Karim Gharbi

Gene mapping in fishes: a means to an end

Genetic research in fishes is poised to contribute a vast amount of information on the structural organization and function of vertebrate genomes. Recent advances in molecular biology have made possible the widescale characterization of genomes in all living organisms. This includes defining chromosomes at the cytological level down to their linear composition at individual nucleotide base pairs. Pioneering gene mapping studies into the genomes of fishes will only serve as the starting point for more detailed studies into the function of these genomes. Future research directed at understanding the mechanisms of gene actions and interactions will benefit all areas of biology, including ecology, ethology, evolution, and physiology. Gene mapping data from brown trout and rainbow trout are used to exemplify how basic information on gene transmission in a species may help to localize centromeres onto a genetic map and identify chromosomal regions possessing a high degree of segregation distortion. Genetic maps may also be used to identify differences in recombination levels among individuals and between the sexes when multiple mapping families are utilized in studies. Observations of this type are the antecedents to more complex biological investigations on the genetic architecture underlying these phenomena.

Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout ( Oncorhynchus mykiss )

BackgroundComparative genomics, through the integration of genetic maps from species of interest with whole genome sequences of other species, will facilitate the identification of genes affecting phenotypes of interest. The development of microsatellite markers from expressed sequence tags will serve to increase marker densities on current salmonid genetic maps and initiate in silico comparative maps with species whose genomes have been fully sequenced.ResultsEighty-nine polymorphic microsatellite markers were generated for rainbow trout of which at least 74 amplify in other salmonids. Fifty-five have been associated with functional annotation and 30 were mapped on existing genetic maps. Homologous sequences were identified for 20 of the EST containing microsatellites to identify comparative assignments within the tetraodon, mouse, and/or human genomes.ConclusionThe addition of microsatellite markers constructed from expressed sequence tag data will facilitate the development of high-density genetic maps for rainbow trout and comparative maps with other salmonids and better studied species.

Characterization of Na, K-ATPase genes in Atlantic salmon (Salmo salar) and comparative genomic organization with rainbow trout (Oncorhynchus mykiss)

A combination of molecular and in silico approaches was employed to assemble a survey of Na, K-ATPase genes contained in the ancestrally tetraploid genome of the Atlantic salmon (Salmo salar). Molecular characterization of genomic clones coding for the α subunit revealed two single genes (α1a and α2) and two pairs of presumably homeologous genes (α1b/i-ii and α1c/i-ii). Each of the six genes showed high sequence similarity to isoforms previously isolated from rainbow trout and extensive structural differences relative to putative orthologs in the human genome. In silico analysis of expressed sequence tag (EST) collections indicated that at least five α (α1a, α1b, α1c, α2, and α3) and four β (β1a, β1b, β2, and β3b) subunit isoforms are expressed in Atlantic salmon. Meiotic linkage analysis further showed that Na, K-ATPase genes are dispersed throughout the salmon genome, with the exception of two multigene clusters on linkage groups AS-22 and AS-28. Duplicate gene copies for the isoform α1b were assigned to linkage groups with multiple homeologous anchors (AS-22 and AS-23), while β2 duplicates suggested a new homeologous affinity between AS-05 and AS-28. In addition, the comparison of linkage arrangements with rainbow trout also showed that the genomic organization of Na, K-ATPase genes is consistent with the evolutionary conservation of syntenic chromosome regions between these species.