Project Number: 1930-31000-008-10
Project Type: Grant

Start Date: May 04, 2007
End Date: Dec 31, 2009

Objective:
The proposed work is part of a joint effort to construct an integrated physical and genetic map for the rainbow trout genome. 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:
A total of 110,592 BAC clones (6X 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 the 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. Dr. Palti will coordinate the physical map assembly at the NCCCWA and will be responsible for developing microsatellite markers from BACs that represent contigs of interest to enable integration of the physical and genetic maps. Additionally, Dr. Luo will receive appropriate funding through this agreement to obtain additional 10X genome coverage BAC library or two 5X BAC libraries using partial digestion of Swanson genomic DNA with restriction enzymes that will complement the current HindIII library (e.g. EcoRI and BamHI).