance of the new microarray platform was evaluated by analyzing the expression of genes for which we had previous expectations of being involved in rainbow trout muscle degradation. These chips can be ordered from Agilent using design number 016320. This microarray is anticipated to open new avenues of research that will aid in the development of novel strategies to enhance efficiency of growth and quality in food fish.

Last Modified: 9/1/2014
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