Cyprinids

Genome Mapping and Genomics in Animals

Volumn 2, Issue , 2008, Pages 45-83

  Orban, Laszlo ^a,b   Wu, Qingjiang ^c  

^a TEMASEK LIFE SCIENCES LABORATORY   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c INSTITUTE OF HYDROBIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 70249096024     PISSN: None     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Chapter

References (345)

1. Adjaye J, Herwig R, Herrmann D, Wruck W, BenKahla A, Brink TC, Nowak M, Carnwath JW, Hultschig C, Niemann Het al. (2004) Cross-species hybridisation of human and bovine orthologous genes on high density cDNA microarrays. BMC Genomics 5:83
2. Aldridge FJ, Marston RQ, Shireman JV (1990) Induced triploids and tetraploids in bighead carp, Hypophthalmichthys nobilis, verified by multiembryo cytofluorometric analysis. Aquaculture 87:121-131
3. Aliah RS, Takagi M, Dong S, Teoh CT, Taniguchi N (1999) Isolation and inheritance of microsatellite markers in the common carp Cyprinus carpio. Fish Sci 65:235-239
4. Alves MJ, Coelho MM, Collares-Pereira MJ (2001) Evolution in action through hybridisation and polyploidy in an Iberian freshwater fish: a genetic review. Genetica 111:375-385
5. Amemiya CT, Zhong TP, Silverman GA, Fishman MC, Zon LI (1999) Zebrafish YAC, BAC, and PAC genomic libraries. In: The Zebrafish: Genetics and Genomics. Detrich HW, WesterfieldMand Zon LI (eds) Academic Press, SanDiego, CA, USA, pp 235-258
6. Amemiya CT, Zon LI (1999) Generation of a zebrafish P1 artificial chromosome library. Genomics 58:211-213
7. Amores A, Postlethwait JH (1999) Banded chromosomes and the zebrafish karyotype. In: The Zebrafish: Genetics and Genomics. Detrich HW, Westerfield M and Zon LI (eds) Academic Press, San Diego, CA, USA, pp 323-338
8. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A et al. (2002)Wholegenome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301-1310
9. Avise JC (2000) Phylogeography: The history and formation of species, Harvard University Press, Cambridge, MA, USA, pp 1-447
10. Bahary N, Davidson A, Ransom D, Shepard J, Stern H, Trede N, Zhou Y, Barut B, Zon LI (2004) The Zon laboratory guide to positional cloning in zebrafish. In: Zebrafish: 2nd Edition. Genetics Genomics and Informatics. DetrichHW, Westerfield M and Zon LI (eds) Elsevier Academic Press, Amsterdam, The Netherlands, pp 305-329
11. Bakos J, Gorda S (1995) Genetic improvement of common carp strains using intraspecific hybridization. Aquaculture 129:183-186
12. Balon EK (1995) Origin and domestication of the wild carp, Cyprinus carpio - fromRoman gourmets to the swimming flowers. Aquaculture 129:3-48
13. Bartfai R, Egedi S, Yue GH, Kovacs B, Urbanyi B, Tamas G, Horvath L, Orban L (2003) Genetic analysis of twocommon carp broodstocks by RAPD and microsatellite markers. Aquaculture 219:157-167
14. Ben-Dom N, Cherfas NB, Gomelsky B, Avtalion RR, Moav B, Hulata G (2001) Production of heterozygous and homozygous clones of common carp (Cyprinus carpio L.): Evidence fromDNAfingerprinting andmixed leukocyte reaction. Isr J Aquacult - Bamidgeh 53:89-100
15. Bensch S, Akesson M (2005) Ten years of AFLP in ecology and evolution: why so few animals? Mol Ecol 14:2899-2914
16. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2005) GenBank. Nucleic Acids Res 33:D34-D38
17. Benter T, Papadopoulos S, Pape M, Manns M, Poliwoda H (1995) Optimization and reproducibility of Random Amplified Polymorphic DNA in human. Anal Biochem 230:92-100
18. Bercsenyi M, Magyary I, Urbanyi B, Orban L, Horvath L (1998) Hatching out goldfish from common carp eggs: interspecific androgenesis between two cyprinid species. Genome 41:573-579
19. Berg LS (1964) Freshwater fishes of the USSR and adjacent countries, Vol. 2, IsraeliProgramfor ScientificTranslations, Jerusalem, Israel, pp 1-496
20. Boguski MS, Lowe TMJ, Tolstoshev CM (1993) dbEST - Database for expressed sequence tags. Nat Genet 4:332-333
21. Bonar SA, Bolding B, Divens M (2002) Effects of triploid grass carp on aquatic plants, water quality, and public satisfaction in Washington State. North Am J Fish Management 22:96-105
22. Bongers ABJ, BenAyed MZ, Doulabi BZ, Komen J, Richter CJJ (1997) Origin of variation in isogenic, gynogenetic, and androgenetic strains of common carp, Cyprinus carpio. J Exp Zool 277:72-79
23. Bongers ABJ, Intveld EPC, Abohashema K, Bremmer IM, Eding EH, Komen J, Richter CJJ (1994) Androgenesis in common carp (Cyprinus carpio L) using UV irradiation in a synthetic ovarian fluid and heat shocks. Aquaculture 122:119-132
24. Bongers ABJ, Sukkel M, Gort G, Komen J, Richter CJJ (1998) Development and use of genetically uniform strains of common carp in experimental animal research. Lab Anim 32:349-363
25. Bongers ABJ, Zandieh-Doulabi B, Richter CJJ, Komen J (1999) Viable androgeneticYYgenotypes of common carp (Cyprinus carpio L.). J Hered 90:195-198
26. Bowtell DDL (1999) Options available - from start to finish - for obtaining expression data by microarray. Nat Genet 21:25-32
27. Bradley KM, Elmore JB, Breyer JP, Yaspan BL, Jessen JR, Knapik EW, Smith JR (2007) A major zebrafish polymorphism resource for genetic mapping. Genome Biol 8:R55
28. Briggs R, King TJ (1952) Transplantation of living nuclei from blastula cells into enucleated frog’s eggs. ProcNatl Acad Sci USA 38:455-463
29. Briolay J, Galtier N, Brito RM, Bouvet Y (1998) Molecular phylogeny of Cyprinidae inferred from cytochrome b DNA sequences. Mol Phylogenet Evol 9:100-108
30. Broughton RE, Milam JE, Roe BA (2001) The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res 11:1958-1967
31. Brown P (2005) Carp in Australia, AgFac Fishfacts 4. http://www.irysec.vic.edu.au/sci/introduced/carpfact.html.
32. Brownlie A, Donovan A, Pratt SJ, Paw BH, Oates AC, Brugnara C, Witkowska HE, Sassa S, Zon LI (1998) Positional cloning of the zebrafish sauternes gene: a model for congenital sideroblastic anaemia. Nat Genet 20:244-250
33. Brubaker CL, Paterson AH, Wendel JF (1999) Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome 42:184-203
34. Buchtova H, Svobodova Z, Flajshans M, Vorlova L (2003) Analysis of growth, weight and relevant indices of diploid and triploid population of tench Tinca tinca (Linnaeus 1758). Aquacult Res 34:719-726
35. Burger G, Gray MW, Lang BF (2003) Mitochondrial genomes: anything goes. Trends Genet 19:709-716
36. Burnside J (1999) DNA microarray: Practical approaches and considerations. Biol Reprod 60:70
37. Buth GD, Dowling TE, Gold JR (1991) Molecular and cytological investigations. In:Cyprinid fishes: Systematics, biology and expoitation. Winfield IJ andNelson JS (eds)Chapmann and Hall, London, UK, pp 83-126
38. Butler D (2000) Wellcome Trust funds bid to unravel zebrafish genome. Nature 408:503
39. Cameron DA, Gentile KL, Middleton FA, Yurco P (2005) Gene expression profiles of intact and regenerating zebrafish retina. Mol Vision 11:775-791
40. Cassani JR, Maloney DR, Allaire HP, Kerby JH (1990) Problems associated with tetraploid induction and survival in grass carp, Ctenopharyngodon idella. Aquaculture 88:273-284
41. Cataudella S, Sola L, Accame-Muratori L, Capanna E (1977) The chromosomes of 11 species of Cyprinidae and one Cobitidae fromItaly, with some remarks on the polyploidy in the Cypriniformes. Genetica 47:161-171
42. Chalmers AD, Goldstone K, Smith JC, Gilchrist M, Amaya E, Papalopulu N (2005) A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis. Mech Dev 122:355-363
43. Chan MM, Lu X, Merchant FM, Iglehart JD, Miron PL (2005) Gene expression profiling of NMU-induced rat mammary tumors: cross species comparison with human breast cancer. Carcinogenesis 26:1343-1353
44. Chan YH, Cheng KW, Yu KL, Chan KM (1996) Identification of two prolactin cDNA sequences from a goldfish pituitary cDNA library. Biochim Biophys Acta - Gene Struct Expr 1307:8-12
45. Chang A, Liew WC, Chuah A, Lim Z, Lin Q, Orban L (2007) FluoMEP: A new genotyping method combining the advantages of randomly amplified polymorphic DNA and amplified fragment length polymorphism. Electrophoresis 28:525-534
46. Chapman BA, Bowers JE, Schulze SR, Paterson AH (2004) A comparative phylogenetic approach for dating whole genome duplication events. Bioinformatics 20:180-185
47. Chen HX, Yi YL, Chen MR, Yang XQ (1986) Studies on the developmental potentiality of cultured cell nuclei of fish. Acta Hydrobiol Sinica 10:1-7
48. Chen M, Yan K, Liu H, Yi Y, Yang X, Liu P, Chen H (1987) Preliminary study on artificially induced heterogeneous tetraploid in the hybrid of white crucian carp and red carp. Acta Hydrobiol Sinica 11:96-98
49. Chen M, Yang X, Yu X, Chen H, Chen H, Liu H (1997) Chromosome ploidy manipulation of allotetraploids and their fertility in Japanese phytophagous crucian carp (JPCC) (female) X red crucian carp (RCC) (male). Acta Hydrobiol Sinica 21:197-206
50. Chen X, Cho YG, McCouch SR (2002) Sequence divergence of rice microsatellites in Oryza and other plant species. Mol Gen Genet 268:331-343
51. Cheng K (2004) The experts speak: Views on four key questions about zebrafish research. Zebrafish 1:85-103
52. Cherfas NB (1975) Studies on diploid gynogenesis in the carp. I. Experiments on the mass production of the diploid gynogenetic offspring (in Russian). Genetika (Moscow) 11:78-86
53. Cherfas NB (1977) Studies on diploid gynogenesis in the carp. II. Segregation with respect to certainmorphological traits in gynogenetic offsprings (inRussian). Genetika (Moscow) 13:811-820
54. Cherfas NB, Gomelsky B, Bendom N, Peretz Y, Hulata G (1994) Assessment of triploid common carp (Cyprinus carpio L) for culture. Aquaculture 127:11-18
55. Cherfas NB, Gomelsky B, Peretz Y, Bendom N, Hulata G, Moav B (1993) Induced gynogenesis and polyploidy in the Israeli common carp line Dor-70. Isr J Aquacult - Bamidgeh 45:59-72
56. Cherfas NB, Kozinsky O, Rothbard S, Hulata G (1990) Induced diploidgynogenesis andtriploidy inornamental (koi) carp, Cyprinus carpio L .1. Experiments on the timing of temperature shock. Isr J Aquacult - Bamidgeh 42:3-9
57. Chiba T, Kurihama N, Kenichi Y (1966) Culture of common carp (in Japanese). Green Book House Publisher, Tokyo, Japan, pp 1-222
58. Chourrout D, Chevassus B, Krieg F, Happe A, Burger G, Renard P (1986) Production of second generation triploid and tetraploid rainbow trout by mating tetraploid males and diploid females - potential of tetraploid fish. Theor Appl Genet 72:193-206
59. Chrisanfova GG, Ludanny RI, Slynko YV, Yakovlev VN, Semyenova SK (2004) RAPD fingerprinting of common bream Abramis brama L., roach Rutilus rutilus L., and their F-1 hybrids (A. brama × R. rutilus and R. rutilus × A. brama). Russian J Genet 40:1182-1185
60. Christoffels A, Bartfai R, Srinivasan H, Komen H, Orban L (2006) Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome. BMC Bioinformatics 7 (Suppl. 5):S2
61. Christoffels A, Koh EGL, Chia JM, Brenner S, Aparicio S, Venkatesh B (2004) Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol Biol Evol 21:1146-1151
62. Clark MD, Hennig S, Herwig R, Clifton SW, Marra MA, Lehrach H, Johnson SL (2001) An oligonucleotide fingerprint normalized and expressed sequence tag characterized zebrafish cDNA library. Genome Res 11:1594-1602
63. Clark MS (2003) Genomics and mapping of Teleostei (bony fish). Comp Funct Genomics 4:182-193
64. Cognie F, Billard R, Chao NH(1989) Cryo-preservation of carp, Cyprinus carpio, sperm. J Appl Ichthyol 5:165-176
65. Coimbra RS, Weil D, Brottier P, Blanchard S, Levi M, Hardelin JP, Weissenbach J, Petit C (2002) A subtracted cDNA library from the zebrafish (Danio rerio) embryonic inner ear. Genome Res 12:1007-1011
66. Collares-Pereira MJ, Coelho MM (1989) Polyploidy versus diploidy: a new model for the karyological evolution of Cyprinidae. Arq Mus Bocage, NS 1:375-383
67. Collares-Pereira MJ, DaCosta LM (1999) Intraspecificandinterspecific genome size variation in Iberian Cyprinidae and the problem of diploidy and polyploidy, with review of genome sizes within the family. Folia Zool 48:61-76
68. Corley-Smith GE, Brandhorst BP (1999) Preservation of endangered species and populations: A role for genome banking, somatic cell cloning, and androgenesis? Mol Reprod Dev 53:363-367
69. Corley-Smith GE, Brandhorst BP, Walker C, Postlethwait JH (1999) Production of haploid and diploid androgenetic zebrafish (including methodology for delayed in vitro fertilization). In:TheZebrafish: Genetics andGenomics. Detrich HW, Westerfield M and Zon LI (eds) Academic Press, San Diego, CA, USA, pp 45-60
70. Corley-Smith GE, Lim CTJ, Brandhorst BP (1996) Production of androgenetic zebrafish (Danio rerio). Genetics 142:1265-1276
71. Cossins AR, Crawford DL (2005) Opinion - Fish as models for environmental genomics. Nat Rev Genet 6:324-333
72. Crooijmans R, Bierbooms VAF, Komen J, VanderPoel JJ, Groenen MAM (1997) Microsatellite markers in common carp (Cyprinus carpio L). Anim Genet 28:129-134
73. Csizmadia C, Jeney Z, Szerencses I, Gorda S (1995) Transferrin polymorphismof someraces ina live genebankof common carp. Aquaculture 129:193-198
74. David L, Blum S, Feldman MW, Lavi U, Hillel J (2003) Recent duplication of the, common carp (Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci. Mol Biol Evol 20:1425-1434
75. David L, Rajasekaran P, Fang J, Hillel J, Lavi U (2001) Polymorphism in ornamental and common carp strains (Cyprinus carpio L.) as revealed by AFLP analysis and a new set of microsatellite markers. Mol Gen Genet 266:353-362
76. David L, Rosenberg NA, Lavi U, Feldman MW, Hillel J (2007) Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp, Cyprinus carpio L. Genet Select Evol 39:319-340
77. David L, Rothbard S, Rubinstein I, Katzman H, Hulata G, Hillel J, Lavi U (2004) Aspects of red and black color inheritance in the Japanese ornamental (koi) carp (Cyprinus carpio L.). Aquaculture 233:129-147
78. Day F (1880) The fishes of Great Britain and Ireland (Vol. 2.), Williams and Norgate, London, UK, pp 1-388
79. Desvignes JF, Laroche J, Durand JD, Bouvet Y (2001) Genetic variability in reared stocks of common carp (Cyprinus carpio L.) based onallozymes and microsatellites. Aquaculture 194:291-301
80. Diter A, Guyomard R, Chourrout D (1988) Gene segregation in induced tetraploid rainbow trout - Genetic evidence of preferential pairing of homologous chromosomes. Genome 30:547-553
81. Dodd A, Curtis PM, Williams LC, Love DA (2000) Zebrafish: bridging the gap between development and disease. Hum Mol Genet 9:2443-2449
82. Dong S, Ohara K, Taniguchi N (1997) Introduction of sperm of common carp Cyprinus carpio into eggs of ginbuna Carassius langsdorfii by heat shock treatment and its confirmation by DNA markers. Nippon Suisan Gakkaishi 63:201-206
83. Dong S, Taniguchi N (1996) Clonal nature of offspings of ginbuna, Carassius langsdorfii by RAPD-PCR and isozyme patterns. Nippon Suisan Gakkaishi 62:891-896
84. Dong S, Taniguchi N, Tsuji S (1996) Identification of clones of ginbuna, Carassius langsdorfii by DNA fingerprinting and isozyme pattern. Nippon Suisan Gakkaishi 62:747-753
85. Dong Z, Zhou E (1998) Application of the random amplified polymorphicDNAtechnique in a study of heterosis in common carp, Cyprinus carpio L. Aquacult Res 29:595-600
86. Dooley K, Zon LI (2000) Zebrafish: amodel systemfor the study of human disease. Curr Opin Genet Dev 10:252-256
87. Driever W, Solnica-Krezel L, Schier AF, Neuhauss SCF, Malicki J, Stemple DL, Stainier DYR, Zwartkruis F, Abdelilah S, Rangini Z et al. (1996) A genetic screen for mutations affecting embryogenesis in zebrafish. Development 123:37-46
88. Durand JD, Tsigenopoulos CS, Unlu E, Berrebi P (2002) Phylogeny and biogeography of the family Cyprinidae in the Middle East inferred from cytochrome b DNA - Evolutionary significance of this region. Mol Phylogenet Evol 22:91-100
89. Ellegren H (2004) Microsatellites: Simple sequences with complex evolution. Nat Rev Genet 5:435-445
90. Emelyanov A, Gao Y, Naqvi NI, Parinov S (2006) Trans-kingdom transposition of the maize Dissociation element. Genetics 174:1095-1104
91. Engeszer RE, Patterson RB, Rao AA, Parichy DM (2007) Zebrafish in the wild: A review of natural history and new notes from the field. Zebrafish 4:1-8
92. Ferris SD, Witt GS (1977) The evolution of duplicate gene expression in the carp (Cyprinus carpio). Experientia 33:1299-1301
93. Flajshans M, Kvasnicka P, Rab P (1993a) Genetic studies intench (Tinca tinca L) - High incidence of spontaneous triploidy. Aquaculture 110:243-248
94. Flajshans M, Linhart O, Kvasnicka P (1993b) Genetic studies of tench (Tinca tinca L) - Induced triploidy and tetraploidy and first performance data. Aquaculture 113:301-312
95. Flajshans M, Linhart O, Slechtova V, Slechta V (1999) Genetic resources of commercially important fish species in the Czech Republic: present state and future strategy. Aquaculture 173:471-483
96. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32:W273-279
97. Froese R, Pauly DE (2005) FishBase.WorldWideWeb electronic publication. In: www.fishbase.org, version (06/2005)
98. Froufe E, Magyary I, Lehoczky I, Weiss S (2002) mtDNA sequence data supports an Asian ancestry and single introduction of common carp into theDanube basin. J Fish Biol 61:301-304
99. Fu H, Wu C (2001) Nuclear transfer in leach (Paramisgurnus dabryanus Sauvage) by cell-to-cell electrofusion. Aquacult Res 32:267-275
100. Geisler R, Rauch GJ, Baier H, van Bebber F, Bross L, Dekens MPS, Finger K, Fricke C, Gates MA, Geiger H et al. (1999) A radiation hybrid map of the zebrafish genome. Nat Genet 23:86-89
101. Gervai J, Peter S, Nagy A, Csanyi V (1980) Induced triploidy in carp, Cyprinus carpio L. J Fish Biol 17:667-671
102. Gilles A, Lecointre G, Faure E, Chappaz R, Brun G (1998) Mitochondrial phylogeny of the European cyprinids: Implications for their systematics, reticulate evolution, and colonization time. Mol Phylogenet Evol 10:132-143
103. Gilles A, Lecointre G, Miquelis A, Loerstcher M, Chappaz R, Brun G (2001) Partial combination applied to phylogeny of European cyprinids using the mitochondrial control region. Mol Phylogenet Evol 19:22-33
104. Goff DJ, Galvin K, Katz H, Westerfield M, Lander ES, Tabin CJ (1992) Identification of polymorphic simple sequence repeats in the genome of the zebrafish. Genomics 14:200-202
105. Gomelsky B (2003) Chromosomesetmanipulation and sex control in common carp: a review. Aquat Liv Res 16:408-415
106. Gorda S, Bakos J, Liska J, Kakuk C (1995) Live gene bank of common carp strains at the FishCultureResearch Institute, Szarvas. Aquaculture 129:199-202
107. Gracey AY, Fraser EJ, Li WZ, Fang YX, Taylor RR, Rogers J, Brass A, Cossins AR (2004) Copingwith cold:Anintegrative,multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci USA 101:16970-16975
108. Granjeaud S, Bertucci F, Jordan BR (1999) Expression profiling: DNA arrays in many guises. Bioessays 21:781-790
109. Gregory RT, Mable BK (2005) Polyploidy in animals. In: The evolution of the genome. Gregory TR (ed) Elsevier Academic Press, Amsterdam, The Netherlands, pp 427-517
110. Gregory TR (2005a) Animal Genome Size Database. http://www.genomesize.com/, Last accessed: July 25, 2005
111. Gregory TR (2005b) Synergy between sequence and size in large-scale genomics. Nat Rev Genet 6:699-708
112. Grigoryev DN, Ma SF, Irizarry RA, Ye SQ, Quackenbush J, Garcia JGN (2004) Orthologous gene-expression profiling in multi-speciesmodels: search for candidate genes. Genome Biol 5:R34
113. Gross R, Kohlmann K, Kersten P (2002) PCR-RFLP analysis of the mitochondrial ND-3/4 and ND-5/6 gene polymorphisms in the European and East Asian subspecies of common carp (Cyprinus carpio L.). Aquaculture 204:507-516
114. Grunina AS, Gomelski BI, Neyfakh AA (1990) Diploid androgenesis in carp. Genetika (Moscow) 26:2037-2043
115. Grunina AS, Gomelski BI, Neyfakh AA (1991) Production of androgenetic diploid hybrids between common carp and crucian carp. Genetika (Moscow) 27:1612-1616
116. Grunwald DJ, Eisen JS (2002) Headwaters of the zebrafish emergence of a new model vertebrate. Nat Rev Genet 3:717-724
117. Gui JF, Sun J, Liang S, Huang W, Jiang Y (1991) Studies on genome manipulation in fish. II. Tetraploidy induced by hydrostatic pressure treatment and a combination of hydrostatic pressure and cold treatments in transparent colored crucian carp. Acta Hydrobiol Sinica 15:342-347
118. Günther A (1868) Catalogue of the fishes in the British Museum, Vol. 7, Trustees of the BritishMuseum, London, UK, pp 1-512
119. Gurdon JB (1962) Adult frogs derived from the nuclei of single somatic cells. J Exp Embryol Morph 4:256-273
120. Haffter P, Granato M, Brand M, Mullins MC, Hammerschmidt M, Kane DA, Odenthal J, van Eeden FJM, Jiang YJ, Heisenberg CP. (1996) The identificationof geneswith unique and essential functions in the development of the zebrafish, Danio rerio. Development 123:1-36
121. Haga H, Yamada R, Ohnishi Y, Nakamura Y, Tanaka T (2002) Gene-based SNP discovery as part of the Japanese Millennium Genome Project: identification of 190562 genetic variations in the human genome. J Hum Genet 47:605-610
122. Handley-Goldstone HM, Grow MW, Stegeman JJ (2005) Cardiovascular gene expression profiles of dioxin exposure in zebrafish embryos. Tox Sci 85:683-693
123. Hillier L, Lennon G, Becker M, Bonaldo MF, Chiapelli B, Chissoe S, Dietrich N, DuBuque T, Favello A, Gish W et al. (1996) Generation and analysis of 280,000 human expressed sequence tags. Genome Res 6:807-828
124. Hollebecq MG, Chourrout D, Wohlfarth G, Billard R (1986) Diploid gynogenesis induced by heat shocks after inactivation with UV-irradiated sperm in common carp. Aquaculture 54:69-76
125. Horvat S, Medrano JF (1996) Fine geneticmapping of the region surrounding the high growth (hg) locus inmouseChromosome 10: Targeting random amplified polymorphic DNA (RAPD) markers. Mammal Genome 7:312-314
126. Horvath A, Miskolczi E, Urbanyi B (2003) Cryopreservation of common carp sperm. Aquat Liv Res 16:457-460
127. Horvath L, Orban L (1995) Genome and gene manipulation in the common carp. Aquaculture 129:157-181
128. Horvath L, Tamas G, Tolg I (1984) Special methods in pond fish husbandry, Akademiai Kiado and Halver Corporation, Budapest, Hungary and Seattle, WA, USA, pp 1-148
129. Howes GJ (1991) Systematics and biogeography: an overview. In: Cyprinid fishes: Systematics, biology and exploitation. Winfield IJ and Nelson JS (eds) Chapman & Hall, London, UK, pp 1-33
130. Hukriede N, Fisher D, Epstein J, Joly L, Tellis P, Zhou Y, Barbazuk B, Cox K, Fenton-Noriega L,. (2001) TheLN54 radiation hybrid map of zebrafish expressed sequences. Genome Res 11:2127-2132
131. Hulata G (1995a) The history and current status of aquaculture genetics in Israel. Isr J Aquacult - Bamidgeh 47:142-154
132. Hulata G (1995b) A review of genetic improvement of the common carp (Cyprinus carpio L.) and other cyprinids by crossbreeding, hybridization and selection. Aquaculture 129:143-155
133. Hulata G (2001) Geneticmanipulations in aquaculture: a review of stock improvement by classical and modern technologies. Genetica 111:155-173
134. Hurley IA, Mueller RL, Dunn KA, Schmidt EJ, Friedman M, Ho RK, Prince VE, Yang Z, Thomas MG, Coates MI (2007) A new time-scale for ray-finned fish evolution. Proc Roy Soc B 274:489-498
135. Ihssen PE, McKay LR, McMillan I, Phillips RB (1990) Ploidy manipulation and gynogenesis in fishes - Cytogenetic and fisheries applications. Trans Am Fish Soc 119:698-717
136. Jackson K, Goldberg D, Yehuda Y, Degani G (2000) Molecular DNA variation in koi (Cyprinus carpio) of various color patterns. Isr J Aquacult - Bamidgeh 52:151-158
137. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A et al. (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate protokaryotype. Nature 431:946-957
138. Jeffreys AJ (2005) Genetic fingerprinting. Nat Med 11:1035-1039
139. Jeffreys AJ, Wilson V, Thein SL (1985a) Hypervariable ‘minisatellite’ regions in human DNA. Nature 314:67-73
140. Jeffreys AJ, Wilson V, Thein SL (1985b) Individual-specific ‘fingerprints’ of human DNA. Nature 316:76-79
141. Jekosch K (2004) The zebrafish genome project: Sequence analysis and annotation. In: Zebrafish: 2nd Edition. Genetics Genomics and Informatics.DetrichHW,WesterfieldMand Zon LI (eds) Elsevier Academic Press, Amsterdam, The Netherlands, pp 225-239
142. Jhingran VG, Pullin RSV (1988) A hatchery manual for the common, Chinese and Indian major carps. ICLARM Stud Rev 11:1-191
143. Ji W, Zhou WL, Gregg K, Yu N, Davis S (2004) A method for cross-species gene expression analysis with high-density oligonucleotide arrays. Nucleic Acids Res 32:e93
144. Johnson SL, Midson CN, Ballinger EW, Postlethwait JH (1994) Identification of RAPD primers that reveal extensive polymorphisms between laboratory strains of zebrafish. Genomics 19:152-156
145. Ju B, Huang H, Lee KY, Lin S (2004a) Cloning the zebrafish. In: Fish development and genetics: The zebrafish and medaka models. Gong Z and Korzh V (eds)World Scientific Pub. Co., Singapore, pp 581-611
146. Ju BS, Huang HG, Lee KY, Lin S (2004b) Cloning zebrafish by nuclear transfer. In: Zebrafish: 2nd Edition. Genetics Genomics and Informatics.DetrichHW,WesterfieldMand Zon LI (eds) Elsevier Academic Press, Amsterdam, The Netherlands, pp 403-411
147. Katagiri T, Asakawa S, Minagawa S, Shimizu N, Hirono I, Aoki T (2001) Construction and characterization of BAC libraries for three fish species; rainbow trout, carp and tilapia. Anim Genet 32:200-204
148. Kawakami K, Shima A (1999) Identification of the Tol2 transposase of the medaka fish Oryzias latipes that catalyzes excision of a nonautonomous Tol2 element in zebrafish Danio rerio. Gene 240:239-244
149. Kawakami K, Takeda H, Kawakami N, Kobayashi M, Matsuda N, Mishina M (2004) A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish. Dev Cell 7:133-144
150. Kelly PD, Chu F, Woods IG, Ngo-Hazelett P, Cardozo T, Huang H, Kimm F, Liao LY, Yan YL, Zhou YY et al. (2000) Genetic linkage mapping of zebrafish genes and ESTs. Genome Res 10:558-567
151. Kelsh RN (2004) Genetics and evolution of pigment patterns in fish. Pigment Cell Res 17:326-336
152. Kingsley DM, Zhu BL, Osoegawa K, De Jong PJ, Schein J, Marra M, Peichel C, Amamiya C, Schluter D, Balabhadra S et al. (2004) New genomic tools for molecular studies of evolutionary change in threespine sticklebacks. Behaviour 141:1331-1344
153. Kirankumar S, Pandian TJ (2004a) Interspecific androgenetic restoration of rosy barb using cadaveric sperm. Genome 47:66-73
154. Kirankumar S, Pandian TJ (2004b) Use of heterologous sperm for the dispermic induction of androgenesis in barbs. J Fish Biol 64:1485-1497
155. Kirpichnikov VS (1967) Homologous hereditary variation and evolution of wild common carp Cyprinus carpio (in Russian). Genetika (Moscow) 8:65-72
156. Kirpichnikov VS (1999) Genetics and breeding of commoncarp, Billard R, Reperant J, Rio JP andWard R (eds), INRA, Paris, France, pp 1-97
157. Kirpichnikov VS, Ilyasov JI, Shart LA, Vikhman AA, Ganchenko MV, Ostashevsky AL, Simonov VM, Tikhonov GF, Tjurin VV (1993) Selection of Krasnodar common carp (Cyprinus carpio L) for resistance to dropsy - Principal results and prospects. Aquaculture 111:7-20
158. Klinkhardt M, Tesche M, Greven H (1995) Database of fish chromosomes, Westarp Wissenschaften, Magdeburg, East Germany, pp 1-237
159. Knapik EW, Goodman A, Atkinson OS, Roberts CT, Shiozawa M, Sim CU, WekslerZangen S, Trolliet MR, Futrell C, Innes BA et al. (1996) A reference cross DNA panel for zebrafish (Danio rerio) anchored with simple sequence length polymorphisms. Development 123:451-460
160. Knapik EW, Goodman A, Ekker M, Chevrette M, Delgado J, Neuhauss S, Shimoda N, Driever W, Fishman MC, Jacob HJ (1998) A microsatellite genetic linkage map for zebrafish (Danio rerio). Nat Genet 18:338-343
161. Kobayashi K, Nakano K, Nakamura M (1977) On the hybrids, 4n ginbuna (Carassius auratus langsdorfii) X kinbuna (C. auratus subsp.) and their chromosomes. Bull Jap Soc Sci Fish 43:31-37
162. Koch R, Rauch GJ, Humphray S, Geisler R, Plasterk R (2004) Bacterial artificial chromosome (BAC) clones and the current clone map of the zebrafish genome. In: Zebrafish: 2nd Edition. Genetics Genomics and Informatics. DetrichHW, Westerfield M and Zon LI (eds) Elsevier Academic Press, Amsterdam, The Netherlands, pp 295-304
163. Kohlmann K, Gross R, Murakaeva A, Kersten P (2003) Genetic variability and structure of common carp (Cyprinus carpio) populations throughout the distribution range inferred from allozyme, microsatellite and mitochondrial DNA markers. Aquat Liv Res 16:421-431
164. Kohlmann K, Kersten P (1999) Genetic variability of German andforeigncommoncarp(Cyprinus carpio L.)populations. Aquaculture 173:435-445
165. Kohlmann K, Kersten P, Flajshans M (2005) Microsatellitebased genetic variability and differentiation of domesticated, wild and feral common carp (Cyprinus carpio L.) populations. Aquaculture 247:253-266
166. Komen J (1990) Clones of common carp, Cyprinus carpio. Doctoral Thesis,Wageningen University, The Netherlands
167. Lachner EA, Robins CR, Courtenay WRJ (1970) Exotic fishes and other aquatic organisms introduced into North America. Smithsonian Contribut Zool 59:1-29
168. Lang BF, Gray MW, Burger G (1999) Mitochondrial genome evolution and the origin of eukaryotes. Ann Rev Genet 33:351-397
169. Larhammar D, Risinger C (1994) Molecular genetic aspects of tetraploidy in the common carp Cyprinus carpio. Mol Phylogenet Evol 3:59-68
170. Lee C, Smith A (2004) Molecular cytogenetic methodologies and a bacterial artificial chromosome (BAC) probe panel resource for genomic analyses in zebrafish. In: Zebrafish: 2nd Edition. Genetics Genomics and Informatics. Detrich HW, Westerfield M and Zon LI (eds) Elsevier Academic Press, Amsterdam, The Netherlands, pp 241-254
171. Lehoczky I, Magyary I, Hancz C, Weiss S (2005) Preliminary studies on the genetic variability of sixHungarian common carp strains using microsatellite DNA markers. Hydrobiologia 533:223-228
172. Lele Z, Krone PH (1996) The zebrafish as a model system in developmental, toxicological and transgenic research. Biotechnol Adv 14:57-72
173. Leung AYH, Mendenhall EM, Kwan TTF, Liang R, Eckfeldt C, Chen E, Hammerschmidt M, Grindley S, Ekker SC, Verfaillie CM (2005) Characterization of expanded intermediate cell mass in zebrafish chordinmorphant embryos.Dev Biol 277:235-254
174. Lever C (1996) Naturalized fishes of the world. Academic Press, San Diego, CA, USA, pp 1-408
175. Li Y, Chia JM, Bartfai R, Christoffels A, Yue GH, Ding K, Ho MY, Hill JA, Stupka E, Orban L (2004) Comparative analysis of the testis and ovary transcriptomes in zebrafish by combining experimental and computational tools. Comp Funct Genomics 5:403-418
176. Li Y, Mao S (1990) Establishment of cell strain AHZC88 resistant to pathogenic viruses of grass carp hemorrhage by ultraviolet (UV) inducement. J Fish China 14:89-94
177. Lien CL, Schebesta M, Makino S, Weber GJ, Keating MT (2006) Gene expression analysis of zebrafish heart regeneration. PLoS Biol 4:1386-1396
178. Linney E, Dobbs-McAuliffe B, Sajadi H, Malek RL (2004) Microarray gene expressionprofilingduringthe segmentation phase of zebrafish development. Comp Biochem Physiol C - Toxicol Pharmacol 138:351-362
179. Liu BH (1998) Statistical genomics: Linkage, mapping and QTL analysis, CRC Press, Boca Raton, FL, USA, pp 1-596
180. Liu JK, He BW (1992) Cultivation of Chinese Freshwater Fishes (in Chinese), Science Press, Beijing, People’s Republic of China, pp 1-750
181. Liu P, Yi YL, Liu HQ, Chen HX (1988) Preliminary study on electric fusion of fish cells (in Chinese). Acta Hydrobiol Sinica 12:94-96
182. Liu SJ, Liu Y, Zhou GJ, Zhang XJ, Luo C, Feng H, He XX, Zhu GH, Yang H (2001) The formation of tetraploid stocks of red crucian carp × common carp hybrids as an effect of interspecific hybridization. Aquaculture 192:171-186
183. Liu SJ, Sun YD, Zhang C, Luo KK, Liu Y (2004) Production of gynogenetic progeny from allotetraploid hybrids red crucian carp × common carp. Aquaculture 236:193-200
184. Lo J, Lee SC, Xu M, Liu F, Ruan H, Eun A, He YW, Ma WP, Wang WF, Wen ZL et al. (2003) 15,000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Genome Res 13:455-466
185. Lu R, Chen H (1993) Advances in fish cell engineering in China. Aquaculture 111:41-50
186. Lubzens E, Daube N, Pekarsky I, Magnus Y, Cohen A, Yusefovich F, Feigin P (1997) Carp (Cyprinus carpio L.) spermatozoa cryobanks - strategies in research and application. Aquaculture 155:13-30
187. Luo J, Lang M, Salzburger W, Siegel N, Stolting KN, Meyer A (2006) A BAC library for the goldfish Carassius auratus auratus (Cyprinidae, Cypriniformes). J Exp Zool B - Mol Dev Evol 306B:567-574
188. Luo J, Zhang YP, Zhu CL, Xiao WH, Huang SY (1999) Genetic diversity in crucian carp (Carassius auratus). Biochem Genet 37:267-279
189. Mabuchi K, Miya M, Senou H, Suzuki T, Nishida M (2006) Complete mitochondrial DNA sequence of the Lake Biwa wild strain of common carp (Cyprinus carpio L.): further evidence for an ancient origin. Aquaculture 257:68-77
190. Mabuchi K, Senou H, Suzuki T, Nishida M (2005) Discovery of an ancient lineage of Cyprinus carpio fromLake Biwa, central Japan, based on mtDNA sequence data, with reference to possiblemultiple origins of koi. J Fish Biol 66:1516-1528
191. Magyary I, Urbanyi B, Horvath L (1996) Cryopreservation of common carp (Cyprinus carpio L) sperm. 2. Optimal conditions for fertilization. J Appl Ichthyol 12:117-119
192. Marra MA, Kucaba TA, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier LW, McPherson JD, Waterston RH(1997)High throughput fingerprint analysis of large-insert clones. Genome Res 7:1072-1084
193. Martyniuk CJ, Xiong HL, Crump K, Chiu S, Sardana R, Nadler A, Gerrie ER, Xia XH, Trudeau VL (2006) Gene expression profiling in the neuroendocrine brain of male goldfish (Carassius auratus) exposed to 17 alpha-ethinylestradiol. Physiol Genomics 27:328-336
194. Mathavan S, Lee SGP, Mak A, Miller MD, Murthy KRK, Govindarajan KR, Tong Y, Wu YL, Lam SH, Yang H et al. (2005) Transcriptome analysis of zebrafish embryogenesis using microarrays. PLoS Genet 1:e29
195. Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, Dubchak I (2000) VISTA: visualizing global DNA sequence alignments of arbitrary length. Bioinformatics 16:1046-1047
196. Meyer A (1993) Evolution of mitochondrial DNA in fishes. In: Molecular biology frontiers. Hochacka PW andMommsen TP (eds) Elsevier, Amsterdam, The Netherlands, pp 1-38
197. Mia MY, Taggart JB, Gilmour AE, Gheyas AA, Das TK, Kohinoor AHM, Rahman MA, Sattar MA, Hussain MG, Mazid MA et al. (2005) Detection of hybridization between Chinese carp species (Hypophthalmichthys molitrix and Aristichthys nobilis) in hatchery broodstock in Bangladesh, using DNA microsatellite loci. Aquaculture 247:267-273
198. Miller RD, Phillips MS, Jo I, Donaldson MA, Studebaker JF, Addleman N, Alfisi SV, Ankener WM, Bhatti HA, Callahan CE et al. (2005) High-density single-nucleotidepolymorphism maps of the human genome. Genomics 86:117-126
199. Mills CA (1991) Reproduction and life history. In: Cyprinid fishes: Systematics, biology and exploitation. Winfield IJ and Nelson JS (eds) Chapman & Hall, London, UK, pp 483-508
200. Moens LN, vanderVen K, VanRemorte IP, Del-Favero J, DeCoen WM (2006) Expression profiling of endocrine-disrupting compounds using a customized Cyprinus carpio cDNA microarray. Toxicol Sci 93:298-310
201. Moyle PB (1976) Inland fishes of California, University of California Press, Berkeley, CA, USA, pp 1-405
202. Murakami M, Fujitani H (1997) A family of highly repetitive DNAs from “Ginbuna” (Carassius auratus langsdorfi) genome common to Carassius auratus populations. Zool Sci 14:763-769
203. Murakami M, Yamashita Y, Fujitani H (1998) The complete sequence of mitochondrial genome from a gynogenetic triploid “ginbuna” (Carassius auratus langsdorfi). Zool Sci 15:335-337
204. Nagy A (1987) Genetic manipulations performed on warmwater fish. In: Proceedings of the World Symposium on Selection, Hybridization and Genetic Engineering in Aquaculture, Vol. II, Berlin, East Germany, pp 163-174
205. Nagy A, Csanyi V (1984) A new breeding system using gynogenesis and sex-reversal for fast inbreeding of carp. Theor Appl Genet 67:485-490
206. Nagy A, Rajki L, Horvath L, Csanyi V (1978) Investigation on carp, Cyprinus carpio L., gynogenesis. J Fish Biol 13:215-114
207. Naruse K, Takeda H (2006) Draft genome sequence of medaka: Evolution of fish genome. Zool Sci 23:1126-1126
208. Nechiporuk A, Poss KD, Johnson SL, Keating MT (2003) Positional cloning of a temperature-sensitivemutant emmental reveals a role for sly1 during cell proliferation in zebrafish fin regeneration. Dev Biol 258:291-306
209. Neyfakh AA (1956) The effect of ionizing radiation on the gametes of the loach (Misgurnus fossilis L.). Dokl Akad Nauk (USSR) 111:585-588
210. Noonan JP, Grimwood J, Danke J, Schmutz J, Dickson M, Amemiya CT, Myers RM (2004) Coelacanth genome sequence reveals the evolutionary history of vertebrate genes. Genome Res 14:2397-2405
211. Ohara K, Dong S, Taniguchi N (1999) High proportion of heterozygotes in microsatellite DNA loci of wild clonal silver crucian carp, Carassius langsdorfii. Zool Sci 16:909-913
212. Ojima Y, Makino S (1978) Triploidy induced by cold shock in fertilized eggs of the carp. Proc Jap Acad Sci B 54:359-362
213. Ojima Y, Takai A (1981) A karyotype study of colored carp (Cyprinus carpio). A preliminary report. Proc Jap Acad Sci B 57:7-12
214. Opperman K (1913) Die Entwicklung von Vorelleneiern nach Befrunchtung mit radiumbestrahlten Samenfaden (in German). Arch Mikrosk Anat 83:141-189
215. Paaver TK (1983) Cyprinus carpio L. Biochemical genetics of commoncarp(inRussian),ValgusPublishers,Tallin,USSR, pp 1-122
216. Padhi BK, Mandal RK (1997) Inadvertenthybridizationin a carp hatchery as detected by nuclear DNA RFLP. J Fish Biol 50:906-909
217. Pandian TJ, Koteeswaran R (1998) Ploidy induction and sex control in fish. Hydrobiologia 384:167-243
218. Pandian TJ, Venugopal T, Koteeswaran R (1999) Problems and prospects of hormone, chromosome and gene manipulations in fish. Curr Sci 76:369-386
219. Parinov S, Kondrichin I, Korzh V, Emelyanov A (2004) Tol2 transposon-mediated enhancer trap to identify developmentally regulated zebrafish genes in vivo. Dev Dyn 231:449-459
220. Penman DJ (2005) Progress in carp genetics research. In: Carp genetic resources for aquaculture in Asia. Penman DJ, Gupta MV and Dey MM (eds) WorldFish Center, Penang, Malaysia, pp 82-113
221. Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA, Boyce-Jacino M (1999) Milling SNPs from EST databases. Genome Res 9:167-174
222. Pine RT, Anderson LWJ, Hung SSO (1990) Control of aquatic plants in static and flowing water by yearling triploid grass carp. J Aquat Plant Management 28:36-40
223. Postlethwait J (2004) The evolution of zebrafish genome. In: Fish development and genetics: The zebrafish and medaka models. Gong Z and Korzh V (eds)World Scientific Pub. Co., Singapore, pp 581-611
224. Postlethwait JH, Johnson SL, Midson CN, Talbot WS, Gates M, Ballinger EW, Africa D, Andrews R, Carl T, Eisen JS et al. (1994) A genetic linkage map for the zebrafish. Science 264:699-703
225. Postlethwait JH, Yan YL, Gates MA, Horne S, Amores A, Brownlie A, Donovan A, Egan ES, Force A, Gong ZY et al. (1998) Vertebrate genome evolution and the zebrafish gene map. Nat Genet 18:345-349
226. Poustka AJ, Groth D, Hennig S, Thamm S, Cameron A, Beck A, Reinhardt R, Herwig R, Panopoulou G, Lehrach H (2003) Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters. Genome Res 13:2736-2746
227. Primrose SB (1998) Principles of genome analysis. 2nd Edition, Blackwell Science Ltd., Oxford, UK, pp 1-187
228. Purdom CE (1969) Radiation-induced gynogenesis and androgenesis in fish. Heredity 24:431-444
229. Qian F, Zhen FH, Ong C, Jin SW, Soo HM, Stainier DYR, Lin S, Peng JR, Wen ZL (2005) Microarray analysis of zebrafish cloche mutant using amplified cDNA and identification of potential downstream target genes. Dev Dyn 233:1163-1172
230. Rab P, Collares-Pereira MJ (1995) Chromosomes of European cyprinid fishes (Cyprinidae, Cypriniformes) - a review. Fol Zool 44:193-214
231. Rakus KL, Wiegertjes GF, Stet RJM, Savelkoul HFJ, Pilarczyk A, Irnazarow I (2003) Polymorphism of major histocompatibility complex class IIB genes in different lines of the common carp (Cyprinus carpio). Aquat Liv Res 16:432-437
232. Ransom DG, Zon LI (1999) Mapping zebrafish mutations by AFLP. In: The Zebrafish: Genetics and Genomics. Detrich HW, Westerfield M and Zon LI (eds) Academic Press, San Diego, CA, USA, pp 195-211
233. Recoubratsky AV, Gomelsky BI, Emelyanova OV, Pankratyeva EV (1992) Triploid common carp produced by heat shock with industrial fish-farm technology. Aquaculture 108:13-19
234. Reid BB (2002) Genomeinsider:Aconversationwith SeanEddy. HHMI Bull September 2002:13
235. Renn SCP, Aubin-Horth N, Hofmann HA (2004) Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genomics 5:42
236. Reynders H, van der Ven K, Moens LN, van Remortel P, De Coen WM, Blust R (2006) Patterns of gene expression in carp liver after exposure to a mixture of waterborne and dietary cadmium using a custom-made microarray. Aquat Tox 80:180-193
237. Roberts J, Tilzey R (1997) Controlling carp: Exploring the options for Australia, CSIRO Land and Water, Griffith, NSW, Australia, pp 1-128
238. Rockett JC, Luft JC, Garges JB, Krawetz SA, Hughes MR, Kim KH, Oudes AJ, Dix DJ (2001) Development of a 950-gene DNA array for examining gene expression patterns in mouse testis. Genome Biol 2:0014.0011-0014.0019
239. Rodriguez-Gutierrez MEM (1995) Inducing triploid in grass carp (Ctenopharyngodon idella) utilizing cold shock thermic. Aquaculture 137:154-155
240. Romashov DD, Golovinskaya KA, Belyaeva VN, Bakulina ED, Pokrovskaya GL, Cherfas NB (1960) Radiation diploid gynogenesis in fish. Biophysics 5:461-468
241. Rong J, Bowers JE, Schulze SR, Waghmare VN, Rogers CJ, Pierce GJ, Zhang H, Estill JC, Paterson AH (2005) Comparative genomics of Gossypiumand Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy. Genome Res 15:1198-1210
242. Rothbard S, Shelton WL, Kulikovsky Z, Rubinshtein I, Hagani Y, Moav B (1997) Chromosome set manipulations in the black carp. Aquacult Int 5:51-64
243. Rothbard S, Shelton WL, Rubinshtein I, Hinits Y, David L (2000) Induction of all-female triploids in grass carp (Ctenopharyngodon idella) by integration of hormonal sex inversion and ploidy manipulation. Isr JAquac - Bamidgeh 52:133-150
244. Saitoh K, Miya M, Inoue JG, Ishiguro NB, Nishida M (2003) Mitochondrial genomics of ostariophysan fishes: Perspectives on phylogeny and biogeography. J Mol Evol 56:464-472
245. Saitoh K, Sado T, Mayden RL, Hanzawa N, Nakamura K, Nishida M, Miya M (2006) Mitogenomic evolution and interrelationships of the cypriniformes (Actinopterygii : Ostariophysi): The first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences. J Mol Evol 63:826-841
246. Sambrook J, Russell D (2001) Molecular cloning: A laboratory manual. ColdSpringHarborLaboratoryPress,ColdSpring Harbor, NY, USA, pp 1-2344
247. Schena M (1996) Genome analysis with gene expression microarrays. Bioessays 18:427-431
248. Schmid M, Nandra I, Guttenbach M, Steinlein C, Hoehn H, Schartl M, Haaf T, Weigend S, Fries R, Buerstedde JM et al. (2000) First report on chicken genes and chromosomes 2000. Cytogenet Cell Genet 90:169-218
249. Shart LA, Iljasov J (1979) Types of transferrins and esterases in spawners of common carp selected fro resistance to dropsy (in Russian). In: Biochemical and population genetics of fishes. Kirpitchnikov VS (ed) Academy of Sciences, USSR, Leningrad, pp 147-151
250. Shimoda N, Knapik EW, Ziniti J, Sim C, Yamada E, Kaplan S, Jackson D, de Sauvage F, Jacob H, Fishman MC (1999) Zebrafish genetic map with 2000 microsatellite markers. Genomics 58:219-232
251. Singh SK, Mittal AK (1990) A comparative study of the epidermis of the common carp and the three Indian major carps. J Fish Biol 36:9-19
252. Slater GSC (1998) Human EST sequences. In: Guide to human genome computing. Bishop MJ (ed) Academic Press, San Diego, CA, USA, pp 205-214
253. Smartt J, Bundell JH (1996) Goldfish breeding and genetics, T.F.H. Publications, Neptune City, NJ, USA, pp 1-256
254. Smith CT, Elfstrom CM, Seeb LW, Seeb JE (2005a) Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Mol Ecol 14:4193-4203
255. Smith CT, Templin WD, Seeb JE, Seeb UW (2005b) Single nucleotide polymorphisms provide rapid and accurate estimates of the proportions of US and Canadian Chinook salmon caught in Yukon River fisheries. North Am J Fish Management 25:944-953
256. Sola L, Gornung E (2001) Classical and molecular cytogenetics of the zebrafish, Danio rerio (Cyprinidae, Cypriniformes): an overview. Genetica 111:397-412
257. Sreenivasan R, Cai M, Bartfai R, Wang XG, Christoffels A, Orban L (2008) Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. PLoS ONE 3:e1791
258. Stanley JG (1976) Production of hybrid, androgenetic, and gynogenetic grass carp and carp. Trans Am Fish Soc 105:10-16
259. Stears SL, Martinsky T, Schena M (2003) Trends in microarray analysis. Nat Med 9:140-145
260. Steffens W (1999) The carp (in German). Westarp Wissenschaften, Heidelberg, Germany, pp 1-215
261. Streisinger G, Walker C, Dower N, Knauber D, Singer F (1981) Production of clones of homozygous diploid zebra fish (Brachydanio rerio). Nature 291:293-296
262. Sumanas S, Jorniak T, Lin S (2005) Identification of novel vascular endothelial-specific genes by the microarray analysis of the zebrafish cloche mutants. Blood 106:534-541
263. Sun XW, Liang LQ (2004) A genetic linkage map of common carp (Cyprinus carpio L.) andmapping of a locus associated with cold tolerance. Aquaculture 238:165-172
264. Svetovidov AN (1933) Uber den europaischen und ostasiatischen Karpfen (Cyprinus carpio) (in German). Zool Anzeiger 104:269-292
265. Talbot WS, Schier AF (1999) Positional cloning of mutated zebrafish genes. In: The Zebrafish: Genetics and Genomics. Detrich HW, Westerfield M and Zon LI (eds) Academic Press, San Diego, CA, USA, pp 259-286
266. Tamaru Y, Wakasa T, Akiyama S, Tanaka T (2005) Transcriptome analysis on an antidepressant drug, imipramine by zebrafish DNA microarray. J Pharm Sci 97:76P
267. Tanck MWT, Claes T, Bovenhuis H, Komen J (2002) Exploring the genetic background of stress using isogenic progenies of common carp selected for high or low stress-related cortisol response. Aquaculture 204:419-434
268. Taniguchi N, Kijima A, Tamura T, Takegami K, Yamasaki I (1986) Color, growth and maturation in ploidymanipulated fancy carp. Aquaculture 57:321-328
269. Taylor JS, Braasch I, Frickey T, Meyer A, de Peer YV (2003) Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res 13:382-390
270. Taylor JS, Van de Peer Y, Braasch I, Meyer A (2001) Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos Trans R Soc Lond Ser B - Biol Sci 356:1661-1679
271. Thompson BZ, Wattendorf RJ, Hestand RS, Underwood JL (1987) Triploid grass carp production. Progress Fish-Cult 49:213-217
272. Tomasiewicz HG, Flaherty DB, Soria JP, Wood JG (2002) Transgenic zebrafish model of neurodegeneration. J Neurosci Res 70:734-745
273. Ton C, Stamatiou D, Dzau VJ, Liew CC (2002) Construction of a zebrafish cDNA microarray: gene expression profiling of the zebrafish during development. Biochem Biophys Res Commun 296:1134-1142
274. Ton C, Stamatiou D, Liew CC (2003) Gene expression profile of zebrafish exposed to hypoxia during development. Physiol Genomics 13:97-106
275. Tong J, Wang Z, Yu X, Wu Q, Chu KH (2002) Cross-species amplification in silver carp and bighead carp with microsatellite primers of common carp. Mol Ecol Notes 2:245-247
276. Tong J, Yu X, Liao X (2005) Characterization of a highly conserved microsatellite marker with utility potentials in cyprinid fishes. J Appl Ichthyol 21:232-235
277. Torres-Vazquez J, Kamei M, Pine H, Berk JD, Weinstein BM (2003) An F3 genetic screen using transgenic zebrafish to uncover mutations affecting vascular development. Arterioscl Thromb Vasc Biol 23:A32
278. Toth B, Varkonyi E, Hidas A, Meleg EE, Varadi L (2005) Genetic analysis of offspring from intra- and interspecific crosses of Carassius auratus gibelio by chromosome and RAPD analysis. J Fish Biol 66:784-797
279. Truveller KA, Maslennikova NA, Moscovkin LA, Romanova LI (1973) Variability in disc-electrophoretic patterns of muscle myogens in carp (Cyprinus carpio L.) (in Russian). In: Biochemical and population genetics of fishes. Kirpitchnikov VS (ed) Academy of Sciences, USSR, Leningrad, pp 113-119
280. Tung TC, Wu SQ, Ye YF, Yan SY, Du M, Lu DY (1963) Nuclear transplantation of fish. Chin Sci Bull 7:60-61
281. Udvadia AJ, Linney E (2003) Windows into development: historic, current, and future perspectives on transgenic zebrafish. Dev Biol 256:1-17
282. Umino T, Arai K, Maeda K, Zhang QQ, Sakae K, Niwase I, Nakagawa H (1997) Natural clones detected by multilocus DNA fingerprinting in gynogenetic triploid ginbuna Carassius langsdorfii in Kurose River, Hiroshima. Fish Sci 63:147-148
283. Valenta M, Stratil A, Slechtova V, Kalal L, Slechta V (1976) Polymorphism of transferrin in carp (Cyprinus carpio L.): genetic determination, isolation, and partial characterization. Biochem Genet 14:27-45
284. Van de Peer Y, Meyer A (2005) Large-scale gene and ancient genome duplications. In: The evolution of the genome. Gregory TR(ed) ElsevierAcademic Press,Amsterdam, The Netherlands, pp 329-368
285. vanderVen K, Keil D, Moens LN, VanLeemput K, VanRemortelt P, De Coen WM (2006) Neuropharmaceuticals in the environment: Mianserin-induced neuroendocrine disruption in zebrafish (Danio rerio) using cDNA microarrays. Env Tox Chem 25:2645-2652
286. van Eenennaam J, Stocker RK, Thiery RG, Hagstrom NT, Doroshov SI (1990) Egg fertility, early development and survival from crosses of diploid female X triploid male grass carp (Ctenopharyngodon idella). Aquaculture 86:111-125
287. Vandepoele K, De Vos W, Taylor JS, Meyer A, Van de Peer Y (2004) Major events in the genomeevolution of vertebrates: paranome age and size differ considerably between rayfinned fishes and land vertebrates. Proc Natl Acad SciUSA 101:1638-1643
288. Vandeputte M (2003) Selective breeding of quantitative traits in the common carp (Cyprinus carpio): a review. Aquat Liv Res 16:399-407
289. Venkatesh B, Kirkness EF, Loh YH, Halpern AL, Lee AP, Johnson J, Dandona N, Viswanathan LD, Tay A, Venter JC et al. (2007) Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol 5:932-944
290. Venter AJA, Schoonbee HJ (1991) The use of triploid grass carp, Ctenopharyngodon idella(Val), inthe controlof submerged aquatic weeds in the Florida Lake, Roodepoort, Transvaal. Water SA 17:321-326
291. Vignal A, Milan D, SanCristobal M, Eggen A (2002) A review on SNP and other types ofmolecularmarkers and their use in animal genetics. Genet Select Evol 34:275-305
292. Voelker D, Vess C, Tillmann M, Nagel R, Otto GW, Geisler R, Schirmer K, Scholz S (2007) Differential gene expression as a toxicant-sensitive endpoint in zebrafish embryos and larvae. Aquat Toxicol 81:355-364
293. von Schalburg KR, Rise ML, Cooper GA, Brown GD, Gibbs AR, Nelson CC, Davidson WS, Koop BF (2005) Fish and chips: Various methodologies demonstrate utility of a 16,006- gene salmonid microarray. BMC Genomics 6:126
294. Vooren CM (1972) Ecological aspects of the introduction of fish species into natural habitats in Europe, with special reference to the Netherlands and literature survey. J Fish Biol 4:565-583
295. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M et al. (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414
296. Walter MA, Spillett DJ, Thomas P, Weissenbach J, Goodfellow PN (1994) A method for constructing radiation hybrid maps of whole genomes. Nat Genet 7:22-28
297. Wang T, Chen H, Liu H, Guo W (1993) Characterization of a cell clone resistant to grass carp hemorrhagic virus. Aquaculture 111:307
298. Wang XZ, Li JB, He SP (2007) Molecular evidence for themonophylyofEastAsiangroupsof Cyprinidae (Teleostei:Cypriniformes) derived fromthe nuclear recombination activating gene 2 sequences. Mol Phylogenet Evol 42:157-170
299. Wang ZY, Futami K, Nishihara A, Okamoto N (2005) Four types of Smad4 found in the common carp, Cyprinus carpio. J Exp Zool B - Mol Dev Evol 304:250-258
300. Watson A, Mazumder A, Stewart M, Balasubramanian S (1998) Technology for microarray analysis of gene expression. Curr Opin Biotechnol 9:609-614
301. Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213-7218
302. Wiegertjes GF, Bongers ABJ, Voorthuis P, Doulabi BZ, Groeneveld A, VanMuiswinkel WB, Stet RJM (1996) Characterization of isogenic carp (Cyprinus carpio L.) lineswith a genetically determined high or low antibody production. Anim Genet 27:313-319
303. Wienholds E, Schulte-Merker S, Walderich B, Plasterk RHA (2002) Target-selected inactivation of the zebrafish rag1 gene. Science 297:99-102
304. Wienholds E, van Eeden F, Kosters M, Mudde J, Plasterk RHA, Cuppen E (2003) Efficient target-selected mutagenesis in zebrafish. Genome Res 13:2700-2707
305. Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531-6535
306. Williams D, Li W, Hughes MA, Gonzalez SF, Vernon C, Vidal MC, Bartfai R, Orban L, Rogers J, Matthews L et al. (2008) Genomic resources and microarrays for the common carp (Cyprinus carpio L.). J Fish Biol (in press)
307. Wingert R, Fraenkel P, Dooley K, Brownlie A, Foott H, Axe J, Schmid B, Davidson A (2003) Forward genetic screen to identify zebrafish mutants with defects in hemoglobin production. Blood Cells Mol Dis 31:168-169
308. Woods IG, Kelly PD, Chu F, Ngo-Hazelett P, Yan YL, Huang H, Postlethwait JH, Talbot WS (2000) A comparative map of the zebrafish genome. Genome Res 10:1903-1914
309. Woods IG, Wilson C, Friedlander B, Chang P, Reyes DK, Nix R, Kelly PD, Chu F, Postlethwait JH, Talbot WS (2005) The zebrafish gene map defines ancestral vertebrate chromosomes. Genome Res 15:1307-1314
310. Woynarovich E (1961) Hatching carp eggs in Zuger glasses and breeding of carp larvae until the age of 10 days. Isr J Aquacult - Bamidgeh 4:38-46
311. Wu C, Ye Y, Chen R, Liu X (1993) An artificial multiple triploid carp and its biological characteristics. Aquaculture 111:255-262
312. Wu G, Sun YH, Zhu ZY (2003a) Growth hormone gene transfer in common carp. Aquat Liv Res 16:416-420
313. Wu H-W (1977) The cyprinid fishes of China (in Chinese). People’s Press, Shanghai, People’s Republic of China, pp 1-598
314. Wu Q, Chen R, Ye Y, Ke H (1981) Investigation on the carp gynogenesis with reference to establishing a pure line. Acta Genet Sinica 8:50-55
315. Wu Q, Gui JF (1999) Fish genetics and breeding engineering (in Chinese), Scientific and Technical Publisher, Shanghai, People’s Republic of China, pp 1-278
316. Wu Q, Ke H, Chen R, Ye Y (1979) Seeking for the way of maintaining the vigor of progeny in the hybrid between two varieties of common carp (in Chinese). Acta Hydrobiol Sinica 5:445-450
317. Wu Q, Ye Y, Chen R (1986)Genomemanipulationin carp(Cyprinus carpio). Aquaculture 54:57-61
318. Wu Q, Ye Y, Chen R, Tong J (1991) The production of pure line red carp 8305 and its biological characteristics. Oceanol Limnol Sinica 22:295-299
319. Wu QJ, Ye YZ, Dong XH (2003b) Two unisexual artificial polyploid clones constructed by genome addition of common carp (Cyprinus carpio) and crucian carp (Carassius auratus). Sci China C - Life Sci 46:595-604
320. Xia QY, Zhou ZY, Lu C, Cheng DJ, Dai FY, Li B, Zhao P, Zha XF, Cheng TC, Chai CL et al. (2004) A draft sequence for the genome of the domesticated silkworm(Bombyx mori). Science 306:1937-1940
321. Xiao T, Roeser T, Staub W, Baier H (2005) A GFP-based genetic screen reveals mutations that disrupt the architecture of the zebrafish retinotectal projection. Development 132:2955-2967
322. Yan JP, Liu SJ, Sun YD, Zhang C, Luo KK, Liu Y (2005) RAPD and microsatellite analysis of diploid gynogens from allotetraploid hybrids of red crucian carp (Carassius auratus) × common carp (Cyprinus carpio). Aquaculture 243:49-60
323. Yan S (1998) Cloning in fish: Nucleocytoplasmic hybrids, IUBS Educational and Cultural Press Ltd., Hong Kong, People’s Republic of China, pp 1-130
324. Ye YZ, Zhou JF, Wang XH, Wu QJ (2002) Reproduction mode of an artificial allotetraploid carp (Pisces;Cyprinidae).Hereditas 137:140-144
325. Yoon JM, Park HY (2002) Genetic similarity and variation in the cultured and wild crucian carp (Carassius carassius) estimated with Random Amplified Polymorphic DNA. Asian- Australasian J Anim Sci 15:470-476
326. Yoon SJ, Hallerman EM, Gross ML, Liu Z, Schneider JF, Faras AJ, Hackett PB, Kapuscinski AR, Guise KS (1990) Transfer of the gene for neomycin resistance into goldfish, Carassius auratus. Aquaculture 85:21-33
327. Yu J, Hu SN, Wang J, Wong GKS, Li SG, Liu B, Deng YJ, Dai L, Zhou Y, Zhang XQ et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296:79-92
328. Yu X, Zhou T, Li K, Li Y, Zhou M (1987) On the karyosystematics of cyprinid fishes and a summary of fish chromosome studies in China. Genetica 72:225-236
329. Yue GH, Ho MY, Orban L, Komen J (2004) Microsatelliteswithin genes and ESTs of common carp and their applicability in silver crucian carp. Aquaculture 234:85-98
330. Yue GH, Orban L (2002) Polymorphicmicrosatellites fromsilver crucian carp (Carassius auratus gibelio Bloch) and crossamplification in common carp (Cyprinus carpio L.). Mol Ecol Notes 2:534-536
331. Yue GH, Orban L (2004) Characterization of microsatellites located within the genes of goldfish (Carassius auratus auratus). Mol Ecol Notes 4:404-405
332. Zardoya R, Doadrio I (1998) Phylogenetic relationships of Iberian cyprinids: systematic and biogeographical implications. Proc Roy Soc London B - Biol Sci 265:1365-1372
333. Zardoya R, Doadrio I (1999) Molecular evidence on the evolutionary and biogeographical patterns of European cyprinids. J Mol Evol 49:227-237
334. Zardoya R, Economidis PS, Doadrio I (1999) Phylogenetic relationships of Greek Cyprinidae:Molecular evidence for at least two origins of the Greek cyprinid fauna. Mol Phylogenet Evol 13:122-131
335. Zhang H, Okamoto N, Ikeda Y (1995) Two c-myc genes from a tetraploid fish, the common carp (Cyprinus carpio). Gene 153:231-236
336. Zhang JJ, Talbot WS, Schier AF (1998) Positional cloning identifies zebrafishone-eyedpinhead as apermissiveEGF-related ligand required during gastrulation. Cell 92:241-251
337. Zheng W, Stacey NE, Coffin J, Strobeck C (1995) Isolation and characterization of microsatellite loci in the goldfish Carassius auratus. Mol Ecol 4:791-792
338. Zhong JY, Wang YP, Zhu ZY (2002) Introduction of the human lactoferrin gene into grass carp (Ctenopharyngodon idellus) to increase resistance against GCH virus. Aquaculture 214:93-101
339. Zhong TP, Kaphingst K, Akella U, Haldi M, Lander ES, Fishman MC (1998) Zebrafish genomic library in yeast artificial chromosomes. Genomics 48:136-138
340. Zhou J, Wu Q, Wang Z, Ye Y (2004a) Genetic variation analysis within and among six varieties of common carp (Cyprinus carpio L.) in China using microsatellite markers. Russian J Genet 40:1389-1393
341. Zhou J, Wu Q, Wang Z, Ye Y (2004b) Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA. J Zool Syst Evol Res 42:266-269
342. Zhou JF, Wang ZW, Ye YZ, Wu QJ (2003a) PCR-RFLP analysis of mitochondrial DNA ND5/6 region among 3 subspecies of common carp (Cyprinus carpio L.) and its application to genetic discrimination of subspecies. Chinese Sci Bull 48:465-468
343. Zhou JF, Wu QJ, Ye YZ, Tong JG (2003b) Genetic divergence between Cyprinus carpio carpio and Cyprinus carpio haematopterus as assessed by mitochondrial DNA analysis, with emphasis on origin of European domestic carp. Genetica 119:93-97
344. Zhou L, Wang Y, Gui JF (2000) Genetic evidence for gonochoristic reproduction in gynogenetic silver crucian carp (Carassius auratus gibelio Bloch) as revealed by RAPD assays. J Mol Evol 51:498-506
345. Zhu Z, Li G, He L, Chen S (1985) Novel gene transfer into the fertilized eggs of gold fish (Carassius auratus L. 1758). Z Angew Ichthyol 1:31-34