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Open Access Research article

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

Richard Guyon1, Michaelle Rakotomanga1, Naoual Azzouzi1, Jean Pierre Coutanceau3, Celine Bonillo4, Helena D’Cotta5, Elodie Pepey3, Lucile Soler3, Marguerite Rodier-Goud4, Angelique D’Hont4, Matthew A Conte5, Nikkie EM van Bers6, David J Penman7, Christophe Hitte1, Richard PMA Crooijmans6, Thomas D Kocher5, Catherine Ozouf-Costaz2, Jean Francois Baroiller3 and Francis Galibert18*

Author Affiliations

1 Institut Génétique et Développement (UMR 6061) CNRS/Université de Rennes 1, Rennes, France

2 Systématique, Adaptation, Evolution (UMR 7138) CNRS, Muséum National d'Histoire Naturelle, 75231, Paris, FRANCE

3 INTREPID (INTensification Raisonnée et Ecologique pour une PIsciculture Durable) (UMR110) Cirad/Ifremer, 34398, Montpellier, France

4 CIRAD, UMR AGAP, F-34398 Montpellier, France cedex, Montpellier, France

5 Department of Biology, University of Maryland, College Park, MD 20742, Maryland, USA

6 Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, Wageningen, 6709 PG, The Netherlands

7 Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, Scotland, UK

8 UMR CNRS 6061, Faculté de Médecine, Université de Rennes 1, Rennes, France

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BMC Genomics 2012, 13:222  doi:10.1186/1471-2164-13-222

Published: 6 June 2012



The 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.


We 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.


The 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.