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Title: Development of a 37K high-density oligo-nucleotide microarray for rainbow trout

Author
item SALEM, MOHAMED - WEST VIRGINIA UNIVERSITY
item KENNEY, BRETT - WEST VIRGINIA UNIVERSITY
item Rexroad, Caird
item YAO, JIANBO - WEST VIRGINIA UNIVERSTIY

Submitted to: Journal of Fish Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/14/2008
Publication Date: 6/1/2008
Citation: Salem, M., Kenney, B., Rexroad III, C.E., Yao, J. 2008. Development of a 37K high-density oligo-nucleotide microarray for rainbow trout. Journal of Fish Biology. 72:(9)2187-2206.

Interpretive Summary: Progress in aquaculture is hindered by a limited knowledge about the biochemical processes affecting fish production efficiency and quality. Rainbow trout is the most widely cultivated cold freshwater fish in the US and is often used as a model organism for carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition research. Interests in this species have facilitated the continued development of the rainbow trout genomic resources including a number of different microarray platforms. Recently, we created one such resource and demonstrated its usefulness in investigating muscle growth and flesh quality in rainbow trout. A high-density oligonucleotide microarray was generated to represent as many rainbow trout genes as possible. Our data revealed a number of candidate genes that are associated with fish muscle growth and fillet quality. In addition, we have shown that muscle deterioration as a physiological response to the energetic demands of fish sexual maturation represents a unique model for studying the mechanisms of muscle degradation in fishes. This resource will facilitate discovery of genes which impact important aquaculture production traits.

Technical Abstract: We have constructed a rainbow trout 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 all publicly available data from international rainbow trout genomic 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 gene expression associated with the rainbow trout vitellogenesis-induced muscle atrophy. 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 for genetic improvement for economically important traits benefiting the salmonid aquaculture industries.