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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: Progress Toward An Immunogenetic Map for Rainbow Trout

Authors
item Fincham, Michele
item Wiens, Gregory
item Rexroad, Caird
item Vallejo, Roger
item Palti, Yniv

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: March 30, 2007
Publication Date: May 2, 2007
Citation: Fincham, M.R., Wiens, G.D., Rexroad III, C.E., Vallejo, R.L., Palti, Y. 2007. Progress toward an immunogenetic map for rainbow trout. Meeting Abstract.

Technical Abstract: QTL (quantitative trait loci) mapping utilizes a series of methods for finding pieces of DNA that are closely linked to genes that confer a desired phenotype. One of our research goals is to map QTL in rainbow trout that associate with innate resistance to Flavobacterium psychrophilum. A high density genetic map of over 1200 microsatellite markers has been recently constructed in our lab to enable whole genome association studies. We are now adding candidate immune response genes to the genetic map. The process begins by using known mouse and human immune genes to identify putative homologous genes in the trout and salmon expressed-sequence-transcript (EST) datasets. PCR primers are then developed from the partial or complete coding sequences to screen a rainbow trout BAC (bacterial artificial chromosome) library in order to isolate clones that harbor the genes of interest. The selected BACs are mapped by HindIII restriction enzyme digestion to construct locus specific physical maps (contigs). These physical maps are used to link a single gene to a single locus of the trout genome. A representative BAC from each locus is fragmented, sub-cloned, and partially sequenced to isolate microsatellites that are then added onto the genetic map. To date we have mapped 10 loci that contain immune response genes using this process and we are currently in the process of isolating microsatellites for another set of 14 genes. Our immuno-focused genetic map will be used as a cost effective tool in future studies that seek to associate rainbow trout genetic variations with disease resistance. Additionally, it will provide useful information for comparative genome mapping with other model fish species and for integration of the physical and genetic maps of rainbow trout.

Last Modified: 8/22/2014
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