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

Autor: Helena D'Cotta, Nikkie E. M. Van Bers, Jean-François Baroiller, Richard Guyon, Jean Pierre Coutanceau, Thomas D. Kocher, Matthew A. Conte, Lucile Soler, Naoual Azzouzi, Francis Galibert, Marguerite Rodier-Goud, Angélique D'Hont, Christophe Hitte, Céline Bonillo, Michaelle Rakotomanga, Richard P. M. A. Crooijmans, David J. Penman, Elodie Pepey, Catherine Ozouf-Costaz
Přispěvatelé: Galibert, Francis, Institut de Génétique et Développement de Rennes (IGDR), Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Intensification raisonnée et écologique pour une pisciculture durable (UMR INTREPID), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Biology, University of Maryland [College Park], University of Maryland System-University of Maryland System, Animal Breeding and Genomics Centre, Wageningen University and Research [Wageningen] (WUR), Institute of Aquaculture, University of Stirling, Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), This work was supported by grant to COC, JFB and CH (ANR-07-GANI-005) from ANR (Agence Nationale de la Recherche, France)., ANR-07-GANI-0005,PERCIMAP,Construction of a high-density Tilapia RH map(2007), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-IFR140-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Wageningen University and Research Centre [Wageningen] (WUR), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), ANR-07-GANI-0005,GANI,Construction of a high-density Tilapia RH map(2007), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), De Villemeur, Hervé, Genanimal - Construction of a high-density Tilapia RH map - - PERCIMAP2007 - ANR-07-GANI-0005 - GANI - VALID
Jazyk: angličtina
Rok vydání: 2012
Předmět:
tetraodon-nigroviridis
0106 biological sciences
Chromosomes
Artificial
Bacterial
oreochromis-niloticus
Genetic Linkage
tilapia
Polymorphisme génétique
sex determination
01 natural sciences
Genome
Nile tilapia
poisson d'élevage
Marqueur génétique
évolution
Expressed Sequence Tags
Genetics
Comparative Genomic Hybridization
0303 health sciences
Expressed sequence tag
biology
Oreochromis niloticus
Chromosome Mapping
Cichlids
genetic-linkage map
Oreochromis
[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry
Molecular Biology/Genomics [q-bio.GN]
Research Article
Biotechnology
construction
Locus des caractères quantitatifs
lcsh:QH426-470
Genotype
Perciformes (199XXXXXXX013)
lcsh:Biotechnology
Fish farming
Animal Breeding and Genomics
Quantitative trait locus
Polymorphism
Single Nucleotide
010603 evolutionary biology
03 medical and health sciences
Fish physiology
lcsh:TP248.13-248.65
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Genomics [q-bio.GN]
evolution
Animals
Fokkerij en Genomica
14. Life underwater
030304 developmental biology
Génie génétique
fish
Radiation Hybrid Mapping
génome
Microsatellite
sequence
L10 - Génétique et amélioration des animaux
biology.organism_classification
radiation hybrid map
Haplochromine
lcsh:Genetics
Evolutionary biology
cartographie du génome
Carte génétique
WIAS
M12 - Production de l'aquaculture
zebrafish genome
cichlidae
Microsatellite Repeats
Zdroj: BMC Genomics 1 (13), 222-239. (2012)
BMC Genomics
BMC Genomics, BioMed Central, 2012, 13 (1), pp.222. ⟨10.1186/1471-2164-13-222⟩
BMC Genomics, 2012, 13 (1), pp.222. ⟨10.1186/1471-2164-13-222⟩
BMC Genomics, Vol 13, Iss 1, p 222 (2012)
BMC Genomics 13 (2012)
BMC Genomics, 13
ISSN: 1471-2164
DOI: 10.1186/1471-2164-13-222⟩
Popis: 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.
Databáze: OpenAIRE
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