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Zebrafish as a model organism for nutrition and growth: towards comparative studies of nutritional genomics applied to aquacultured fishes

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Abstract

Zebrafish (Danio rerio) is a common research model in fish studies of toxicology, developmental biology, neurobiology and molecular genetics; it has been proposed as a possible model organism for nutrition and growth studies in fish. The advantages of working with zebrafish in these areas are their small size, short generation time (12–14 weeks) and their capacity to produce numerous eggs (100–200 eggs/clutch). Since a wide variety of molecular tools and information are available for genomic analysis, zebrafish has also been proposed as a model for nutritional genomic studies in fish. The detailed study of every species employed as a model organism is important because these species are used to generalize how several biological processes occur in related organisms, and contribute considerably toward improving our understanding of the mechanisms involved in nutrition and growth. The objective of this review is to show the relevant aspects of the nutrition and growth in zebrafish that support its utility as a model organism for nutritional genomics studies. We made a particular emphasis that gene expression and genetic variants in response to zebrafish nutrition will shed light on similar processes in aquacultured fish.

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References

  • Accini G (2009) Estimación de heredabilidad e identificación de marcadores RAPD asociados a tasa de crecimiento en zebrafish (Danio rerio). Tesis de Ingeniero Agrónomo, Facultad de Ciencias Agronómicas, Universidad de Chile, p 33

  • Acosta J, Carpio Y, Borroto I, Gonzalez O, Estrada M (2005) Myostatin gene silenced by RNAi show a zebrafish giant phenotype. J Biotechnol 119:324–331

    Article  PubMed  CAS  Google Scholar 

  • Alami-Durante H, Médale F, Cluzeaud M, Kaushik S (2010a) Skeletal muscle growth dynamics and expression of related genes in white and red muscle of rainbow trout fed diets with graded levels of a mixture of plant protein sources as substitutes for fishmeal. Aquaculture 303:50–58

    Article  CAS  Google Scholar 

  • Alami-Durante H, Wrutniak-Cabello C, Kaushik SJ, Médale F (2010b) Skeletal muscle cellularuty and expression of myogenic regulatory factors and myosin heavy chains in rainbow trout (Oncorhynchus mykiss): effects of changes in dietary plant protein sources and amino acid profiles. Comp Biochem Physiol A 156:561–568

    Article  CAS  Google Scholar 

  • Albertson R, Payne-Ferreira T, Postlethwait J, Yelick P (2005) Zebrafish acvr2a and acvr2b exhibit distinct roles in craniofacial development. Dev Dyn 233:1405–1418

    Article  PubMed  CAS  Google Scholar 

  • Aleström P, Holter J, Nourizadeh-Lillabadi R (2006) Zebrafish in functional genomics and aquatic biomedicine. Trends Biotechnol 24:15–21

    Article  PubMed  CAS  Google Scholar 

  • Allendorf F, Thorgaard G (1984) Tetraploidy and the evolution of salmonid fishes. In: Turner B (ed) Evolutionary genetics of fishes. Plenum Press, New York, pp 1–46

    Google Scholar 

  • Aparicio S, Chapman J, Stupka E, Putnam N, Chia J, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Sollewinjn Gelpke M, Roach J, Oh T, Ho IY, Wong M, Detter CH, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith S, Clark M, Edwards YJK, Doggett N, Zharkikh A, Tavtigian S, Pruss D, Barnstead M, Evans CH, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan H, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301–1310

    Article  PubMed  CAS  Google Scholar 

  • Araneda C, Neira R, Lam N, Iturra P (2008) Salmonids. In: Kocher TD, Kole C (eds) Genome mapping and genomics in fishes and aquatic animals. Springer-Verlag, Berlin, Heidelberg, pp 1–43

    Chapter  Google Scholar 

  • Atchley W, Fitch W, Bronnerfraser M (1994) Molecular evolution of the Myod family of transcription factors. Proc Natl Acad Sci USA 91:11522–11526

    Article  PubMed  CAS  Google Scholar 

  • Barbazuk W, Korf I, Kadavi I, Heyen J, Tate S, Wun E, Bedell J, McPherson J, Johnson S (2000) The syntenic relationship of the zebrafish and human genomes. Genome Res 10:1351–1358

    Article  PubMed  CAS  Google Scholar 

  • Bell M (2001) Lateral plate evolution in the threespine stickleback: getting nowhere fast. Genetica 1:445–461

    Article  Google Scholar 

  • Bergeron S, Milla L, Villegas R, Shen M-C, Burgess S, Allende M, Palma V, Karlstrom R (2008) Expression profiling identifies novel Hh/Gli regulated genes in developing zebrafish embryos. Genomics 91:165–177

    Article  PubMed  CAS  Google Scholar 

  • Biga P, Goetz F (2006) Zebrafish and giant danio as models for muscle growth: determinate versus indeterminate growth as determined by morphometric analysis. Am J Physiol Regul Integr Comp Physiol 291:1327–1337

    Article  CAS  Google Scholar 

  • Boulding EG, Culling M, Glebe B, Berg PR, Lien S, Moen T (2008) Conservation genomics of Atlantic salmon: SNPs associated with QTLs for adaptative traits in parr from four trans-Atlantic backcrosses. Heredity 101:381–391

    Article  PubMed  CAS  Google Scholar 

  • Bower N, Li X, Taylor R, Johnston A (2008) Switching to fast growth: the insulin-like growth factor (IGF) system in skeletal muscle of Atlantic salmon. J Exp Biol 211:3859–3870

    Article  PubMed  CAS  Google Scholar 

  • Bradley K, Elmore B, Breyer J, Yaspan B, Jessen J, Knapik E, Smith J (2007) A major zebrafish polymorphism resource for genetic mapping. Genome Biol 8:55–65

    Article  CAS  Google Scholar 

  • Breder C, Rosen D (1966) Modes of reproduction in fishes. The Natural History Press, New York, p 941

    Google Scholar 

  • Briggs J (2002) The zebrafish: a new model organism for integrative physiology. Am J Physiol Regul Integr Comp Physiol 282:R3–R9

    PubMed  CAS  Google Scholar 

  • Brown M (1957) Experimental studies on growth. In: Brown M (ed) The physiology of fishes. Academic Press, New York, pp 261–400

    Google Scholar 

  • Carpio Y, Acosta J, Morales R, Santisteban Y, Sanchéz A, Estrada M (2009) Regulation of body mass growth through activin type IIB receptor in teleosts fish. Gen Comp Endocrinol 160:158–167

    Article  PubMed  CAS  Google Scholar 

  • Carvalho A, Sá R, Oliva-Teles A, Bergot P (2004) Solubility and peptide profile affect the utilization of dietary protein by common carp (Cuprinus carpio) during early larval stages. Aquaculture 234:319–333

    Article  CAS  Google Scholar 

  • Carvalho A, Araujo L, Santos M (2006) Rearing zebrafish (Danio rerio) larvae without live food: evaluation of a commercial, a practical, and a purified starter diet on larval performance. Aquacult Res 37:1107–1111

    Article  CAS  Google Scholar 

  • Cenadelli S, Maran V, Bongioni G, Fusetti L, Parma P, Aleandri R (2007) Identification of nuclear SNPs in gilthead seabream. J Fish Biol 70:399–405

    Article  CAS  Google Scholar 

  • Chapalamadugu K, Robison B, Drew R, Powell M, Hill R, Amberg J, Rodnick K, Hardy R, Hill M, Murdoch G (2009) Dietary carbohydrate level affects transcription factor expression that regulates skeletal muscle myogenesis in rainbow trout. Comp Biochem Physiol B 153:66–72

    Article  PubMed  CAS  Google Scholar 

  • Chauvigné F, Gabillard J, Weil C, Rescan P (2003) Effect of refeeding on IGFI, IGFII, IGF receptors, FGF2, FGF6 and myostatin mRNA expression in rainbow trout myotomal muscle. Gen Comp Endocrinol 132:209–215

    Article  PubMed  CAS  Google Scholar 

  • Chen Y, Lee W, Liu C, Tsai H (2001) Molecular structure, dynamic expression, and promoter analysis of zebrafish (Danio rerio) Myf-5 gene. Genesis 29:22–35

    Article  PubMed  CAS  Google Scholar 

  • Chen F, Lee Y, Jiang Y, Wang S, Peatman E, Abernathy J, Liu H, Liu SK, Kucuktas H, Ke CH, Liu Z (2010) Identification and characterization of Full-Length cDNAs in Channel Catfish (Ictalurus punctatus) and Blue Catfish (Ictalurus furcatus). Plos One 12e: 11543

  • Clark M (2003) Genomics and mapping of teleostei. Comp Funct Genomics 4:182–193

    Article  PubMed  CAS  Google Scholar 

  • Cossins A, Crawford D (2005) Fish as model for environmental genomics. Nat Rev Genet 6:324–340

    Article  PubMed  CAS  Google Scholar 

  • Cowey C, Sargent J (1976) Lipid nutrition in fish. Comp Biochem Physiol 57B:269–273

    Google Scholar 

  • Cresko W, McGuigan K, Phillips P, Postlethwait J (2007) Studies of threespine stickleback developmental evolution: progress and promise. Genetica 129:105–126

    Article  PubMed  Google Scholar 

  • Crollius H, Weissenbach J (2008) Fish genomics and biology. Genome Res 15:1675–1682

    Article  CAS  Google Scholar 

  • Dabrowski K, Hliwa P, Gomulka P, Sienicki M, Carvalho AP, Ostaszewska T, Terjesen B (2005) Studies on the utilization of free amino acid, casein-based, or commercial diets in rearing common carp larvae. Abstr of Aquac Am 344, New Orleans, USA

  • Daga R, Thode G, Amores A (1996) Chromosome complement, C-banding, Ag-NOR and replication banding in the zebrafish Danio rerio. Chromosome Res 4:29–32

    Article  PubMed  CAS  Google Scholar 

  • Dahm R (2002) Atlas of embryonic stages of development in the zebrafish. In: Nusslein-Volhard C, Dahm R (eds) Zebrafish: a practical approach. Oxford University Press, Oxford, pp 219–236

    Google Scholar 

  • Dahm R, Geisler R (2006) Learning from small fry: the zebrafish as a genetic model organism for aquaculture fish species. Mar Biotechnol 0:1–17

    Google Scholar 

  • Davidson W, Koop B, Jones S, Iturra P, Vidal R, Maass A, Jonassen I, Lien S, Omholt S (2010) Sequencing the genome of the Atlantic salmon (Salmo salar). Genome Biol 11:403

    PubMed  Google Scholar 

  • Davis GP, Hetzel DJ (2000) Integrating molecular genetics technology with traditional approaches for genetic improvement in aquaculture species. Aquacult Res 31:3–10

    Article  Google Scholar 

  • De-Santis C, Jerry D (2007) Candidate growth genes in finfish—Where should we be looking? Aquaculture 272:22–38

    Article  CAS  Google Scholar 

  • Dominik S, Henshall J, Kube P, King H, Lien S, Kent M, Elliott N (2010) Evaluation of an Atlantic salmon SNP chip as a genomic tool for the application in a Tasmanian Atlantic salmon (Salmo salar) breeding population. Aquaculture 308:S56–S61

    Article  CAS  Google Scholar 

  • Douglas S (2006) Microarray studies of genes expression in fish. J Integr Biol 10(4):474–489

    CAS  Google Scholar 

  • Drew R, Rodnick K, Settles M, Wacyk J, Churchill E, Powell M, Hardy R, Murdoch G, Hill R, Barrie R (2008) Effect of starvation on the transcriptomes of the brain and liver in adult female zebrafish. Physiol Genomics 35:283–295

    Article  PubMed  CAS  Google Scholar 

  • Driever W, Stemple D, Schier A, Solnica-Krezel L (1994) Zebrafish: genetic tools for studying vertebrate development. Trends Genet 10:152–159

    Article  PubMed  CAS  Google Scholar 

  • Du SH (2004) Molecular regulation of fish muscle development and growth. In: Gong Z, Korzh V (eds) Molecular aspects of fish and marine biology, volume 2, fish development and genetics the zebrafish and medaka models. World Scientific, Singapure, pp 581–611

    Google Scholar 

  • Dumas A, Frane J, Bureau D (2010) Modelling growth and body composition in fish nutrition: where have we been and where are we going? Aquacult Res 41:161–181

    Article  Google Scholar 

  • Dutta S (1993) Food and feeding habits of Danio rerio (Ham. Buch.) inhabiting gadigarh stream, Jammu. J Freshw Biol 5:165–168

    Google Scholar 

  • Eaton R, Farley R (1974a) Spawning cycle and egg production of zebrafish, Brachydanio rerio, in the laboratory. Copeia 1:195–204

    Article  Google Scholar 

  • Eaton R, Farley R (1974b) Growth and the reduction of depensation of zebrafish, Brachedanio rerio reared in the laboratory. Copeia 1:204–209

    Article  Google Scholar 

  • Ehrlich J, Sankoff D, Nadeau J (1997) Synteny conservation and chromosome rearrangements during mammalian evolution. Genetics 147:289–296

    PubMed  CAS  Google Scholar 

  • Erbay E, Park I, Nuzzi P, Schoenherr C, Chen J (2003) IGF-II transcription in skeletal myogenesis is controlled by mTOR and nutrients. J Cell Biol 163:931–936

    Article  PubMed  CAS  Google Scholar 

  • Estay F, Cerisola H, Téllez V (1994) Biologia del desarrollo y reproducción artificial en la trucha arcoíris. Publicación del grupo de investigación de la Universidad de Chile, Universidad Católica de Valparaíso y del Instituto Fomento Pesquero, Chile, pp 1–28

  • Falconer D, MacKay T (1996) Introduction to quantitative genetics. Longman Group Ltda, Malasia, p 464

    Google Scholar 

  • Fiogbé E, Kestemont P (1995) An assessment of the protein and amino acid requirement in goldfish (Carassius auratus) larvae. J Appl Ichthyol 11:282–289

    Article  Google Scholar 

  • Fjalestad KT, Moen T, Gomez-Raya L (2003) Prospects for genetic technology in salmon breeding programmes. Aquacult Res 34:397–406

    Article  CAS  Google Scholar 

  • Franch R, Louro B, Tsalavouta M, Chatziplis D, Tsigenopoulos S, Sorropoulou E, Antonello J, Magoulas A, Mylonas C, Babbucci M, Patarnello T, Power D, Kotoulas G, Bargelloni L (2006) A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L. Genetics 174:851–861

    Article  PubMed  CAS  Google Scholar 

  • Froystad M, Lilleeng E, Bakke-Mckellep A, Vekterud K, Hemre G, Krogdahl A (2008) Gene expression in distal intestine of Atlantic salmon (Salmo salar L.) fed genetically modified soybean meal. Aquacult Nutr 14:204–214

    Article  CAS  Google Scholar 

  • Froystad M, Lilleeng E, Bakke-Mckellep A, Vekterud K, Valen E, Hemre G, Krogdahl A (2009) Distal intestinal gene expression in Atlantic salmon (Salmo salar L.) fed genetically modified maize. Aquacult Nutr 15:104–115

    Article  CAS  Google Scholar 

  • German D, Horn M (2006) Gut length and mass in herbivorous and carnivorous prickleback fishes (Teleostei: Stichaeidae): ontogenetic, dietary, and phylogenetic effects. Mar Biol 148:1123–1134

    Article  Google Scholar 

  • Goll D, Thompson V, Li H, Wei W, Cong J (2003) The calpain system. Physiol Rev 83:731–801

    PubMed  CAS  Google Scholar 

  • Goolish E, Okutake K, Lesure S (1999) Growth and Survivorship of larval zebrafish Danio rerio on processed diets. N Am J Aquacult 61:189–198

    Article  Google Scholar 

  • Gornung E, Gabrielli I, Cataudella S, Sola L (1997) CMA3—banding pattern and fluorescence in situ hybridization with 18S rRNA genes in zebrafish chromosomes. Chromosome Res 5:40–46

    Article  PubMed  CAS  Google Scholar 

  • Govoroun M, Le Gac F, Guiguen Y (2006) Generation of a large scale repertoire of Expressed Sequence Tags (ESTs) from normalized rainbow trout cDNA libraries. BCM Genomics 7:196

    Article  Google Scholar 

  • Grunwald D, Eisen J (2002) Headwaters of the zebrafish—emergence of a new model vertebrate. Nat Rev Genet 3:717–724

    Article  PubMed  CAS  Google Scholar 

  • Hahlbeck E, Katsiadaki I, Mayer I, Adolfsson-Erici M, James J, Bengtsson B (2004) The juvenile three-spined stickleback (Gasterosteus aculeatus L.) as a model organism for endocrine disruption II-kidney hypertrophy, vitellogenin and spiggin induction. Aquat Toxicol 70:311–326

    Article  PubMed  CAS  Google Scholar 

  • Hardy R (2010) Utilization of plant proteins in fish diets: effects of global demand and supplies of fishmeal. Aquacult Res 41:770–776

    Article  CAS  Google Scholar 

  • Hayes B, Laerdahl JK, Lien S, Moen T, Berg P, Hindar K, Davison WS, Koop BF, Adzhubei A, Hoyheim B (2007) An extensive resources of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences. Aquaculture 265:82–90

    Article  CAS  Google Scholar 

  • Hedges S (2002) The origin and evolution of model organisms. Nat Rev Genet 3:838–843

    Article  PubMed  CAS  Google Scholar 

  • Helterline D, Garikipati D, Stenkamp D, Rodgers D (2006) Embryonic and tissue-specific regulation of myostatin-1 and-2 gene expression in zebrafish. Gen Comp Endocrinol 151(1):90–97

    Article  CAS  Google Scholar 

  • Hinegardner R, Rosen DE (1972) Cellular DNA content and the evolution of teleostean fishes. Am Nat 106:621–644

    Article  CAS  Google Scholar 

  • Hinits Y, Osborn D, Carvajal J, Rigby P, Hughes M (2007) Mrf4 (myf6) is dynamically expressed in differentiated zebrafish skeletal muscle. Gene Expr Patterns 7:738–745

    Article  PubMed  CAS  Google Scholar 

  • Horn M, Gawlicka A, German D, Logothetis E, Cavanagh J, Boyle K (2006) Structure and function of the stomachless digestive system in three related species of New World silverside fishes (Atherinopsidae) representing herbivory, omnivory, and carnivory. Mar Biol 149:1237–1245

    Article  Google Scholar 

  • Huising M, Geven E, Kruiswijk C, Nabuurs S, Stolte E, Spanings F, Verburg-van Kemenade B, Flik G (2006) Increased leptin expression in common carp (Cyprinus carpio) after food intake but not after fasting or feeding to satiation. Endocrinology 147:5786–5797

    Article  PubMed  CAS  Google Scholar 

  • Janvier P (1996) Early vertebrates. Oxford Science Publications, Clarendon Press, New York 375

    Google Scholar 

  • Johansen K, Overturf K (2005) Sequence, conservation, and quantitative expression of rainbow trout Myf-5. Comp Biochem Physiol B: Biochem Mol Biol 140:533–541

    Article  CAS  Google Scholar 

  • Johansen S, Coucheron D, Andreassen M, Ove Karlsen B, Furmanek T, Jorgensen T, Emblem A, Breines R, Nordeide J, Moun T, Nederbragt A, Stenseth N, Jakobsen K (2009) Large-scale sequence analyses of Atlantic cod. New Biotechnol 25:263–271

    Article  CAS  Google Scholar 

  • Johnson R, Johnson T, Londraville R (2000) Evidence for leptin expression in fishes. J Exp Zool A: Comp Exp Biol 286:718–724

    Article  CAS  Google Scholar 

  • Johnston I (1999) Muscle development and growth: potential implications for flesh quality in fish. Aquaculture 177:99–115

    Article  Google Scholar 

  • Johnston I, Macqueen D, Watabe S (2008) Molecular biotechnology of development and growth in fish muscle. In: Tsukamoto K, Kawamura T, Takeuchi T, Douglas Beard T, Kaiser M (eds) Fisheries for global welfare and environment. 5th World Fisheries Congress, Scotland, pp 241–262

    Google Scholar 

  • Kaput J, Rodriguez RL (2003) Nutritional Genomics: the next frontier in the postgenomic era. Physiol Genomics 16:166–177

    Article  Google Scholar 

  • Kasahara M, Naruse K, Sasaki SH, Nakatani Y, Qu W, Ahsan B, Yamada T, Nagayasu Y, Doi K, Kasai Y, Jindo T, Kobayashi D, Shamida A, Toyoda A, Kuroki Y, Fujiyama A, Sasaki T, Shimizu A, Asakawa SH, Shimizu N, Hashimoto SH, Jun Yang, Lee Y, Matsushima K, Sugano S, Sakaisumi M, Takanori N, Ohishi K, Haga SH, Ohta F, Nomoto H, Nogata K, Morishita T, Endo T, Shin-I T, Takeda H, Morishita SH, Kohara Y (2007) The medaka draft genome and insigts into vertebrate genome evolution. Nature 447:714–719

    Article  PubMed  CAS  Google Scholar 

  • Katsiadaki I, Scott AP, Mayer I (2002) The potential of the three-spined stickleback (Gasterosteus aculeatus L.) as a combined biomarker for oestrogens and androgens in European waters. Mar Environ Res 54:725–728

    Article  PubMed  CAS  Google Scholar 

  • Kimmel C, Ballard W, Kimmel S, Ullmann B, Schilling T (1995) Stages of embryonic development of the zebrafish. Dev Dyn 203:253–310

    Article  PubMed  CAS  Google Scholar 

  • Kobiyama A, Nihei Y, Hirayama Y, Kikuchi K, Suetake H, Johnston I, Watabe S (1998) Molecular cloning and developmental expression patterns of the MyoD and MEF2 families of muscle transcription factors in the carp. J Exp Biol 201:2801–2813

    CAS  Google Scholar 

  • Kurokawa T, Uji S, Suzuki T (2005a) Identification of pepsinogen gene in the genome of stomachless fish. Takifugu rubripes Comp Biochem and Physiol Part B: Biochem Mol Biol 140:133–140

    Article  CAS  Google Scholar 

  • Kurokawa T, Uji S, Suzuki T (2005b) Identification of cDNA coding for a homologue to mammalian leptin from pufferfish, Takifugu rubripes. Peptides 26:745–750

    Article  PubMed  CAS  Google Scholar 

  • Lauder G, Liem K (1989) The evolution and interrelationships of the Actinopterygian fishes. Bull Mus Comp Zool 150:95–187

    Google Scholar 

  • Lawrence C (2007) The husbandry of zebrafish (Danio rerio): a review. Aquaculture 269:1–20

    Article  Google Scholar 

  • Lee S, McPherron A (2001) Regulation of myostatin activity and muscle growth. PNAS 16:9306–9311

    Article  Google Scholar 

  • Leong J, Jantzen S, Von Schalburg K, Cooper G, Messmer A, Liao N, Munro S, Moore R, Holt R, Jones S, Davison W, Koop B (2010) Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome. BCM Genomics 11:279

    Article  CAS  Google Scholar 

  • Li P, Peatman E, Wang SH, Feng J, He CH, Baoprsertkul P, Xu P, Kucuktas H, Nandi S, Somridhivej B, Serapion J, Simmons M, Turan C, Liu L, Muir W, Dunham R, Brady Y, Grizzle J, Liu Z (2007) Towards the ictalurid catfish transcriptome: generation and analysis of 31, 215 catfish ESTs. BCM Genomics 8:117

    Article  CAS  Google Scholar 

  • Lilleeng E, Froystad M, Ostby G, Valen E, Krogdahl A (2007) Effects of diet containing soybean meal on trypsin mRNA expression and activity in Atlantic salmon (Salmo salar L.). Comp Biochem Physiol Part A: Mol Integr Physiol 147:25–36

    Article  CAS  Google Scholar 

  • Liu Z, Cordes J (2004) DNA marker technologies and their applicationsin aquaculture genetics. Aquaculture 238:1–37

    Article  CAS  Google Scholar 

  • Liu H, Jiang Y, Wang SH, Ninwichian P, Somridhivej B, Xu P, Abernathy J, Kucuktas H, Liu Z (2009) Comparative analysis of catfish BAC end sequences with the zebrafish genome. BCM Genomics 10:592

    Article  CAS  Google Scholar 

  • Lo Pestri R, Lisa C, Di Stasio L (2009) Molecular genetics in aquaculture. Ital J of Anim Sci 8:299–313

    Google Scholar 

  • Lochman R, Phillips H (1996) Nutrition and feeding of baitfish. Aquacult Mag 4:87–89

    Google Scholar 

  • Lu J, Peatman E, Yang Q, Wang SH, Hu Z, Reecy J, Kucuktas H, Liu Z (2010) The catfish genome database cBARBEL: an informatics platform for genome biology of ictalurid catfish. Nucleic Acids Res 39:D815–D821

    Article  PubMed  Google Scholar 

  • Maccatrozzo L, Bargelloni L, Cardazzo B, Rizzo G, Patarnello T (2001) A novel second myostatin gene is present in teleost fish. FEBS Lett 509:36–40

    Article  PubMed  CAS  Google Scholar 

  • Macqueen D, Johnston I (2008) Evolution of follistatin in teleosts revealed through phylogenetic, genomic and expression analyses. Dev Genes Evol 218:1–14

    Article  PubMed  CAS  Google Scholar 

  • Marti M, Moreno-Aliaga M, Zulet A, Martinez J (2005) Avances en nutrición molecular: nutrigenómica y nutrigenética. Nutr Hosp 3:157–164

    Google Scholar 

  • McClure M, McIntyre P, McCune A (2006) Notes on the natural diet and habitat of eight danioin fishes, including the zebrafish Danio rerio. J Fish Biol 69:553–570

    Article  Google Scholar 

  • McPherron A, Lawler A, Lee S (1997) Regulation of skeletal muscle mass in mice by a new TGF-beta superfamily member. Nature 387:83–90

    Article  PubMed  CAS  Google Scholar 

  • Meinelt T, Schultz C, Worth M, Kurzinger H, Steinberg C (1999) Dietary fatty acid composition influences the fertilization rate of zebrafish (Danio rerio Hamilton-Buchanon). J Appl Ichthyol 15:19–23

    Article  CAS  Google Scholar 

  • Meinelt T, Schultz C, Worth M, Kurzinger H, Steinberg C (2000) Correlation of diets high in n6-polyunsaturated fatty acids with high growth rate in zebrafish (Danio rerio). Comp Med 50:43–45

    PubMed  CAS  Google Scholar 

  • Meli R, Prasad A, Patowary A, Lalwani K, Maini J, Sharma M, Singh A, Kumar G, Jadhav V, Scaria V, Sivasubbu S (2008) FishMap: a community resource for zebrafish genomics. Zebrafish 5:125–130

    Article  PubMed  CAS  Google Scholar 

  • Metscher B, Ahlberg P (1999) Zebrafish in context: uses of a laboraty model in comparative studies. Dev Biol 210:1–4

    Article  PubMed  CAS  Google Scholar 

  • Moen T, Hayes B, Baranski M, Berg P, Kjoglum S, Koop B, Davidson W, Omholt S, Lien S (2008a) A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BCM Genomics 9:223–237

    Article  CAS  Google Scholar 

  • Moen T, Hayes B, Nilsen F, Delghandi M, Fjalestad K, Fevolden SE, Berg PR, Lien S (2008b) Identification and characterization of novel SNP markers in Atlantic cod: evidence for directional selection. BMC Genetics 9:18

    Article  PubMed  CAS  Google Scholar 

  • Mommsen T (2001) Paradigms of growth in fish. Comp Biochem Physiol B 129:207–219

    Article  PubMed  CAS  Google Scholar 

  • Moriyama S, Ayson F, Kawauchi H (2000) Growth regulation by insulin-like growth factor-I in fish. Biosci Biotechnol Biochem 64(8):1553–1562

    Article  PubMed  CAS  Google Scholar 

  • Moyle P, Cech J (2000) Fishes. An introduction to ichthyology. Prentice Hall Inc., USA, p 612

    Google Scholar 

  • Müller M, Kersten S (2003) Nutrigenomics: goals and strategies. Nat Rev Genet 4:315–322

    Article  PubMed  CAS  Google Scholar 

  • Mutch M, Wahli W, Williamson G (2005) Nutrigenomics and nutrigenetics: the emerging faces of nutrition. The FASEB J 19:1602–1615

    Article  CAS  Google Scholar 

  • Naruse K, Tanaka M, Mita K, Shima A, Postlethwait J, Mitani H (2004) A medaka gen map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping. Genome Res 14:820–828

    Article  PubMed  CAS  Google Scholar 

  • Nielsen E, Hansen M, Meldrup D (2006) Evidence of microsatellite hitch-hiking selection in Atlantic cod (Gadus morhua L.): implications for inferring population structure in nonmodel organisms. Mol Ecol 15:3219–3229

    Article  PubMed  CAS  Google Scholar 

  • NRC National Research Council (1993) Nutrient requeriments of coldwater fishes. National Academy of Science, Washington, DC USA 63

    Google Scholar 

  • Ojima Y (1983) Fish cytogenetics. Suiko-sha, Tokyo, Japan 453

    Google Scholar 

  • Orban L, Wu Q (2008) Cyprinids. In: Kocher TD, Kole C (eds) Genome mapping and genomics in fishes and aquatic animal, volume 2. Springer-Verlag, Berlin, Heidelberg, pp 45–97

    Chapter  Google Scholar 

  • Ostbye T, Bardal T, Vegusdal A, Frang O, Kjorsvik E, Andersen O (2007) Molecular cloning of the Atlantic salmon activin receptor IIB cDNA-Localization of the receptor and myostatin in vivo and in vitro in muscle cells. Comp Biochem Physiol 2:101–111

    Google Scholar 

  • Panserat S, Kaushik S (2010) Regulation of gene expression by nutritional factors in fish. Aquacult Res 41:751–762

    Article  CAS  Google Scholar 

  • Panserat S, Kirchner S, Kaushik S (2007) Nutrigenomics. In: Nakagawa H, Sato M, Gatlin D III (eds) Dietary supplements for the health and quality of cultured fish. CAB International North America, USA, pp 210–229

    Chapter  Google Scholar 

  • Panserat S, Ducasse-Cabanot S, Plagnes-Juan E, Srivastava P, Kolditz C, Piumi F, Esquerré D, Kaushik S (2008) Dietary fat level modifies the expression of hepatic genes in juvenile rainbow trout (Oncorhynchus mykiss) as revealed by microarray analysis. Aquaculture 275:235–241

    Article  CAS  Google Scholar 

  • Phillips D, Krestor D (1998) Follistatin: a multifunctional regulatory protein. Front Neuroendocrinol 19:287–322

    Article  PubMed  CAS  Google Scholar 

  • Postlethwait J (2004) Evolution of the zebrafish genome. In: Gong Z, Korzh V (eds) Molecular Aspects of Fish and Marine Biology, volume 2, fish development and genetics the zebrafish and medaka models. World Scientific, Singapure, pp 581–611

    Chapter  Google Scholar 

  • Quinn N, Levenkova N, Chow W, Bouffard P, Boroevich K, Knight J, Jarvie T, Lubieniecki K, Desany B, Koop B, Harkins T, Davidson W (2008) Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome. BMC Genomics 9:404

    Article  PubMed  CAS  Google Scholar 

  • Rebbapragada A, Benchabane H, Wrana J, Celeste A, Attisano L (2003) Myostatin signals through a transforming growth factor beta-like signaling pathway to block adipogenesis. Mol Cell Biol 23:7230–7242

    Article  PubMed  CAS  Google Scholar 

  • Reid DP, Santo A, Glebe B, Danzmann RG, Ferguson M (2005) QTL for body weight and condition factor in Atlantc salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Artic charr (Salvelinus alpinus). Heredity 94:166–172

    Article  PubMed  CAS  Google Scholar 

  • Rexroad CE III, Lee Y, Keele JW, Karamycheva S, Brown G, Koop B, Gahr SA, Palti Y, Quackenbush J (2003) Sequence analysis of a rainbow trout cDNA library and creation of a gene index. Cytogenet Genome Res 102:347–354

    Article  PubMed  Google Scholar 

  • Rexroad C III, Rodriguez M, Coulibaly I, Gharbi K, Danzmann R, DeKoning J, Phillips R, Palti Y (2005) Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss). BCM Genomics 6:54–62

    Article  CAS  Google Scholar 

  • Rexroad C III, Palti Y, Gahr S, Vallejo R (2008) A second generation genetic map for rainbow trout (Oncorhynchus mykiss). BCM Genet 9:74–88

    Google Scholar 

  • Ricker, W (1958) Hanbook of computations for biological statistics of fish populations. Bull Fish Res Bd Canada, p 300

  • Robison B, Drew R, Murdoch G, Powell M, Rodnick K, Settles M, Stone D, Churchill E, Hill R, Papasani M, Lewis S, Hardy R (2008) Sexual dimorphism in hepatic gene expression and the response to dietary carbohydrate manipulation in the zebrafish (Danio rerio). Comp Bichem Physiol Part D 2:141–154

    Google Scholar 

  • Roush W (1996) Zebrafish embryology builds a better model vertebrate. Science 272:1103

    Article  PubMed  CAS  Google Scholar 

  • Rust M (2002) Nutritional physiology. In: Halver J, Hardy R (eds) Fish nutrition, 3rd edn. Academic press, USA, pp 368–446

    Google Scholar 

  • Ryynänen HJ, Primmer C (2006) Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantc salmon (salmo salar) and other salmon fishes. BCM Genomics 7:192

    Article  CAS  Google Scholar 

  • Salem M, Nath J, Rexroad C, Killefer J, Yao J (2005a) Identification and molecular characterization of the rainbow trout calpains (Capn1 and Calp2): their expression in muscle wasting during starvation. Comp Biochem Physiol B: Biochem Mol Biol 140:63–71

    Article  CAS  Google Scholar 

  • Salem M, Yao J, Rexroad C, Kenney P, Semmens K, Killefer J, Nath J (2005b) Characterization of calpastatin gene in fish: its potential role in muscle growth and fillet quality. Comp Biochem Physiol B: Biochem Mol Biol 141:488–497

    Article  CAS  Google Scholar 

  • Salem M, Silverstein J, Rexroad C III, Yao J (2007) Effect of starvation on global gene expression and proteolysis in rainbow trout (Oncorhynchus mykiss). BCM Genomics 8:328–344

    Article  CAS  Google Scholar 

  • Santigosa E, Sánchez J, Médale F, Kaushik S, Peréz-Sánchez J, Gallardo M (2008) Modifications of digestive enzymes in trout (Oncorhynchus mykiss) and sea bream (Sparus aurata) in response to dietary fish meal replacement by plant protein sources. Aquaculture 282:68–74

    Article  CAS  Google Scholar 

  • Santos M, Micael J, Carvalho A, Morabito R, Booy P, Massanisso P, Lamoree M, Reis-Henriques M (2006) Estrogens counteract the masculinizing efect of tributyltin in zebrafish. Comp Biochem and Physiol C: Toxicol Pharmacol 142:151–155

    Article  CAS  Google Scholar 

  • Sarropoulou E, Power DM, Magoulas A, Geisler R, Kotoulas G (2005) Comparative analysis and characterization of expressed sequence tags in gilthead sea bream (Sparus aurata) liver and embryos. Aquaculture 243:69–81

    Article  CAS  Google Scholar 

  • Sarropoulou E, Franch R, Louro B, Power D, Bargelloni L, Magoulas AN, Senger F, Tsalavouta M, Patarnello T, Galibert F, Kotoulas G, Geisler R (2007) A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis. BCM Genomics 8:44

    Article  CAS  Google Scholar 

  • Seiliez I, Gabillard J, Skiba-Cassy S et al (2008) An in vivo and in vitro assessment of TOR signaling cascade in rainbow trout (Onchorinchus mykiss). Am J Physiol Regul Integr Comp Physiol 295:329–335

    Article  CAS  Google Scholar 

  • Senger F, Priat C, Hitte CH, Sarropoulou E, Franch R, Geisler R, Bargelloni L, Power D, Galibert F (2006) The first radiation hybrid map of perch-like fish: the gilthead seabream (Sparus aurata L.). Genomics 87:793–800

    Article  PubMed  CAS  Google Scholar 

  • Smith C, Elfstrom C, Seeb L, Seeb J (2005) Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Mol Ecol 14:4193–4203

    Article  PubMed  CAS  Google Scholar 

  • Spence R, Fatema M, Ellis S, Ahmed Z, Smith C (2007) Diet, growth and recruitment of wild zebrafish in Bangladesh. J Fish Biol 71:304–309

    Article  Google Scholar 

  • Stickney H, Schmutz J, Woods I, Holtzer C, Dickson M, Kelly P, Myers R, Talbot W (2002) Rapid mapping of zebrafish mutations with SNPs and oligonuleotide microarrays. Genome Res 12:1929–1934

    Article  PubMed  CAS  Google Scholar 

  • Tan X, Hoang L, Du S (2002) Characterization of muscleregulatory genes, Myf5 and myogenin, from striped bass and promoter analysis of muscle-specific expression. Mar Biotechnol 4:537–545

    Article  PubMed  CAS  Google Scholar 

  • Tave D (1993) Genetics for fish hatchery managers. An AVI book, New York, p 415

    Google Scholar 

  • Thorsen J, Zhu B, Frengen E, Osoegawa K, Jong PJ, Koop BF, Davidson W, Hoyheim B (2005) A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects. BCM Genomics 6:50

    Article  CAS  Google Scholar 

  • Turchini G, Torstensen B, Ng W-K (2009) Fish oil replacement in finfish nutrition. Rev Aquacult 1:10–57

    Article  Google Scholar 

  • Vignal A, Milan D, San Cristobal M, Eggen A (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol 34:275–305

    Article  PubMed  CAS  Google Scholar 

  • Volff J (2005) Genome evolution and biodiversity in teleost fish. Heredity 94:280–294

    Article  PubMed  CAS  Google Scholar 

  • Von Hertell U, Hörstgen-Schwarrk G, Langholz H, Jung B (1990) Family studies on genetic variability in growth and reproductive performance between and within test fish populations of the zebrafish, Brachydanio rerio. Aquaculture 85:307–315

    Article  Google Scholar 

  • Wang Y, Li C, Lee G, Tsay H, Tsai H, Chen Y (2008) Inactivation of zebrafish mrf4 leads to myofibril misalignment and motor axon growth disorganization. Dev Dyn 237:1043–1050

    Article  PubMed  CAS  Google Scholar 

  • Wang S, Peatman E, Abernathy J, Waldbieser G, Lindquist E, Richardson P, Lucas S, Wang M, Li P, Thimmapuram J, Liu L, Vullaganti D, Kucuktas H, Murdock CH, Small B, Wilson M, Liu H, Jiang Y, Lee Y, Chen F, Lu J, Wang W, Xu P, Somridhivej B, Baoprasertkul P, Quilang J, Sha Z, Bao B, Wang Y, Wang Q, Takano T, Nandi S, Liu S, Wong L, Kaltenboeck L, Quiniou S, Bengten E, Miller N, Trant J, Rockhsar D, Liu Z, The Catfish Genome Consortium (2010) Assembly of 500, 000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol 11:R8

    Article  PubMed  CAS  Google Scholar 

  • Watanabe T (1981) Lipid nutrition in fish. Comp Biochem Physiol B 73:3–15

    Article  Google Scholar 

  • Watanabe T, Kitajima C, Fujita S (1983) Nutritional values of live organisms used in Japan for mass propagation of fish: a review. Aquaculture 34:115–145

    Article  CAS  Google Scholar 

  • Wegrzyn D, Ortubay S (2009) Salmonidos en patagonia, volumen 1. Mar del plata, Argentina, p 164

    Google Scholar 

  • Wesmajervi MS, Tafese T, Stenvik J, Fjalested KT, Damsgard B, Delghandi M (2007) Eight new microsatellite markers in Atlantic cod (Gadus morhua L.) derived from an enriched genomic library. Mol Ecol 7:138–140

    CAS  Google Scholar 

  • Westerfield M (2000) The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio). University of Oregon Press, Eugene, Oregon USA, p 385

    Google Scholar 

  • Wittbrodt J, Shima A, Schartl M (2002) Medaka—a model organism from the far east. Nat Rev Genet 3:53–64

    Article  PubMed  CAS  Google Scholar 

  • Woods G, Wilson C, Friedlander B, Chang P, Reyes K, Nix R, Kelly D, Chu F, Postlethwait H, Talbot W (2005) The zebrafish gene map defines ancestral vertebrate chromosomes. Genome Res 15:1307–1314

    Article  PubMed  CAS  Google Scholar 

  • Wright D, Nakamichi R, Krause J, Butlin R (2006) QTL analysis of behavioral and morphological differentiation between wild and laboratory zebrafish (Danio rerio). Behav Genet 36:271–284

    Article  PubMed  Google Scholar 

  • Xu P, Wang SH, Liu L, Thorsen J, Kukuktas H, Liu Z (2007) A BAC-based physical map of the channel catfish genome. Genomics 90:380–388

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

This work was supported by the following fellowships to PU: Conicyt AT-24091052 and Doctoral fellowship from the Consorcio Empresarial de Genética y Desarrollo Biotecnológico para la Industria Salmonera (Aquainnovo S.A.) and, Grant DI I2 04/05-2 Universidad de Chile to CA. The authors acknowledge the help of Daniela Romo and Francisco Estay (Piscicola Hulilco Ltda.) for your assistance in photography. PU also wishes to thank the Programa de Doctorado en Ciencias de Recursos Naturales of the Universidad de La Frontera. We are especially grateful to Rashida Lathan for the English editing in the final version of this work.

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  1. Departamento de Ciencias Químicas, Programa de Doctorado en Ciencias de Recursos Naturales, Facultad de Ciencias Ingeniería y Administración, Universidad de La Frontera, Casilla 54-D, Temuco, Chile

    Pilar E. Ulloa

  2. Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Casilla 1004, Santiago, Chile

    Patricia Iturra

  3. Departamento de Producción Animal, Facultad de Ciencias Agronómicas, Universidad de Chile, Casilla 70061-7, Santiago, Chile

    Pilar E. Ulloa, Roberto Neira & Cristian Araneda

  4. AQUAINNOVO S.A., Polpaico 037, Puerto Montt, Chile

    Roberto Neira

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  1. Pilar E. Ulloa
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  2. Patricia Iturra
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Correspondence to Pilar E. Ulloa.

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Ulloa, P.E., Iturra, P., Neira, R. et al. Zebrafish as a model organism for nutrition and growth: towards comparative studies of nutritional genomics applied to aquacultured fishes. Rev Fish Biol Fisheries 21, 649–666 (2011). https://doi.org/10.1007/s11160-011-9203-0

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