A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs.

International audienceABSTRACT: BACKGROUND: The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. Itis also an important model for studies of fish physiology, particularly because of its broadtolerance to an array of environments. It is a good model to study evolutionary mechanismsin vertebrates, because of its close relationship to haplochromine cichlids, which haveundergone rapid speciation in East Africa. The existing genomic resources for Nile tilapiainclude a genetic map, BAC end sequences and ESTs, but comparative genome analysis andmaps of quantitative trait loci (QTL) are still limited. RESULTS: We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia andgenotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC endsequences, 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 sizeof the RH map is 34,084 cR3500 and 937,310 kb. It covers 88 % of the entire genome with anestimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration tothe genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmedthat LG16-LG21 are also merged. The orientation and association of RH groups to eachchromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained smallorphan groups. Synteny relationships were determined between Nile tilapia, stickleback,medaka and pufferfish. CONCLUSION: The RH map and associated FISH map provide a valuable gene-ordered resource for genemapping and QTL studies. All genetic linkage groups with their corresponding RH groupsnow have a corresponding chromosome which can be identified in the karyotype. Placementof conserved segments indicated that multiple inter-chromosomal rearrangements haveoccurred between Nile tilapia and the other model fishes. These maps represent a valuableresource for organizing the forthcoming genome sequence of Nile tilapia, and provide afoundation for evolutionary studies of East African cichlid fishes