. Fao, The State of World Fisheries and Aquaculture, 2010.

D. Randall, C. Wood, S. Perry, H. Bergman, G. Maloiy et al., Urea excretion as a strategy for survival in a fish living in a very alkaline environment, Nature, vol.337, issue.6203, pp.337165-166, 1989.
DOI : 10.1038/337165a0

M. Tine, J. De-lorgeril, D. Cotta, H. Pepey, E. Bonhomme et al., Transcriptional responses of the black-chinned tilapia Sarotherodon melanotheron to salinity extremes, Marine Genomics, vol.1, issue.2, pp.37-46, 2008.
DOI : 10.1016/j.margen.2008.06.001

J. Baroiller, D. Cotta, H. Bezault, E. Wessels, S. Hoerstgen-schwark et al., Tilapia sex determination: Where temperature and genetics meet. Comparative biochemistry and physiology, pp.30-38, 2009.
DOI : 10.1016/j.cbpa.2008.11.018

E. Trewavas, Tilapiine fishes of the genera Sarotherodon Oreochromis and Danakilia, British Museum Natural History, 1983.
DOI : 10.5962/bhl.title.123198

A. Cossins and D. Crawford, Opinion: Fish as models for environmental genomics, Nature Reviews Genetics, vol.24, issue.4, pp.324-333, 2005.
DOI : 10.1046/j.1365-2052.2001.00764.x

T. Kocher, Adaptive evolution and explosive speciation: the cichlid fish model, Nature Reviews Genetics, vol.10, issue.4, pp.288-298, 2004.
DOI : 10.1098/rspb.2002.2153

B. Lee, A. Howe, M. Conte, D. Cotta, H. Pepey et al., An EST resource for tilapia based on 17 normalized libraries and assembly of 116,899 sequence tags, BMC Genomics, vol.11, issue.1, p.278, 2010.
DOI : 10.1186/1471-2164-11-278

L. Soler, M. Conte, T. Katagiri, A. Howe, B. Lee et al., Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus), BMC Genomics, vol.11, issue.1, p.636, 2010.
DOI : 10.1186/1471-2164-11-636

M. Rezk, R. Ponzoni, H. Khaw, E. Kamel, T. Dawood et al., Selective breeding for increased body weight in a synthetic breed of Egyptian Nile tilapia, Oreochromis niloticus: Response to selection and genetic parameters, Aquaculture, vol.293, issue.3-4, pp.3-4187, 2009.
DOI : 10.1016/j.aquaculture.2009.03.019

S. Wessels and G. Hörstgen-schwark, Selection experiments to increase the proportion of males in Nile tilapia (Oreochromis niloticus) by means of temperature treatment, Aquaculture, vol.272, pp.80-87, 2007.
DOI : 10.1016/j.aquaculture.2007.08.009

A. Korol, Z. Frenkel, L. Cohen, E. Lipkin, and M. Soller, Fractioned DNA Pooling: A New Cost-Effective Strategy for Fine Mapping of Quantitative Trait Loci, Genetics, vol.176, issue.4, pp.2611-2623, 2007.
DOI : 10.1534/genetics.106.070011

A. Cnaani, N. Zilberman, S. Tinman, G. Hulata, and R. M. , Genome-scan analysis for quantitative trait loci in an F2 tilapia hybrid, Molecular Genetics and Genomics, vol.272, issue.2, pp.162-172, 2004.
DOI : 10.1007/s00438-004-1045-1

T. Kocher, W. Lee, H. Sobolewska, D. Penman, and B. Mcandrew, A genetic linkage map of a cichlid fish, the tilapia (Oreochromis niloticus), Genetics, vol.148, issue.3, pp.1225-1232, 1998.

B. Lee, W. Lee, J. Streelman, K. Carleton, A. Howe et al., A Second-Generation Genetic Linkage Map of Tilapia (Oreochromis spp.), Genetics, vol.170, issue.1, pp.237-244, 2005.
DOI : 10.1534/genetics.104.035022

K. Majumdar and B. Mcandrew, Relative DNA content of somatic nuclei and chromosomal studies in three genera: Tilapia, Sarotherodon and Oreochromis of the tribe Tilapiini, Genetica, vol.68, pp.165-168, 1986.

A. Shirak, E. Seroussi, A. Cnaani, A. Howe, R. Domokhovsky et al., Amh and Dmrta2 Genes Map to Tilapia (Oreochromis spp.) Linkage Group 23 Within Quantitative Trait Locus Regions for Sex Determination, Genetics, vol.174, issue.3, pp.1573-1581, 2006.
DOI : 10.1534/genetics.106.059030

A. Cnaani, B. Lee, C. Ozouf-costaz, C. Bonillo, J. Baroiller et al., Mapping of sox2 and sox14 in tilapia (Oreochromis spp.). Sex Dev, pp.207-210, 2007.

R. Geisler, G. Rauch, H. Baier, F. Van-bebber, L. Bross et al., A radiation hybrid map of the zebrafish genome, Nature Genetics, vol.23, issue.1, pp.86-89, 1999.
DOI : 10.1038/12692

N. Hukriede, L. Joly, M. Tsang, J. Miles, P. Tellis et al., Radiation hybrid mapping of the zebrafish genome, Proceedings of the National Academy of Sciences, vol.96, issue.17, pp.969745-9750, 1999.
DOI : 10.1073/pnas.96.17.9745

R. Guyon, F. Senger, M. Rakotomanga, N. Sadequi, F. Volckaert et al., A radiation hybrid map of the European sea bass (Dicentrarchus labrax) based on 1581 markers: Synteny analysis with model fish genomes, Genomics, vol.96, issue.4, pp.228-238, 2010.
DOI : 10.1016/j.ygeno.2010.07.007
URL : https://hal.archives-ouvertes.fr/inserm-00511767

F. Senger, C. Priat, C. Hitte, E. Sarropoulou, R. Franch et al., The first radiation hybrid map of a perch-like fish: The gilthead seabream (Sparus aurata L), Genomics, vol.87, issue.6, pp.793-800, 2006.
DOI : 10.1016/j.ygeno.2005.11.019

E. Sarropoulou, R. Franch, B. Louro, D. Power, L. Bargelloni et al., A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis, BMC Genomics, vol.8, issue.1, p.44, 2007.
DOI : 10.1186/1471-2164-8-44

E. Sarropoulou, D. Nousdili, A. Magoulas, and G. Kotoulas, Linking the Genomes of Nonmodel Teleosts Through Comparative Genomics, Marine Biotechnology, vol.90, issue.3, pp.227-233
DOI : 10.1007/s10126-007-9066-5

C. Hitte, J. Madeoy, E. Kirkness, C. Priat, T. Lorentzen et al., Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping, Nature Reviews Genetics, vol.68, issue.8, pp.643-648, 2005.
DOI : 10.1101/gr.2663304

H. Lewin, D. Larkin, J. Pontius, O. Brien, and S. , Every genome sequence needs a good map, Genome Research, vol.19, issue.11, pp.1925-1928, 2009.
DOI : 10.1101/gr.094557.109

S. Aparicio, J. Chapman, E. Stupka, N. Putnam, J. Chia et al., Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes, Science, vol.297, issue.5585, pp.291301-1310, 2002.
DOI : 10.1126/science.1072104

C. Kwok, R. Critcher, and K. Schmitt, Chapter 16 Construction and Characterization of Zebrafish Whole Genome Radiation Hybrids, pp.287-302, 1999.
DOI : 10.1016/S0091-679X(08)61906-8

W. Kent, BLAT---The BLAST-Like Alignment Tool, Genome Research, vol.12, issue.4, pp.656-664, 2002.
DOI : 10.1101/gr.229202

W. Chen and R. Mayden, A Phylogenomic Perspective on the New Era of Ichthyology, BioScience, vol.60, issue.6, pp.421-432, 2010.
DOI : 10.1525/bio.2010.60.6.6

T. Gregory, Animal Genome Size Database, 2011.

J. Chew, C. Oliveira, J. Wright, and M. Dobson, Molecular and cytogenetic analysis of the telomeric (TTAGGG) n repetitive sequences in the Nile tilapia, Oreochromis niloticus (Teleostei: Cichlidae), Chromosoma, vol.111, issue.1, pp.45-52, 2002.
DOI : 10.1007/s00412-002-0187-3

J. Mota-velasco, I. Ferreira, M. Cioffi, K. Ocalewicz, R. Campos-ramos et al., Characterisation of the chromosome fusions in Oreochromis karongae, Chromosome Research, vol.90, issue.3, pp.575-586, 2010.
DOI : 10.1007/s10577-010-9141-z

I. Ferreira, A. Poletto, T. Kocher, J. Mota-velasco, D. Penman et al., Chromosome evolution in African cichlid fish: contributions from the physical mapping of repeated DNAs. Cytogenetic and genome research, pp.314-322, 2010.

O. Brien, S. Womack, J. Lyons, L. Moore, K. Jenkins et al., Anchored reference loci for comparative genome mapping in mammals, Nature Genetics, vol.11, issue.2, pp.103-112, 1993.
DOI : 10.1016/0092-8674(87)90595-2

W. Murphy, S. Sun, Z. Chen, N. Yuhki, D. Hirschmann et al., A Radiation Hybrid Map of the Cat Genome: Implications for Comparative Mapping, Genome Research, vol.10, issue.5
DOI : 10.1101/gr.10.5.691

J. Volff, Genome evolution and biodiversity in teleost fish, Heredity, vol.94, issue.3, pp.280-294, 2005.
DOI : 10.1038/sj.hdy.6800635

R. Li, W. Fan, G. Tian, H. Zhu, L. He et al., The sequence and de novo assembly of the giant panda genome, Nature, issue.7279, pp.463311-317, 2010.

J. Kwintkiewicz, Z. Cai, and C. Stocco, Follicle-Stimulating Hormone-Induced Activation of Gata4 Contributes in the Up-Regulation of Cyp19 Expression in Rat Granulosa Cells, Molecular Endocrinology, vol.21, issue.4, pp.933-947, 2007.
DOI : 10.1210/me.2006-0446

A. Cnaani, B. Lee, N. Zilberman, C. Ozouf-costaz, G. Hulata et al., Genetics of Sex Determination in Tilapiine Species, Sexual Development, vol.2, issue.1, pp.43-54, 2008.
DOI : 10.1159/000117718
URL : https://hal.archives-ouvertes.fr/hal-00420120

R. Roberts, J. Ser, and T. Kocher, Sexual Conflict Resolved by Invasion of a Novel Sex Determiner in Lake Malawi Cichlid Fishes, Science, vol.326, issue.5955, pp.998-1001, 2009.
DOI : 10.1126/science.1174705

J. Ser, R. Roberts, and T. Kocher, Multiple interacting loci control sex determination in lake Malawi cichlid fish. Evolution; international journal of organic evolution, pp.486-501, 2010.

K. Yoshida, Y. Terai, S. Mizoiri, M. Aibara, H. Nishihara et al., B Chromosomes Have a Functional Effect on Female Sex Determination in Lake Victoria Cichlid Fishes, PLoS Genetics, vol.106, issue.113, p.1002203, 2011.
DOI : 10.1371/journal.pgen.1002203.s013

L. Hauser, M. Baird, R. Hilborn, L. Seeb, and J. Seeb, An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population. Molecular ecology resources, pp.150-161, 2011.

M. Sarder, D. Penman, J. Myers, and B. Mcandrew, Production and propagation of fully inbred clonal lines in the Nile tilapia (Oreochromis niloticus L.). The Journal of experimental zoology, pp.675-685, 1999.

F. Vignaux, C. Hitte, C. Priat, J. Chuat, C. Andre et al., Construction and optimization of a dog whole-genome radiation hybrid panel, Mammalian Genome, vol.10, issue.9, pp.888-894, 1999.
DOI : 10.1007/s003359901109

A. Smit, R. Hubley, and P. Green, RepeatMasker Open-3.0, 1996.

X. Huang and A. Madan, CAP3: A DNA Sequence Assembly Program, Genome Research, vol.9, issue.9, pp.868-877, 1999.
DOI : 10.1101/gr.9.9.868

G. Slater and E. Birney, Automated generation of heuristics for biological sequence comparison, BMC Bioinformatics, vol.6, issue.1, p.31, 2005.
DOI : 10.1186/1471-2105-6-31

R. Warren, G. Sutton, S. Jones, and R. Holt, Assembling millions of short DNA sequences using SSAKE, Bioinformatics, vol.23, issue.4, pp.500-501, 2007.
DOI : 10.1093/bioinformatics/btl629

H. Li, J. Ruan, and R. Durbin, Mapping short DNA sequencing reads and calling variants using mapping quality scores, Genome Research, vol.18, issue.11, pp.1851-1858, 2008.
DOI : 10.1101/gr.078212.108
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577856

S. Mckay, R. Schnabel, B. Murdoch, J. Aerts, C. Gill et al., Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping, Animal Genetics, vol.8, issue.2, pp.120-125, 2007.
DOI : 10.1111/j.1365-2052.2006.01564.x

T. Schiex and C. Gaspin, CARTHAGENE: constructing and joining maximum likelihood genetic maps, Proceedings/International Conference on Intelligent Systems for Molecular Biology, pp.258-267, 1997.

T. Derrien, C. Andre, F. Galibert, and C. Hitte, AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps, Bioinformatics, vol.23, issue.4, pp.498-499, 2007.
DOI : 10.1093/bioinformatics/btl618

K. Youens-clark, B. Faga, I. Yap, L. Stein, and D. Ware, CMap 1.01: a comparative mapping application for the Internet, Bioinformatics, vol.25, issue.22, pp.253040-304, 2009.
DOI : 10.1093/bioinformatics/btp458

M. Sanetra, F. Henning, S. Fukamachi, and A. Meyer, A Microsatellite-Based Genetic Linkage Map of the Cichlid Fish, Astatotilapia burtoni (Teleostei): A Comparison of Genomic Architectures Among Rapidly Speciating Cichlids, Genetics, vol.182, issue.1, pp.387-397, 2009.
DOI : 10.1534/genetics.108.089367

R. Albertson, J. Streelman, and T. Kocher, Directional selection has shaped the oral jaws of Lake Malawi cichlid fishes, Proceedings of the National Academy of Sciences, vol.100, issue.9, pp.5252-5257, 2003.
DOI : 10.1073/pnas.0930235100

C. Fischer, C. Ozouf-costaz, R. Crollius, H. Dasilva, C. Jaillon et al., Karyotype and chromosome location of characteristic tandem repeats in the pufferfish <i>Tetraodon nigroviridis</i>, Cytogenetic and Genome Research, vol.88, issue.1-2, pp.50-55, 2000.
DOI : 10.1159/000015484

T. Katagiri, C. Kidd, E. Tomasino, J. Davis, C. Wishon et al., A BAC-based physical map of the Nile tilapia genome, BMC Genomics, vol.6, issue.1, p.89, 2005.
DOI : 10.1186/1471-2164-6-89