Abstract
BackgroundThe Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited.ResultsWe have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish.ConclusionThe RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.
Highlights
The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide
Because tilapia are closely related to the cichlid fishes in the Great Lakes of East Africa, which have undergone a spectacular radiation, they will contribute to our understanding of evolutionary mechanisms
radiation hybrid (RH) panel We fused Hprt— derivative CHO host cells with Nile tilapia splenocytes γ-irradiated at 3500 rad
Summary
The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. Tilapia have a short generation time, are sufficiently large in size for physiological studies and can be reared making them a perfect model system They exhibit a versatile adaptability to different environmental conditions to match the vast array of their ecological habitats. The 2000 cichlid species in these lakes represent a collection of natural mutants that may provide insight into the genetic mechanisms of speciation and adaptation [7] These unique biological features have motivated the development of a range of genomic tools for the Nile tilapia, Oreochromis niloticus, one of the most farmed tilapia species. Likewise the analysis of 106,259 BAC end sequences and their alignment on the genome sequence of four model fish species (stickleback, medaka, pufferfish and zebrafish) provides a valuable intermediate resource for the mapping of genes in cichlids [9] The culmination of these efforts is the whole genome sequence currently being assembled by the Broad Institute (Cambridge, USA)
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