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United States Department of Agriculture

Agricultural Research Service

Research Project: PRODUCTION OF AN INTREGRATED PHYSICAL AND GENETIC MAP FOR RAINBOW TROUT
2007 Annual Report


1a.Objectives (from AD-416)
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.


1b.Approach (from AD-416)
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).


3.Progress Report
This serves to document research conducted under a specific cooperative agreement between ARS and the University of California, Davis entitled, “Production of a physical map for the rainbow trout genome using high throughput DNA fingerprinting” and a reimbursable agreement between ARS and CSREES-NRI, entitled “Production of an integrated physical and genetic map for rainbow trout.” Over 100,000 bacterial artificial chromosome clones (5.5X genome coverage) were evaluated by DNA fingerprinting to initiate construction of a rainbow trout physical map to be integrated with the current genetic map. The ADODR is in frequent contact with the cooperator through phone calls, email, and annual site visits in addition to receipt of written reports.


Last Modified: 10/25/2014
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