Project Number: 1930-31000-008-12
Project Type: Specific Cooperative Agreement

Start Date: Sep 22, 2008
End Date: Aug 31, 2009

Objective:
The objective of the research outlined in this agreement focuses on a joint effort a to construct an 2nd generation integrated physical and genetic map for the rainbow trout genome, which will enable identification, isolation and characterization of genes that affect economically important traits of rainbow trout.

Approach:
A total of 5,376 BAC clones from the new 5X BamHI Swanson rainbow trout BAC library (SRTM1) will be fingerprinted using the SNaPshot fingerprinting method sequenced from both insert ends using T7 and SP6 primers at the Cooperator's lab. Four-color (multiple restriction pattern) fingerprinting profile and DNA sequence chromatograms from each insert end will be generated for each BAC clone. The output will be GeneMapper and Sequence Analysis data files of standard ABI format. The data will be combined with the data from previous fingerprinting and BAC end sequencing projects at the NCCCWA using the FP Miner software package to edit the data and the program FPC to conduct a pairwise search for overlaps between BAC fingerprints and to build contigs. ARS will coordinate the assembly of the 2nd generation physical map and will be responsible for developing microsatellite markers from BAC end sequences to fill in gaps and expand the current integrated physical and genetic map.