Project Number: 1930-31000-008-05
Project Type: Specific Cooperative Agreement

Start Date: Sep 01, 2005
End Date: Sep 30, 2006

Objective:
A major constraint to increasing the production efficiency of the Nation's cool and cold water aquaculture industry is the lack of genetically improved strains of fish for aquaculture. There is only limited genetic information on traits that will enhance production efficiency and yield a better quality fish. Identification and characterization of genes affecting aquaculture production traits will facilitate the development of genetically improved strains to increase aquaculture production efficiency. The objective of the research outlined in this agreement focus on a joint effort to construct an integrated physical and genetic map for the rainbow trout genome, which will enable identification, isolation and characterization of genes that affect economically important traits.

Approach:
Collaborators at the USDA/ARS/NCCCWA and University of California, Davis have worked to develop resources for an integrated physical and genetic map for the rainbow trout genome. A total of 9,216 BAC clones (0.5X genome coverage) from the Swanson rainbow trout BAC library will be fingerprinted using the SNaPshot fingerprinting method at the lab of Dr. Luo in UC Davis. Four-color (multiple restriction pattern) fingerprint profile for each BAC clone will be generated. The output will be data files of standard ABI format (.fsa). The data will be combined with data from previous fingerprinting projects at the NCCCWA using the Genoprofiler and FP Miner software packages to edit the data and the program FPC to conduct a pairwise search for overlaps between BAC fingerprints and to build contigs. Microsatellite markers will be isolated at the NCCCWA from BACs that represent contigs of interest to enable integration of the physical and genetic maps.