Development of genomic resources for genetic enhancement of channel catfish (Ictalurus punctatus)

Genetic enhancement of channel catfish (Ictalurus punctatus) is essential for increasing their production and sustainability. To this end, my dissertation focused on the development of new genomic resources useful for catfish genetic research including genetically engineered transposon system Sleeping Beauty (SB), expressed sequence tags (ESTs), and systematic analysis of 40S ribosomal protein (RP) genes.; Transposon vectors are widely used in prokaryotic and lower eukaryotic systems. However, they were not available for use in vertebrate animals until the recent molecular reconstruction of a synthetic fish transposon SB. This transposon system has been tested for its applicability in channel catfish transgenic research. Initially, the activity of SB transposon system has been confirmed and the effect of transposon size on the activity of SB transposase has been analyzed using mouse NIH3T3 cells. Knowing the size limitations of a newly introduced transposon system is crucial for gene transfer studies. The activity of SB transposase is inversely correlated with the transposon size and there is a maximum limit in transposon size affecting its integration to the host genome. The SB transposase enhanced the integration efficiency effectively when the transposon size was approximately 5.6 kb, but lost its ability to enhance the integration efficiency when the transposon size was increased to 9.1 kb. This result indicates that the SB transposon system is highly applicable for transferring genes with small sizes, but may not be applicable for transferring genes of very large sizes.; Second, 1,909 random EST clones were analyzed and expression profiles were determined. Of the 1,909 ESTs analyzed, 1,376 ESTs were identified as orthologs of known genes representing 496 unique genes, 478 clones were currently unknown, and 55 clones were deleted from the analysis. This research identified 261 new genes and 89 microsatellite-containing genes, which should be useful for the development of polymorphic markers.; Third, a complete set of 40S RP genes was analyzed and their cDNA sequences were made available. This makes channel catfish one of the few species that all 40S RP genes are available. The systematic analysis of all genes involved in specific pathways laid the foundation for evolutionary studies, phylogenetic studies, and comparative genomic studies.