Genomics toolbox for farmed fish

Reviews in Fisheries Science

Volumn 16, Issue SUPPL.1, 2008, Pages 1-13

  Canario, Adelino V M ^a   Bargelloni, Luca ^b   Volckaert, Filip ^c   Houston, R D ^d   Massault, C ^d   Guiguen, Yann ^e  

^a UNIVERSITY OF ALGARVE   (Portugal)

^b UNIVERSITY OF PADOVA   (Italy)

^c UNIVERSITY OF LEUVEN   (Belgium)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

^e CEMAGREF   (France)

Author keywords

Expressed sequence tags; Genetic maps; Genetic markers; Microarray; Quantitative trai loci

Indexed keywords

ANIMALIA;

EID: 52049104452     PISSN: 10641262     EISSN: 15476553     Source Type: Journal    
DOI: 10.1080/10641260802319479     Document Type: Article

References (115)

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