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

Guyon Richard, Rakotomanga Michelle, Azzouzi Naoual, Coutanceau Jean-Pierre, Bonillo Céline, D'Cotta Helena, Pepey Elodie, Soler Lucile, Rodier-Goud Marguerite, D'Hont Angélique, Conte Matthieu, Van Bers Nikkie, Penman David J., Hitte Christophe, Crooijmans Richard, Kocher Thomas D., Ozouf-Costaz Catherine, Baroiller Jean-François, Galibert Francis. 2012. A high-resolution map of the Nile tilapia genome: A resource for studying cichlids and other percomorphs. BMC Genomics, 13 (222), 17 p.

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Abstract : Background: 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. Results: 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. Conclusion: 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. (Résumé d'auteur)

Mots-clés Agrovoc : Oreochromis niloticus, Cichlidae, Perciformes (199XXXXXXX013), Carte génétique, Génome, Marqueur génétique, Microsatellite, Locus des caractères quantitatifs, Polymorphisme génétique, Génie génétique, Évolution

Mots-clés complémentaires : QTL

Classification Agris : L10 - Animal genetics and breeding
M12 - Aquaculture production

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

  • Guyon Richard, Université de Rennes I (FRA)
  • Rakotomanga Michelle, Université de Rennes I (FRA)
  • Azzouzi Naoual, Université de Rennes I (FRA)
  • Coutanceau Jean-Pierre
  • Bonillo Céline
  • Soler Lucile
  • Rodier-Goud Marguerite, CIRAD-DG-EVALUATION (FRA)
  • D'Hont Angélique, CIRAD-BIOS-UMR AGAP (FRA)
  • Conte Matthieu
  • Van Bers Nikkie, Wageningen University (NLD)
  • Penman David J., University of Stirling (GBR)
  • Hitte Christophe, Université de Rennes I (FRA)
  • Crooijmans Richard, Wageningen University (NLD)
  • Kocher Thomas D., University of Maryland (USA)
  • Ozouf-Costaz Catherine, MNHN (FRA)
  • Baroiller Jean-François, CIRAD-PERSYST-UMR INTREPID (FRA) ORCID: 0000-0002-0992-1725
  • Galibert Francis, Université de Rennes I (FRA)

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