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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #161432
Title: PHYSICAL MAPPING OF LOCI OF INTEREST IN RAINBOW TROUT: EVIDENCE FOR GENOME-WIDE DUPLICATION

Author
item Palti, Yniv
item Gahr, Scott
item HANSEN, JOHN - U OF MD BIOTECHNOLOGY
item Rexroad, Caird

Submitted to: Plant and Animal Genome VX Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: 1/10/2004
Publication Date: 1/10/2004
Citation: Palti, Y., Gahr, S.A., Hansen, J., Rexroad III, C.E. 2004. Physical mapping of loci of interest in rainbow trout: evidence for genome-wide duplication. Plant and Animal Genome Abstracts. p.251.

Interpretive Summary:

Technical Abstract: A 10X rainbow trout BAC library was used for physical mapping of loci of interest. The library was derived from the Swanson clonal line (YY male) and consists of 184,704 clones with an average insert size of 137,500 bp (PFGE) or 118,700 bp (DNA fingerprinting). The clones were gridded onto 10 large nylon membranes to produce high-density arrays for screening the library by hybridization. The library was probed with 11 cDNAs from the NCCCWA EST project chosen due to interest in their homology to known gene sequences, 7 known genes, and a Y'specific sex marker. Putative positive clones identified by hybridization were re-arrayed and gridded for secondary confirmation. FPC analysis of HindIII and EcoRV DNA fingerprints and insert end sequencing were used to estimate the level of redundancy in the library, to construct BAC contigs and to detect duplicated loci in the semi-duplicated rainbow trout genome. A good correlation (R2 = 0.7) was found between the number of hits per probe and the number of contigs that were assembled from the positive BACs. The average number of BACs per contig was 9.6, which is in good agreement with 10X genome coverage of the library. Two thirds of the loci screened were predicted to be duplicated as the positive BACs for those genes were assembled into 2 or 3 different contigs, which suggests that most of the rainbow trout genome is still duplicated. The initial physical mapping with this library demonstrates that it is suitable for constructing a whole-genome physical map for rainbow trout due to its wide genome coverage and homozygous origin which enables accurate mapping of duplicated loci.