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United States Department of Agriculture

Agricultural Research Service

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

Location: Cool and Cold Water Aquaculture Research

2008 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

The first physical map for the rainbow trout genome was generated in FY08. The current version of the map is composed of 154,439 clones of which 145,060 are in contigs and 9,379 are singles. It has 4,173 contigs of which only 811 contain Q-clones and only 3 contigs have more then 15% Q-clones. In addition, the BAC library was screened by PCR to identify BACs that harbor 137 genetic markers that represent 25 of the rainbow trout 29 chromosomes, as the first step in the integration of the genetic and physical maps. Additional two 5X BAC libraries that complement the current 10X library were obtained to fill gaps in the new physical map and enable construction of a more comprehensive integrated 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. National Program 106, Component 3, Genetic Improvement.


Last Modified: 7/28/2014
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