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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #160282
Title: GENOMIC CHARACTERIZATION OF A NOVEL PAIR OF ID GENES IN THE RAINBOW TROUT (ONCORHYNCHUS MYKISS)

Author
item Gahr, Scott
item Rexroad, Caird
item Palti, Yniv

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/1/2004
Publication Date: 8/1/2004
Citation: Gahr, S.A., Rexroad III, C.E., Palti, Y. 2004. Genomic characterization of a novel pair of id genes in the rainbow trout (oncorhynchus mykiss). Animal Genetics. 35(4):317-320.

Interpretive Summary: In the current study we have identified and characterized two new family members of inhibitors of differentiation (Id) proteins in rainbow trout and classified them as Trout Id 6-1 and Trout Id 6-2 based on the similarity with the Zebrafish Id6 protein. Using genetic mapping techniques we have been able to show the two genes reside in distinct locations with in the rainbow trout genome. This study represents the initiation into the discovery, determination of genetic location, and tissue distribution of novel genes related to growth and development in the rainbow trout.

Technical Abstract: The Id (Inhibitors of DNA Binding/Differentiation) proteins represent a family of dominant negative regulators of the basic helix-loop-helix transcription factors whose activities result in delayed cell differentiation and prolonged proliferation. A pair of expressed sequence tag clones with homologies to the Id proteins were identified and used to screen a rainbow trout bacterial artificial chromosome library. Phylogenetic analysis of the predicted amino acid sequences revealed closest similarity to the zebrafish Id6 gene, therefore we classified these novel genes as trout Id 6-1 (TId6-1) and Id 6-2 (TId6-2). Genome characterization based on bacterial artificial chromosome sequencing showed each gene having two exons separated by a small intron. The genes are 83% similar in their transcribed regions, yet they are only 64% and 65% similar in the upstream and downstream sequences, respectively. Transcription factor binding sites were identified using TFSEARCH in the five prime proximal region of each gene. Using RT-PCR, we have determined tissue distribution patterns for Id6-1, Id6-2, and their splice variants. Genetic mapping was accomplished by discovery of microsatellites and single nucleotide polymorphisms associated with each gene. Markers for Id6-1 were localized to linkage group 12 and markers for Id6-2 were localized to linkage groups 24 and 29 using two independent reference families.