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United States Department of Agriculture

Agricultural Research Service

Research Project: IDENTIFICATION AND CHARACTERIZATION OF GENES AFFECTING COOL AND COLD WATER AQUACULTURE PRODUCTION

Location: Cool and Cold Water Aquaculture Research

Title: A First Generation BAC Physical Map of the Rainbow Trout Genome

Authors
item Palti, Yniv
item Luo, Ming-Cheng - UNI. OF CALIFORNIA, DAVIS
item Hu, Yuqin - UNI. OF CALIFORNIA, DAVIS
item Genet, Carine - INRA, FRANCE
item Vallejo, Roger
item Rexroad, Caird

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 3, 2008
Publication Date: January 10, 2009
Citation: Palti, Y., Luo, M., Hu, Y., Genet, C., Vallejo, R.L., Rexroad III, C.E. 0209. A first generation bac physical map of the rainbow trout genome. Plant and Animal Genome Conference. Paper No. 100.

Technical Abstract: The physical map was constructed using the high-information content fingerprinting (HICF) method of Luo et al. (2003; Genomics, 82, 378-389). All the clones from the Swanson YY doubled haploid male BAC library (10X coverage; 184,704 clones) were fingerprinted and edited using FPMiner software. Approximately 16% of the clones’ fingerprints did not pass our editing criteria and were removed from the project. The remaining clones were assembled into physical contigs using the finger-printing contig (FPC) program with a tolerance of 5, an initial cutoff of 1E-70 and extensive manual editing. The current version of the map is composed of 154,439 clones of which 145,060 are assembled into 4,173 contigs and 9,379 are singletons. The total number of unique fingerprinting fragments (consensus bands) in contigs is 1,185,157, which corresponds to an estimated physical length of 2.0 Gb (75% - 80% of the rainbow trout genome). The assembly was validated by 1) comparing it to the agarose gel fingerprinting contigs of Palti et al. (2004; Animal Genetics, 35:130-133), and 2) anchoring the largest contigs to the microsatellites genetic linkage map. BAC end sequences (BES) are available for approximately 100,000 clones from the same library. We are currently integrating the physical and genetic maps using microsatellites from BES of clones from the 200 largest contigs. We also integrate the maps by screening PCR super-pools of the BAC library with over 300 markers that represent all the genetic linkage groups.

Last Modified: 7/31/2014
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