Genomics Toolbox for Farmed Fish

REFERENCES

• Altshuler , D. , Pollara , V. J. , Cowles , C. R. , Van Etten , W. J. , Baldwin , J. , Linton , L. and Lander , E. S. 2000 . An SNP map of the human genome generated by reduced representation shotgun sequencing . Nature , 407 : 513 – 516 .
   PubMed Web of Science ®Google Scholar
• Amemiya , C. T. and Zon , L. I. 1999 . Generation of a zebrafish P1 artificial chromosome library . Genomics , 58 : 211 – 213 .
   PubMed Web of Science ®Google Scholar
• Bettini , E. , Porta , A. R. , Dahmen , N. , Wang , H. and Margolis , F. L. 1994 . Expressed sequence tags (EST) identify genes preferentially expressed in catfish chemosensory tissues . Mol. Brain. Res. , 23 : 285 – 291 .
   PubMedGoogle Scholar
• Borevitz , J. O. and Chory , J. 2004 . Genomics tools for QTL analysis and gene discovery . Curr. Opin. Plant Biol. , 7 : 132 – 136 .
   PubMed Web of Science ®Google Scholar
• Bouza , C. , Hermida , M. , Pardo , B. G. , Fernandez , C. , Fortes , G. G. , Castro , J. , Sanchez , L. , Presa , P. , Perez , M. , Sanjuan , A. , De Carlos , A. , Alvarez-Dios , J. A. , Ezcurra , S. , Cal , R. M. , Piferrer , F. and Martinez , P. 2007 . A microsatellite genetic map of the turbot (Scophthalmus maximus) . Genetics , 177 : 2457 – 2467 .
   PubMed Web of Science ®Google Scholar
• Breen , M. , Hitte , C. , Lorentzen , T. D. , Thomas , R. , Cadieu , E. , Sabacan , L. , Scott , A. , Evanno , G. , Parker , H. G. , Kirkness , E. F. , Hudson , R. , Guyon , R. , Mahairas , G. G. , Gelfenbeyn , B. , Fraser , C. M. , Andre , C. , Galibert , F. and Ostrander , E. A. 2004 . An integrated 4249 marker FISH/RH map of the canine genome . BMC Genomics , 5 : 65
   PubMed Web of Science ®Google Scholar
• Castro , J. , Pino , A. , Hermida , M. , Bouza , C. , Riaza , A. , Ferreiro , I. , Sanchez , L. and Martinez , P. A. 2006 . Microsatellite marker tool for parentage analysis in Senegal sole (Solea senegalensis): Genotyping errors, null alleles, and conformance to theoretical assumptions . Aquaculture , 261 : 1194 – 1203 .
   Web of Science ®Google Scholar
• Chistiakov , D. A. , Hellemans , B. , Haley , C. S. , Law , A. S. , Tsigenopoulos , C. S. , Kotoulas , G. , Bertotto , D. , Libertini , A. and Volckaert , F. A. M. 2005 . A microsatellite linkage map of the European sea bass Dicentrarchus labrax L . Genetics , 170 : 1821 – 1826 .
   PubMed Web of Science ®Google Scholar
• Chistiakov , D. A. , Hellemans , B. and Volckaert , F. A. M. 2006 . Microsatellites and their genomic distribution, evolution, function, and applications: A review with special reference to fish genetics . Aquaculture , 255 : 1 – 29 .
   Web of Science ®Google Scholar
• Chourrout , D. 1984 . Pressure-induced retention of second polar body and suppression of 1st cleavage in rainbow trout: Production of all-triploids, all-tetraploids, and heterozygous and homozygous diploid gynogenetics . Aquaculture , 36 : 111 – 126 .
   Web of Science ®Google Scholar
• Cnaani , A. , Hallerman , E. M. , Ron , M. , Weller , J. I. , Indelman , M. , Kashi , Y. , Gall , G. A. E. and Hulata , G. 2003 . Detection of a chromosomal region with two quantitative trait loci, affecting cold tolerance and fish size, in an F-2 tilapia hybrid . Aquaculture , 223 : 117 – 128 .
   Web of Science ®Google Scholar
• Cnaani , A. , Zilberman , N. , Tinman , S. , Hulata , G. and Ron , M. 2004 . Genome-scan analysis for quantitative trait loci in an F-2 tilapia hybrid . Mol. Genet. Genom. , 272 : 162 – 172 .
   PubMed Web of Science ®Google Scholar
• Cohen , R. , Chalifa-Caspi , V. , Williams , T. , Auslander , M. , George , S. , Chipman , J. and Tom , M. 2007 . Estimating the efficiency of fish cross-species cDNA microarray hybridization . Mar. Biotechnol. , 9 : 491 – 499 .
   PubMed Web of Science ®Google Scholar
• Coimbra , M. R. M. , Kobayashi , K. , Koretsugu , S. , Hasegawa , O. , Ohara , E. , Ozaki , A. , Sakamoto , T. , Naruse , K. and Okamoto , N. 2003 . A genetic linkage map of the Japanese flounder, Paralichthys olivaceus . Aquaculture , 220 : 203 – 218 .
   Web of Science ®Google Scholar
• Coulibaly , I. , Gharbi , K. , Danzmann , R. G. , Yao , J. and Rexroad , C. E. 2005 . Characterization and comparison of microsatellites derived from repeat-enriched libraries and expressed sequence tags . Anim. Genet. , 36 : 309 – 315 .
   PubMed Web of Science ®Google Scholar
• Dahm , R. and Geisler , R. 2006 . Learning from small fry: The zebrafish as a genetic model organism for aquaculture fish species . Mar. Biotechnol. , 8 : 329 – 345 .
   PubMed Web of Science ®Google Scholar
• Danzmann , R. G. , Cairney , M. , Davidson , W. S. , Ferguson , M. M. , Gharbi , K. , Guyomard , R. , Holm , L. E. , Leder , E. , Okamoto , N. , Ozaki , A. , Rexroad , C. E. , Sakamoto , T. , Taggart , J. B. and Woram , R. A. A. 2005 . Comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae) . Genome , 48 : 1037 – 1051 .
   PubMed Web of Science ®Google Scholar
• Danzmann , R. G. , Jackson , T. R. and Ferguson , M. M. 1999 . Epistasis in allelic expression at upper temperature tolerance QTL in rainbow trout . Aquaculture , 173 : 45 – 58 .
   Web of Science ®Google Scholar
• De Koning , D.-J. , Archibald , A. and Haley , C. S. 2007 . Livestock genomics: Bridging the gap between mice and men . Trends Biotechnol. , 25 : 483 – 489 .
   PubMed Web of Science ®Google Scholar
• Duarte , C. M. , Marba , N. and Holmer , M. 2007 . Rapid domestication of marine species . Science , 316 : 382 – 383 .
   PubMed Web of Science ®Google Scholar
• Ellegren , H. 2004 . Microsatellites: Simple sequences with complex evolution . Nat. Rev. Genet. , 5 : 435 – 445 .
   PubMed Web of Science ®Google Scholar
• Fadiel , A. , Anidi , I. and Eichenbaum , K. D. 2005 . Farm animal genomics and informatics: An update . Nucl. Acids Res. , 33 : 6308 – 6318 .
   PubMed Web of Science ®Google Scholar
• FAO . 2006 . The State of the World Fisheries and Aquaculture , Rome : Food and Agriculture Organization of the United Nations .
   Google Scholar
• Ferraresso , S. , Vitulo , N. , Mininni , A. N. , Romualdi , C. , Cardazzo , B. , Negrisolo , E. M. , Reinhardt , R. , Canario , A. , Patarnello , T. and Bargelloni , L. 2008 . An integrated platform for mRNA expression profiling in the marine teleost fish Sparus aurata L . BMC Genomics , submitted
   PubMedGoogle Scholar
• Franch , R. , Louro , B. , Tsalavouta , M. , Chatziplis , D. , Tsigenopoulos , C. S. , Sarropoulou , E. , Antonello , J. , Magoulas , A. , Mylonas , C. C. , Babbucci , M. , Patarnello , T. , Power , D. M. , Kotoulas , G. and Bargelloni , L. 2006 . A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L . Genetics , 174 : 851 – 861 .
   PubMed Web of Science ®Google Scholar
• Fuji , K. , Kobayashi , K. , Hasegawa , O. , Coimbra , M. R. M. , Sakamoto , T. and Okamoto , N. 2006 . Identification of a single major genetic locus controlling the resistance to lymphocystis disease in Japanese flounder (Paralichthys olivaceus) . Aquaculture , 254 : 203 – 210 .
   Web of Science ®Google Scholar
• Geisler , R. , Rauch , G. J. , Baier , H. , Van Bebber , F. , Bross , L. , Dekens , M. P. S. , Finger , K. , Fricke , C. , Gates , M. A. , Geiger , H. , Geiger-Rudolph , S. , Gilmour , D. , Glaser , S. , Gnugge , L. , Habeck , H. , Hingst , K. , Holley , S. , Keenan , J. , Kirn , A. , Knaut , H. , Lashkari , D. , Maderspacher , F. , Martyn , U. , Neuhauss , S. , Neumann , C. , Nicolson , T. , Pelegri , F. , Ray , R. , Rick , J. M. , Roehl , H. , Roeser , T. , Schauerte , H. E. , Schier , A. F. , Schonberger , U. , Schonthaler , H. B. , Schulte-Merker , S. , Seydler , C. , Talbot , W. S. , Weiler , C. , Nusslein-Volhard , C. and Haffter , P. 1999 . A radiation hybrid map of the zebrafish genome . Nat. Genet. , 23 : 86 – 89 .
   PubMed Web of Science ®Google Scholar
• Gharbi , K. , Gautier , A. , Danzmann , R. G. , Gharbi , S. , Sakamoto , T. , Hoyheim , B. , Taggart , J. B. , Cairney , M. , Powell , R. , Krieg , F. , Okamoto , N. , Ferguson , M. M. , Holm , L. E. and Guyomard , R. 2006 . A linkage map for brown trout (Salmo trutta): Chromosome homeologies and comparative genome organization with other salmonid fish . Genetics , 172 : 2405 – 2419 .
   PubMed Web of Science ®Google Scholar
• Gilbey , J. , Verspoor , E. , Mclay , A. and Houlihan , D. 2004 . A microsatellite linkage map for Atlantic salmon (Salmo salar) . Anim. Genet. , 35 : 98 – 105 .
   PubMed Web of Science ®Google Scholar
• Gong , Z. Y. 1999 . Zebrafish expressed sequence tags and their applications . Methods Cell Biol. , 60 : 213 – 233 .
   PubMed Web of Science ®Google Scholar
• Guyomard , R. , Mauger , S. , Tabet-Canale , K. , Martineau , S. , Genet , C. , Krieg , F. and Quillet , E. 2006 . A type I and type II microsatellite linkage map of Rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms . BMC Genomics , 7 : 302
   PubMed Web of Science ®Google Scholar
• Hayes , B. J. , Gjuvsland , A. and Omholt , S. 2006 . Power of QTL mapping experiments in commercial Atlantic salmon populations, exploiting linkage and linkage disequilibrium and effect of limited recombination in males . Heredity , 97 : 19 – 26 .
   PubMed Web of Science ®Google Scholar
• Hirono , I. and Aoki , T. 1997 . Expressed sequence tags of medaka (Oryzias latipes) liver mRNA . Mol. Mar. Biol. Biotechnol. , 6 : 345 – 350 .
   PubMedGoogle Scholar
• Houston , R. D. , Guy , D. R. , Hamilton , A. , Ralph , J. , Spreckley , N. , Taggart , J. B. , Mcandrew , B. J. , Haley , C. S. and Bishop , S. C. Detection of major QTL affecting resistance to infectious pancreatic necrosis (IPN) in a commercial Atlantic salmon population . 8th World Congress on Genetics Applied to Livestock Production . Belo Horizonte, MG , Brazil.
   Google Scholar
• Inoue , S. , Nam , B. H. , Hirono , I. and Aoki , T. 1997 . A survey of expressed genes in Japanese flounder (Paralichthys olivaceus) liver and spleen . Mol. Mar. Biol. Biotechnol. , 6 : 376 – 380 .
   PubMedGoogle Scholar
• Jackson , T. R. , Ferguson , M. M. , Danzmann , R. G. , Fishback , A. G. , Ihssen , P. E. , O'Connell , M. and Crease , T. J. 1998 . Identification of two QTL influencing upper temperature tolerance in three rainbow trout (Oncorhynchus mykiss) half-sib families . Heredity , 80 : 143 – 151 .
   Web of Science ®Google Scholar
• Jaillon , O. , Aury , J. M. , Brunet , F. , Petit , J. L. , Stange-Thomann , N. , Mauceli , E. , Bouneau , L. , Fischer , C. , Ozouf-Costaz , C. , Bernot , A. , Nicaud , S. , Jaffe , D. , Fisher , S. , Lutfalla , G. , Dossat , C. , Segurens , B. , Dasilva , C. , Salanoubat , M. , Levy , M. , Boudet , N. , Castellano , S. , Anthouard , R. , Jubin , C. , Castelli , V. , Katinka , M. , Vacherie , B. , Biemont , C. , Skalli , Z. , Cattolico , L. , Poulain , J. , De Berardinis , V. , Cruaud , C. , Duprat , S. , Brottier , P. , Coutanceau , J. P. , Gouzy , J. , Parra , G. , Lardier , G. , Chapple , C. , Mckernan , K. J. , McEwan , P. , Bosak , S. , Kellis , M. , Volff , J. N. , Guigo , R. , Zody , M. C. , Mesirov , J. , Lindblad-Toh , K. , Birren , B. , Nusbaum , C. , Kahn , D. , Robinson-Rechavi , M. , Laudet , V. , Schachter , V. , Quetier , F. , Saurin , W. , Scarpelli , C. , Wincker , P. , Lander , E. S. , Weissenbach , J. and Crollius , H. R. 2004 . Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype . Nature , 431 : 946 – 957 .
   PubMed Web of Science ®Google Scholar
• Ji , W. , Zhou , W. L. , Gregg , K. , Yu , N. , Davis , S. and Davis , S. 2004 . A method for cross-species gene expression analysis with high-density oligonucleotide arrays . Nucleic Acids Res. , 32 : e93
   PubMed Web of Science ®Google Scholar
• Johnson , K. R. , Wright , J. E. and May , B. 1987 . Linkage relationships reflecting ancestral tetraploidy in salmonid fish . Genetics , 116 : 579 – 591 .
   PubMed Web of Science ®Google Scholar
• Johnson , N. A. , Rexroad , C. E. , Hallerman , E. M. , Vallejo , R. L. and Palti , Y. 2007 . Development and evaluation of a new microsatellite multiplex system for parental allocation and management of rainbow trout (Oncorhynchus mykiss) broodstocks . Aquaculture , 266 : 53 – 62 .
   Web of Science ®Google Scholar
• Ju , Z. , Wells , M. , Martinez , A. , Hazlewood , L. and Walter , R. 2005 . An in silico mining for simple sequence repeats from expressed sequence tags of zebrafish, medaka, Fundulus, and Xiphophorus . Silico Biol. , 5 : 439 – 463 .
   PubMedGoogle Scholar
• Kalujnaia , S. , Mcwilliam , I. S. , Zaguinaiko , V. A. , Feilen , A. L. , Nicholson , J. , Hazon , N. , Cutler , C. P. , Balment , R. J. , Cossins , A. R. , Hughes , M. and Cramb , G. 2007 . Salinity adaptation and gene profiling analysis in the European eel (Anguilla anguilla) using microarray technology . Gen. Comp. Endocrinol. , 152 : 274 – 280 .
   PubMed Web of Science ®Google Scholar
• Karsi , A. , Li , P. , Dunham , R. A. and Liu , Z. J. 1998 . Transcriptional activities in the pituitaries of channel catfish before and after induced ovulation by injection of carp pituitary extract as revealed by expressed sequence tag analysis . J. Mol. Endocrinol. , 21 : 121 – 129 .
   PubMed Web of Science ®Google Scholar
• Kasahara , M. , Naruse , K. , Sasaki , S. , Nakatani , Y. , Qu , W. , Ahsan , B. , Yamada , T. , Nagayasu , Y. , Doi , K. , Kasai , Y. , Jindo , T. , Kobayashi , D. , Shimada , A. , Toyoda , A. , Kuroki , Y. , Fujiyama , A. , Sasaki , T. , Shimizu , A. , Asakawa , S. , Shimizu , N. , Hashimoto , S. I. , Yang , J. , Lee , Y. , Matsushima , K. , Sugano , S. , Sakaizumi , M. , Narita , T. , Ohishi , K. , Haga , S. , Ohta , F. , Nomoto , H. , Nogata , K. , Morishita , T. , Endo , T. , Shin-I , T. , Takeda , H. , Morishita , S. and Kohara , Y. 2007 . The medaka draft genome and insights into vertebrate genome evolution . Nature , 447 : 714 – 719 .
   PubMed Web of Science ®Google Scholar
• Kassahn , K. S. , Caley , M. J. , Ward , A. C. , Connolly , A. R. , Stone , G. and Crozier , R. H. 2007 . Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish . Mol. Ecol. , 16 : 1749 – 1763 .
   PubMed Web of Science ®Google Scholar
• Katagiri , T. , Asakawa , S. , Hirono , I. , Aoki , T. and Shimizu , N. 2000 . Genomic bacterial artificial chromosome library of the Japanese flounder Paralichthys olivaceus . Mar. Biotechnol. , 2 : 571 – 576 .
   PubMed Web of Science ®Google Scholar
• Katagiri , T. , Asakawa , S. , Minagawa , S. , Shimizu , N. , Hirono , I. and Aoki , T. 2001 . Construction and characterization of BAC libraries for three fish species: rainbow trout, carp, and tilapia . Anim. Genet. , 32 : 200 – 204 .
   PubMed Web of Science ®Google Scholar
• Katagiri , T. , Kidd , C. , Tomasino , E. , Davis , J. , Wishon , C. , Stern , J. , Carleton , K. , Howe , A. and Kocher , T. 2005 . A BAC-based physical map of the Nile tilapia genome . BMC Genomics , 6 : 89
   PubMed Web of Science ®Google Scholar
• Knott , S. A. , Elsen , J. M. and Haley , C. S. 1996 . Methods for multiple-marker mapping of quantitative trait loci in half-sib populations . Theor. Appl. Genet. , 93 : 71 – 80 .
   PubMed Web of Science ®Google Scholar
• Kolbehdari , D. , Jansen , G. B. , Schaeffer , L. R. and Allen , B. O. 2005 . Power of QTL detection by either fixed or random models in half-sib designs . Genet. Sel. Evol. , 37 : 601 – 614 .
   PubMed Web of Science ®Google Scholar
• Larkin , P. , Villeneuve , D. L. , Knoebl , I. , Miracle , A. L. , Carter , B. J. , Liu , L. , Denslow , N. D. and Ankley , G. T. 2007 . Development and validation of a 2,000-gene microarray for the fathead minnow (Pimephales promelas) . Environ. Toxicol. Chem. , 26 : 1497 – 1506 .
   PubMed Web of Science ®Google Scholar
• Lee , B. Y. , Lee , W. J. , Streelman , J. T. , Carleton , K. L. , Howe , A. E. , Hulata , G. , Slettan , A. , Terai , Y. and Kocher , T. D. 2005 . A second generation genetic linkage map of tilapia (Oreochromis spp.) . Genetics , 170 : 237 – 244 .
   PubMed Web of Science ®Google Scholar
• Lerceteau-Kohler , E. and Weiss , S. 2006 . Development of a multiplex PCR microsatellite assay in brown trout Salmo trutta and its potential application for the genus . Aquaculture , 258 : 641 – 645 .
   Web of Science ®Google Scholar
• Liu , Z. , Karsi , A. , Li , P. , Cao , D. and Dunham , R. 2003 . An AFLP-based genetic linkage map of channel catfish (Ictalurus punctatus) constructed by using an interspecific hybrid resource family . Genetics , 165 : 687 – 694 .
   PubMed Web of Science ®Google Scholar
• Margulies , M. , Egholm , M. , Altman , W. E. , Attiya , S. , Bader , J. S. , Bemben , L. A. , Berka , J. , Braverman , M. S. , Chen , Y.-J. , Chen , Z. , Dewell , S. B. , Du , L. , Fierro , J. M. , Gomes , X. V. , Godwin , B. C. , He , W. , Helgesen , S. , Ho , C. H. , Irzyk , G. P. , Jando , S. C. , Alenquer , M. L. I. , Jarvie , T. P. , Jirage , K. B. , Kim , J.-B. , Knight , J. R. , Lanza , J. R. , Leamon , J. H. , Lefkowitz , S. M. , Lei , M. , Li , J. , Lohman , K. L. , Lu , H. , Makhijani , V. B. , Mcdade , K. E. , Mckenna , M. P. , Myers , E. W. , Nickerson , E. , Nobile , J. R. , Plant , R. , Puc , B. P. , Ronan , M. T. , Roth , G. T. , Sarkis , G. J. , Simons , J. F. , Simpson , J. W. , Srinivasan , M. , Tartaro , K. R. , Tomasz , A. , Vogt , K. A. , Volkmer , G. A. , Wang , S. H. , Wang , Y. , Weiner , M. P. , Yu , P. , Begley , R. F. and Rothberg , J. M. 2005 . Genome sequencing in microfabricated high-density picolitre reactors . Nature , 437 : 376 – 380 .
   PubMed Web of Science ®Google Scholar
• Markert , J. A. , Danley , P. D. and Arnegard , M. E. 2001 . New markers for new species: Microsatellite loci and the East African cichlids . Trends Ecol, Evol. , 16 : 100 – 107 .
   PubMed Web of Science ®Google Scholar
• Marth , G. T. , Korf , I. , Yandell , M. D. , Yeh , R. T. , Gu , Z. J. , Zakeri , H. , Stitziel , N. O. , Hillier , L. , Kwok , P. Y. and Gish , W. R. 1999 . A general approach to single-nucleotide polymorphism discovery . Nat. Genet. , 23 : 452 – 456 .
   PubMed Web of Science ®Google Scholar
• Martinez , V. 2007 . “ Marker-assisted selection in fish and shellfish breeding schemes ” . In Marker-Assisted Selection: Current Status and Future Application in Crops, Livestock, Forestry and Fish. , Edited by: Guimarães , E. , Ruane , J. , Scherf , B. , Sonnino , A. and Dargie , J. Rome : FAO .
   Google Scholar
• Martinez , V. , Thorgaard , G. , Robison , B. and Sillanpaa , M. J. 2005 . Posterior evidence of multiple QTL influencing early development in double haploid lines of rainbow trout . Oncorhynchus mykiss. Aquaculture , 247 : 25
   Web of Science ®Google Scholar
• Matsuyama , T. , Fujiwara , A. , Nakayasu , C. , Kamaishi , T. , Oseko , N. , Tsutsumi , N. , Hirono , I. and Aoki , T. 2007 . Microarray analyses of gene expression in Japanese flounder Paralichthys olivaceus leucocytes during monogenean parasite Neoheterobothrium hirame infection . Dis. Aquat. Organ. , 75 : 79 – 83 .
   PubMed Web of Science ®Google Scholar
• Mcginnity , P. , Prodohl , P. , Ferguson , A. , Hynes , R. , Maoileidigh , N. O. , Baker , N. , Cotter , D. , O'Hea , B. , Cooke , D. , Rogan , G. , Taggart , J. and Cross , T. 2003 . Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon . Proc. Biol. Sci. , 270 : 2443 – 2450 .
   PubMed Web of Science ®Google Scholar
• Meuwissen , T. H. E. , Karlsen , A. , Lien , S. , Olsaker , I. and Goddard , M. E. 2002 . Fine mapping of a quantitative trait locus for twinning rate using combined linkage and linkage disequilibrium mapping . Genetics , 161 : 373 – 379 .
   PubMed Web of Science ®Google Scholar
• Miyake , T. and Amemiya , C. T. 2004 . BAC libraries and comparative genomics of aquatic chordate species . Comp. Biochem. Physiol. C. Comp. Pharmacol. , 138 : 233 – 244 .
   PubMed Web of Science ®Google Scholar
• Moen , T. , Agresti , J. J. , Cnaani , A. , Moses , H. , Famula , T. R. , Hulata , G. , Gall , G. A. E. and May , B. 2004a . A genome scan of a four-way tilapia cross supports the existence of a quantitative trait locus for cold tolerance on linkage group 23 . Aquac. Res. , 35 : 893 – 904 .
   Web of Science ®Google Scholar
• Moen , T. , Fjalestad , K. T. , Munck , H. and Gomez-Raya , L. 2004b . A multistage testing strategy for detection of quantitative trait loci affecting disease resistance in Atlantic salmon . Genetics , 167 : 851 – 858 .
   PubMed Web of Science ®Google Scholar
• Moen , T. , Hoyheim , B. , Munck , H. and Gomez-Raya , L. 2004c . A linkage map of Atlantic salmon (Salmo salar) reveals an uncommonly large difference in recombination rate between the sexes . Anim. Genet. , 35 : 81 – 92 .
   PubMed Web of Science ®Google Scholar
• Moghadam , H. K. , Poissant , J. , Fotherby , H. , Haidle , L. , Ferguson , M. M. and Danzmann , R. G. 2007 . Quantitative trait loci for body weight, condition factor, and age at sexual maturation in Arctic charr (Salvelinus alpinus): Comparative analysis with rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) . Mol. Genet. Genom. , 277 : 647 – 661 .
   PubMed Web of Science ®Google Scholar
• Morizot , D. C. , Slaugenhaupt , S. A. , Kallman , K. D. and Chakravarti , A. 1991 . Genetic linkage map of fishes of the genus Xiphophorus (Teleostei: Poeciliidae) . Genetics , 127 : 399 – 410 .
   PubMed Web of Science ®Google Scholar
• Naylor , R. L. and Burke , M. 2005 . Aquaculture and ocean resources: Raising tigers of the sea . Annu. Rev. Environ. Resour. , 30 : 185 – 218 .
   Web of Science ®Google Scholar
• Naylor , R. L. , Goldburg , R. J. , Primavera , J. H. , Kautsky , N. , Beveridge , M. C. , Clay , J. , Folke , C. , Lubchenco , J. , Mooney , H. and Troell , M. 2000 . Effect of aquaculture on world fish supplies . Nature , 405 : 1017 – 1024 .
   PubMed Web of Science ®Google Scholar
• Naylor , R. L. , Williams , S. L. and Strong , D. R. 2001 . Aquaculture—A gateway for exotic species . Science , 294 : 1655 – 1656 .
   PubMed Web of Science ®Google Scholar
• Ng , S. H. S. , Artieri , C. G. , Bosdet , I. E. , Chiu , R. , Danzmann , R. G. , Davidson , W. S. , Ferguson , M. M. , Fjell , C. D. , Hoyheim , B. , Jones , S. J. M. , De Jong , P. J. , Koop , B. F. , Krzywinski , M. I. , Lubieniecki , K. , Marra , M. A. , Mitchell , L. A. , Mathewson , C. , Osoegawa , K. , Parisotto , S. E. , Phillips , R. B. , Rise , M. L. , Von Schalburg , K. R. , Schein , J. E. , Shin , H. S. , Siddiqui , A. , Thorsen , J. , Wye , N. , Yang , G. and Zhu , B. L. 2005 . A physical map of the genome of Atlantic salmon, Salmo salar . Genomics , 86 : 396 – 404 .
   PubMed Web of Science ®Google Scholar
• Nichols , K. M. , Young , W. P. , Danzmann , R. G. , Robison , B. D. , Rexroad , C. , Noakes , M. , Phillips , R. B. , Bentzen , P. , Spies , I. , Knudsen , K. , Allendorf , F. W. , Cunningham , B. M. , Brunelli , J. , Zhang , H. , Ristow , S. , Drew , R. , Brown , K. H. , Wheeler , P. A. and Thorgaard , G. H. 2003 . A consolidated linkage map for rainbow trout (Oncorhynchus mykiss) . Anim. Genet. , 34 : 102 – 115 .
   PubMed Web of Science ®Google Scholar
• Nieto-Diaz , M. , Pita-Thomas , W. and Nieto-Sampedro , M. 2007 . Cross-species analysis of gene expression in non-model mammals: Reproducibility of hybridization on high density oligonucleotide microarrays . BMC Genom. , 8 : 89
   PubMed Web of Science ®Google Scholar
• O'Malley , K. G. , Sakamoto , T. , Danzmann , R. G. and Ferguson , M. M. 2003 . Quantitative trait loci for spawning date and body weight in rainbow trout: Testing for conserved effects across ancestrally duplicated chromosomes . J. Hered. , 94 : 273 – 284 .
   PubMed Web of Science ®Google Scholar
• Ozaki , A. , Sakamoto , T. , Khoo , S. , Nakamura , K. , Coimbra , M. R. M. , Akutsu , T. and Okamoto , N. 2001 . Quantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss) . Mol. Genet. Genom. , 265 : 23 – 31 .
   PubMed Web of Science ®Google Scholar
• Palti , Y. , Gahr , S. A. , Hansen , J. D. and Rexroad , C. E. 2004 . Characterization of a new BAC library for rainbow trout: Evidence for multi-locus duplication . Anim. Genet. , 35 : 130 – 133 .
   PubMed Web of Science ®Google Scholar
• Pardo , B. G. , Fernandez , C. , Hermida , M. , Vazquez-Lopez , A. , Perez , M. , Presa , P. , Calaza , M. , Alvarez-Dios , J. A. , Comesana , A. S. , Raposo-Guillan , J. , Bouza , C. and Martinez , P. 2007 . Development and characterization of 248 novel microsatellite markers in turbot (Scophthalmus maximus) . Genome , 50 : 329 – 332 .
   PubMed Web of Science ®Google Scholar
• Phillips , R. B. , Nichols , K. M. , Dekoning , J. J. , Morasch , M. R. , Keatley , K. A. , Rexroad , C. III , Gahr , S. A. , Danzmann , R. G. , Drew , R. E. and Thorgaard , G. H. 2006 . Assignment of rainbow trout linkage groups to specific chromosomes . Genetics , 174 : 1661 – 1670 .
   PubMed Web of Science ®Google Scholar
• Quiniou , S. M. , Waldbieser , G. C. and Duke , M. V. 2007 . A first-generation BAC-based physical map of the channel catfish genome . BMC Genom. , 8 : 40
   PubMed Web of Science ®Google Scholar
• Quiniou , S. M. A. , Katagiri , T. , Miller , N. W. , Wilson , M. , Wolters , W. R. and Waldbieser , G. C. 2003 . Construction and characterization of a BAC library from a gynogenetic channel catfish, Ictalurus punctatus . Genet. Sel. Evol. , 35 : 1 – 11 .
   Web of Science ®Google Scholar
• Reid , D. P. , Szanto , A. , Glebe , B. , Danzmann , R. G. and Ferguson , M. M. 2005 . QTL for body weight and condition factor in Atlantic salmon (Salmo salar): Comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus) . Heredity , 94 : 166 – 172 .
   PubMed Web of Science ®Google Scholar
• Renn , S. C. P. , Aubin-Horth , N. and Hofmann , H. A. 2004 . Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray . BMC Genomics , 5 : 42
   PubMed Web of Science ®Google Scholar
• Rexroad , C. E. , Rodriguez , M. F. , Coulibaly , I. , Gharbi , K. , Danzmann , R. G. , De Koning , J. , Phillips , R. and Palti , Y. 2005 . Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss) . BMC Genom. , 6 : 54
   PubMed Web of Science ®Google Scholar
• Roberge , C. , Einum , S. , Guderley , H. and Bernatchez , L. 2006 . Rapid parallel evolutionary changes of gene transcription profiles in farmed Atlantic salmon . Mol. Ecol. , 15 : 9 – 20 .
   PubMed Web of Science ®Google Scholar
• Robison , B. D. , Wheeler , P. A. , Sundin , K. , Sikka , P. and Thorgaard , G. H. 2001 . Composite interval mapping reveals a major locus influencing embryonic development rate in rainbow trout (Oncorhynchus mykiss) . J. Hered. , 92 : 16 – 22 .
   PubMed Web of Science ®Google Scholar
• Rodriguez , M. F. , Lapatra , S. , Williams , S. , Famula , T. and May , B. 2004 . Genetic markers associated with resistance to infectious hematopoietic necrosis in rainbow and steelhead trout (Oncorhynchus mykiss) backcrosses . Aquaculture , 241 : 93 – 115 .
   Web of Science ®Google Scholar
• Sakamoto , T. , Danzmann , R. G. , Gharbi , K. , Howard , P. , Ozaki , A. , Khoo , S. K. , Woram , R. A. , Okamoto , N. , Ferguson , M. M. , Holm , L. E. , Guyomard , R. and Hoyheim , B. 2000 . A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates . Genetics , 155 : 1331 – 1345 .
   PubMed Web of Science ®Google Scholar
• Sakamoto , T. , Danzmann , R. G. , Okamoto , N. , Ferguson , M. M. and Ihssen , P. E. 1999 . Linkage analysis of quantitative trait loci associated with spawning time in rainbow trout (Oncorhynchus mykiss) . Aquaculture , 173 : 33 – 43 .
   Web of Science ®Google Scholar
• Sarropoulou , E. , Franch , R. , Louro , B. , Power , D. M. , Bargelloni , L. , Magoulas , A. , Senger , F. , Tsalavouta , M. , Patarnello , T. , Galibert , F. , Kotoulas , G. and Geisler , R. 2007 . A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis . BMC Genom. , 8 : 44
   PubMed Web of Science ®Google Scholar
• Schlötterer , C. 2004 . The evolution of molecular markers–just a matter of fashion? . Nat. Rev. Genet. , 5 : 63 – 69 .
   PubMed Web of Science ®Google Scholar
• Sellner , E. M. , Kim , J. W. , Mcclure , M. C. , Taylor , K. H. , Schnabel , R. D. and Taylor , J. F. 2007 . Applications of genomic information in livestock . J. Anim. Sci. , 85 : 3148 – 3158 .
   PubMed Web of Science ®Google Scholar
• Senger , F. , Priat , C. , Hitte , C. , Sarropoulou , E. , Franch , R. , Geisler , R. , Bargelloni , L. , Power , D. and Galibert , F. 2006 . The first radiation hybrid map of a perch-like fish: The gilthead seabream (Sparus aurata L) . Genomics , 87 : 793 – 800 .
   PubMed Web of Science ®Google Scholar
• Sobrino , B. , Brion , M. and Carracedo , A. 2005 . SNPs in forensic genetics: A review on SNP typing methodologies . Forensic Sci. Int. , 154 : 181 – 194 .
   PubMed Web of Science ®Google Scholar
• Sonesson , A. K. 2007 . “ Possibilities for marker-assisted selection in aquaculture breeding schemes ” . In Marker-Assisted Selection: Current Status and Future Application in Crops, Livestock, Forestry, and Fish , Edited by: Guimarães , E. , Ruane , J. , Scherf , B. , Sonnino , A. and Dargie , J. Rome : FAO .
   Google Scholar
• Streisinger , G. , Singer , F. , Walker , C. , Knauber , D. and Dower , N. 1986 . Segregation analyses and gene-centromere distances in zebrafish . Genetics , 112 : 311 – 319 .
   PubMed Web of Science ®Google Scholar
• Sun , X. W. and Liang , L. 2004 . Q. A genetic linkage map of common carp (Cyprinus carpio L.) and mapping of a locus associated with cold tolerance . Aquaculture , 238 : 165 – 172 .
   Web of Science ®Google Scholar
• Thorsen , J. , Zhu , B. L. , Frengen , E. , Osoegawa , K. , De Jong , P. J. , Koop , B. F. , Davidson , W. S. and Hoyheim , B. 2005 . A highly redundant BAC library of Atlantic salmon (Salmo salar): An important tool for salmon projects . BMC Genom. , 6 : 50
   PubMed Web of Science ®Google Scholar
• Von Schalburg , K. R. , Rise , M. L. , Cooper , G. A. , Brown , G. D. , Gibbs , A. R. , Nelson , C. C. , Davidson , W. S. and Koop , B. F. 2005 . Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray . BMC Genom. , 6 : 126
   PubMed Web of Science ®Google Scholar
• Waldbieser , G. C. , Bosworth , B. G. , Nonneman , D. J. and Wolters , W. R. 2001 . A microsatellite-based genetic linkage map for channel catfish, Ictalurus punctatus . Genetics , 158 : 727 – 734 .
   PubMed Web of Science ®Google Scholar
• Walker , S. J. , Wang , Y. L. , Grant , K. A. , Chan , F. and Hellmann , G. M. 2006 . Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates . J. Neurosci. Methods , 152 : 179 – 189 .
   PubMed Web of Science ®Google Scholar
• Wang , C. M. , Lo , L. , Feng , F. , Gong , P. , Li , J. , Zhu , Z. , Lin , G. and Yue , G. 2008 . Construction of a BAC library and mapping BAC clones to the linkage map of Barramundi, Lates calcarifer . BMC Genom. , 9 : 139
   PubMed Web of Science ®Google Scholar
• Wang , C. M. , Zhu , Z. Y. , Lo , L. C. , Feng , F. , Lin , G. , Yang , W. T. , Li , J. and Yue , G. H. 2007 . A microsatellite linkage map of Barramundi, Lates calcarifer . Genetics , 175 : 907 – 915 .
   PubMed Web of Science ®Google Scholar
• Wardle , F. C. , Odom , D. T. , Bell , G. W. , Yuan , B. B. , Danford , T. W. , Wiellette , E. L. , Herbolsheimer , E. , Sive , H. L. , Young , R. A. and Smith , J. C. 2006 . Zebrafish promoter microarrays identify actively transcribed embryonic genes . Genome Biol. , 7 : R71
   PubMed Web of Science ®Google Scholar
• Wayne , M. L. and Mcintyre , L. M. 2002 . Combining mapping and arraying: An approach to candidate gene identification . Proc. Natl. Acad. Sci. USA , 99 : 14903 – 14906 .
   PubMed Web of Science ®Google Scholar
• Weber , A. P. M. , Weber , K. L. , Carr , K. , Wilkerson , C. and Ohlrogge , J. B. 2007 . Sampling the arabidopsis transcriptome with massively parallel pyrosequencing . Plant Physiol. , 144 : 32 – 42 .
   PubMed Web of Science ®Google Scholar
• Werner , F. A. O. , Durstewitz , G. , Habermann , F. A. , Thaller , G. , Kramer , W. , Kollers , S. , Buitkamp , J. , Georges , M. , Brem , G. , Mosner , J. and Fries , R. 2004 . Detection and characterization of SNPs useful for identity control and parentage testing in major European dairy breeds . Anim. Genet. , 35 : 44 – 49 .
   PubMed Web of Science ®Google Scholar
• Westgaard , J. I. , Tafese , T. , Wesmajervi , M. A. , Stenvik , J. , Fjalestad , K. T. , Damsgard , B. and Delghandi , M. 2007 . Identification and characterisation of thirteen new microsatellites for Atlantic cod (Gadus morhua L.) from a repeat-enriched library . Conserv. Genet. , 8 : 749 – 751 .
   Web of Science ®Google Scholar
• Whitaker , H. A. , Mcandrew , B. J. and Taggart , J. B. 2006 . Construction and characterization of a BAC library for the European sea bass Dicentrarchus labrax . Anim. Genet. , 37 : 526 – 526 .
   PubMed Web of Science ®Google Scholar
• Williams , T. D. , Diab , A. M. , George , S. G. , Godfrey , R. E. , Sabine , V. , Conesa , A. , Minchin , S. D. , Watts , P. C. and Chipman , J. K. 2006 . Development of the GENIPOL European flounder (Platichthys flesus) microarray and determination of temporal transcriptional responses to cadmium at low dose . Environ. Sci. Technol. , 40 : 6479 – 6488 .
   PubMed Web of Science ®Google Scholar
• Woram , R. A. , Mcgowan , C. , Stout , J. A. , Gharbi , K. , Ferguson , M. M. , Hoyheim , B. , Davidson , E. A. , Davidson , W. S. , Rexroad , C. and Danzmann , R. G. 2004 . A genetic linkage map for Arctic char (Salvelinus alpinus): Evidence for higher recombination rates and segregation distortion in hybrid versus pure strain mapping parents . Genome , 47 : 304 – 315 .
   PubMed Web of Science ®Google Scholar
• Yue , G. H. , Ho , M. Y. , Orban , L. and Komen , J. 2004 . Microsatellites within genes and ESTs of common carp and their applicability in silver crucian carp . Aquaculture , 234 : 85 – 98 .
   Web of Science ®Google Scholar
• Zane , L. , Bargelloni , L. and Patarnello , T. 2002 . Strategies for microsatellite isolation: A review . Mol. Ecol. , 11 : 1 – 16 .
   PubMed Web of Science ®Google Scholar
• Zhang , J. H. , Wheeler , D. A. , Yakub , I. , Wei , S. , Sood , R. , Rowe , W. , Liu , P. P. , Gibbs , R. A. and Buetow , K. H. 2005 . SNPdetector: A software tool for sensitive and accurate SNP detection . PLoS Comput. Biol. , 1 : 395 – 404 .
   Web of Science ®Google Scholar
• Zimmerman , A. M. , Evenhuis , J. P. , Thorgaard , G. H. and Ristow , S. S. 2004 . A single major chromosomal region controls natural killer cell-like activity in rainbow trout . Immunogenetics , 55 : 825 – 835 .
   PubMed Web of Science ®Google Scholar