Functional Genomics Research in Aquaculture: Principles and General Approaches

Functional Genomics in Aquaculture

Volumn , Issue , 2012, Pages 1-40

  Liu, Shikai ^a   Zhang, Yu ^a   Sun, Fanyue ^a   Jiang, Yanliang ^a   Wang, Ruijia ^a   Li, Chao ^a   Zhang, Jiaren ^a   Liu, Zhanjiang John ^a  

^a AUBURN UNIVERSITY   (United States)

Author keywords

Comparative genome pathway, epigenetic using ChIP, and gene expression; Data generation, management and data set mining; Functional genomics research in aquaculture, and general approaches; Functional genomics, genome wide using structural genomics; Functional inference on expression profiling, EST, BLAST and ORF; Gene function determination with ZFN; Gene function on positional analysis, GWAS, QTL, eQTL; Genome mapping, sequencing "structural genomics" and "functional genomics"; RNA Seq in aquaculture, DNA, mRNA, microarray and RNASeq complementary; Vertebrates and conserved synteny and orthology

Indexed keywords

EID: 84879459427     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118350041.ch1     Document Type: Chapter

References (255)

1. Aanes H, Winata CL, Lin CH, Chen JP, Srinivasan KG, Lee SG, Lim AY, Hajan HS, Collas P, Bourque G, Gong Z, Korzh V, Alestrom P, Mathavan S (2011) Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. Genome Research, 21: 1328-1338.
2. Acosta J, Carpio Y, Borroto I, Gonzalez O, Estrada MP (2005) Myostatin gene silenced by RNAi show a zebrafish giant phenotype. Journal of Biotechnology, 119: 324-331.
3. Adams MD, et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science, 252: 1651-1656.
4. AdamsMD, et al. (1995) Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature, 377: 3-174.
5. Amores A, Catchen J, Ferrara A, Fontenot Q, Postlethwait JH (2011) Genome evolution and meiotic maps by massively parallelDNAsequencing: spotted gar, an outgroup for the teleost genome duplication. Genetics, 188: 799-808.
6. Anastasaki C, Longman D, Capper A, Patton EE, Caceres JF (2011) Dhx34 and Nbas function in theNMDpathway and are required for embryonic development in zebrafish. Nucleic Acids Research, 39: 3686-3694.
7. Andersson L, et al. (1996) Comparative genome organization of vertebrates. The First International Workshop on Comparative Genome Organization. Mammalian Genome, 7: 717-734.
8. Aoki T, Wang HC, Unajak S, Santos MD, Kondo H, Hirono I (2011) Microarray analyses of shrimp immune responses. Marine Biotechnology (NY), 13: 629-638.
9. Backes C, Keller A, Kuentzer J, Kneissl B, Comtesse N, Elnakady YA, Muller R, Meese E, Lenhof HP (2007) GeneTrail-advanced gene set enrichment analysis. Nucleic Acids Research, 35: W186-W192.
10. Bae KH, et al. (2003) Human zinc fingers as building blocks in the construction of artificial transcription factors. Nature Biotechnology, 21: 275-280.
11. Baerwald MR, Petersen JL, Hedrick RP, Schisler GJ, May B (2011)Amajor effect quantitative trait locus for whirling disease resistance identified in rainbow trout (Oncorhynchus mykiss). Heredity, 106: 920-926.
12. Bailey LC, Searls DB, Overton GC (1998) Analysis of EST-driven gene annotation in human genomic sequence. Genome Research, 8: 362-376.
13. Baranski M, Moen T, Vage DI (2010) Mapping of quantitative trait loci for flesh colour and growth traits in Atlantic salmon (Salmo salar). Genetics Selection Evolution, 42: 17.
14. Baranski M, Rourke M, Loughnan S, Hayes B, Austin C, Robinson N (2008) Detection of QTL for growth rate in the blacklip abalone (Haliotis rubra Leach) using selective DNA pooling. Animal Genetics, 39: 606-614.
15. Barski A, Cuddapah S, Cui KR, Roh TY, Schones DE, Wang ZB, Wei G, Chepelev I, Zhao KJ (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129: 823-837.
16. Bauer S, Grossmann S, Vingron M, Robinson PN (2008) Ontologizer 2.0-a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics, 24: 1650-1651.
17. Beerli RR, Barbas CF (2002) Engineering polydactyl zinc-finger transcription factors. Nature Biotechnology, 20: 135-141.
18. Bell AC, West AG, Felsenfeld G (1999) The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell, 98: 387-396.
19. Bernstein BE, Humphrey EL, Erlich RL, Schneider R, Bouman P, Liu JS, Kouzarides T, Schreiber SL (2002) Methylation of histone H3 Lys 4 in coding regions of active genes. Proceedings of the National Academy of Sciences of the United States of America, 99: 8695-8700.
20. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ, Gingeras TR, Schreiber SL,Lander ES (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell, 120: 169-181.
21. Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell, 128: 669-681.
22. Beumer K, Bhattacharyya G, Bibikova M, Trautman JK, Carroll D (2006) Efficient gene targeting in Drosophila with zinc-finger nucleases. Genetics, 172: 2391-2403.
23. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes & Development, 16: 6-21.
24. Bonaldo MDF, Lennon G, Soares MB (1996) Normalization and subtraction: Two approaches to facilitate gene discovery. Genome Research, 6: 791-806.
25. Bontems F, Baerlocher L, Mehenni S, Bahechar I, Farinelli L, Dosch R (2011) Efficient mutation identification in zebrafish by microarray capturing and next generation sequencing. Biochemical and Biophysical Research Communications, 405: 373-376.
26. Booman M, Borza T, Feng CY, Hori TS, Higgins B, Culf A, Leger D, Chute IC, Belkaid A, Rise M, Gamperl AK, Hubert S, Kimball J, Ouellette RJ, Johnson SC, Bowman S, Rise ML (2011) Development and experimental validation of a 20K Atlantic Cod (Gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ESTs. Marine Biotechnology, 13: 733-750.
27. Boulding EG, Culling M, Glebe B, Berg PR, Lien S, MoenT(2008) Conservation genomics of Atlantic salmon: SNPs associated with QTLs for adaptive traits in parr from four trans-Atlantic backcrosses. Heredity, 101: 381-391.
28. Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science, 296: 752-755.
29. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, FoyM, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J, Corcoran K (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnology, 18: 630-634.
30. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang JT, Manly KF, Lu L, Chesler EJ, Alberts R, Jansen RC, Williams RW, Cooke MP, de Haan G (2005) Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'. Nature Genetics, 37: 225-232.
31. Chesler EJ, Lu L, Shou SM, Qu YH, Gu J, Wang JT, Hsu HC, Mountz JD, Baldwin NE, Langston MA, Threadgill DW, Manly KF, Williams RW (2005) Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nature Genetics, 37: 233-242.
32. Cheung VG, Conlin LK, Weber TM, Arcaro M, Jen KY, Morley M, Spielman RS (2003) Natural variation in human gene expression assessed in lymphoblastoid cells. Nature Genetics, 33: 422-425.
33. Chini V, Cattaneo AG, Rossi F, Bernardini G, Terova G, Saroglia M, Gornati R (2008) Genes expressed in Blue Fin Tuna (Thunnus thynnus) liver and gonads. Gene, 410: 207-213.
34. Cnaani A, Lee BY, Ozouf-Costaz C, Bonillo C, Baroiller JF, D'Cotta H, Kocher T (2007) Mapping of sox2 and sox14 in tilapia (Oreochromis spp.). Sex Development, 1: 207-210.
35. Cogburn LA, Porter TE, Duclos MJ, Simon J, Burgess SC, Zhu JJ, Cheng HH, Dodgson JB, Burnside J (2007) Functional genomics of the chicken-A model organism. Poultry Science, 86: 2059-2094.
36. Colihueque N, Cardenas R, Ramirez L, Estay F, Araneda C (2010) Analysis of the association between spawning time QTL markers and the biannual spawning behavior in rainbow trout (Oncorhynchus mykiss). Genetics and Molecular Biology, 33: 578-582.
37. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, RoblesM(2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21: 3674-3676.
38. Consoli L, Lefevre A, Zivy M, de Vienne D, Damerval C (2002) QTL analysis of proteome and transcriptome variations for dissecting the genetic architecture of complex traits in maize. Plant Molecular Biology, 48: 575-581.
39. Copf T, Rabet N, Averof M (2006) Knockdown of spalt function by RNAi causes de-repression of Hox genes and homeotic transformations in the crustacean Artemia franciscana. Developmental Biology, 298: 87-94.
40. Coppe A, Pujolar JM, Maes GE, Larsen PF, Hansen MM, Bernatchez L, Zane L, Bortoluzzi S (2010) Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel. BMC Genomics, 11: 635.
41. Cornu TI, Thibodeau-Beganny S, Guhl E, Alwin S, Eichtinger M, Joung J, Cathomen T (2008) DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases. Molecular Therapy, 16: 352-358.
42. Crozat K, Guiton R, Guilliams M, Henri S, Baranek T, Schwartz-Cornil I, Malissen B, DalodM(2010) Comparative genomics as a tool to reveal functional equivalences between human and mouse dendritic cell subsets. Immunological Reviews, 234: 177-198.
43. Cullum R, Alder O, Hoodless PA (2011) The next generation: using new sequencing technologies to analyse gene regulation. Respirology, 16: 210-222.
44. Danzmann RG, Jackson TR, Ferguson MM (1999) Epistasis in allelic expression at upper temperature tolerance QTL in rainbow trout. Aquaculture, 173: 45-58.
45. Derome N, Bougas B, Rogers SM, Whiteley AR, Labbe A, Laroche J, Bernatchez L (2008) Pervasive sex-linked effects on transcription regulation as revealed by expression quantitative trait loci mapping in lake whitefish species pairs (Coregonus sp., sahnonidae). Genetics, 179: 1903-1917.
46. Devlin RH, Yesaki TY, Biagi CA, Donaldson EM, Swanson P, Chan WK (1994) Extraordinary salmon growth. Nature, 371: 209-210.
47. Dheilly NM, Lelong C, Huvet A, Favrel P (2011) Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns. BMC Genomics, 12: 468.
48. Doyon Y, McCammon JM, Miller JC, Faraji F, Ngo C, Katibah GE, Amora R, Hocking TD, Zhang L, Rebar EJ, Gregory PD, Urnov FD, Amacher SL (2008) Heritable targeted gene disruption in zebrafish using designed zinc-finger nucleases. Nature Biotechnology, 26: 702-708.
49. Drivenes O, Taranger GL, Edvardsen RB (2011) Gene expression profiling of Atlantic Cod (Gadus morhua) embryogenesis using microarray. Marine Biotechnology, 14: 167-176.
50. DuSJ, Gong ZY, Fletcher GL, Shears MA, King MJ, Idler DR, Hew CL (1992) Growth enhancement in transgenic Atlantic salmon by the use of an "all fish" chimeric growth hormone gene construct. Bio/Technology, 10: 176-181.
51. Easton AA, Moghadam HK, Danzmann RG, Ferguson MM (2011) The genetic architecture of embryonic developmental rate and genetic covariation with age at maturation in rainbow trout Oncorhynchus mykiss. Journal of Fish Biology, 78: 602-623.
52. Edvardsen RB, Malde K, Mittelholzer C, Taranger GL, Nilsen F (2011) EST resources and establishment and validation of a 16 k cDNA microarray from Atlantic cod (Gadus morhua). Comprative Biochemistry and Physiology Part D Genomics & Proteomics, 6: 23-30.
53. Eichler EE, SankoffD(2003) Structural dynamics of eukaryotic chromosome evolution. Science, 301: 793-797.
54. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genomewide expression patterns. Proceedings of the National Academy of Sciences of the United States of America, 95: 14863-14868.
55. Ekker (2008) SC. Zinc finger-based knockout punches for zebrafish genes. Zebrafish, 5: 121-123.
56. Ellett F, Lieschke GJ (2010) Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology, 10: 563-570.
57. Elnitski L, Jin VX, Farnham PJ, Jones SJ (2006) Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Research, 16: 1455-1464.
58. Esteller M (2006) The necessity of a human epigenome project. Carcinogenesis, 27: 1121-1125.
59. Falconer DS, Mackay TF (1996) Introduction to Quantitative Genetics, 4th edn. Longman, Harlow.
60. Ferraresso S, Vitulo N, Mininni AN, Romualdi C, Cardazzo B, Negrisolo E, Reinhardt R, Canario AVM, Patarnello T, Bargelloni L (2008) Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata). BMC Genomics, 9: 580.
61. Fleury E, Huvet A, Lelong C, de Lorgeril J, Boulo V, Gueguen Y, Bachere E, Tanguy A, Moraga D, Fabioux C, Lindeque P, Shaw J, Reinhardt R, Prunet P, Davey G, Lapegue S, Sauvage C, Corporeau C, Moal J, Gavory F, Wincker P, Moreews F, Klopp C, Mathieu M, Boudry P, Favrel P (2009) Generation and analysis of a 29,745 unique expressed sequence tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase. BMC Genomics, 10: 341.
62. Fraser BA, Weadick CJ, Janowitz I, Rodd FH, Hughes KA (2011) Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome. BMC Genomics, 10: 341.
63. Fu F, Sander JD, Maeder M, Thibodeau-Beganny S, Joung JK, Dobbs D, Miller L, Voytas DF (2009) Zinc finger database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. Nucleic Acids Research, 37: D279-D283.
64. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Team MP (2004) The status, quality, and expansion of the NIH full-length cDNA project: The mammalian gene collection (MGC). Genome Research, 14: 2121-2127.
65. Gheyas AA, Haley CS, Guy DR, Hamilton A, Tinch AE, Mota-Velasco JC, Woolliams JA (2010) Effect of a major QTL affecting IPN resistance on production traits in Atlantic salmon. Animal Genetics, 41: 666-668.
66. Gibson G, Weir B (2005) The quantitative genetics of transcription. Trends in Genetics, 21: 616-623.
67. Goldberg AD, Allis CD, Bernstein E (2007) Epigenetics: A landscape takes shape. Cell, 128: 635-638.
68. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng QD, Chen ZH, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29: 644-652.
69. Greisman HA, Pabo CO (1997) A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science, 275: 657-661.
70. Gross ML, Schneider JF, Moav N, Moav B, Alvarez C, Myster SH, Liu ZJ, Hallerman EM, Hackett PB, Guise KS, Faras AJ, Kapuscinski AR (1992) Molecular analysis and growth evaluation of Northern Pike (Esox-Lucius) microinjected with growth-hormone genes. Aquaculture, 103: 253-273.
71. GuhaThakurta D (2006) Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Research, 34: 3585-3598.
72. Guo X, Li Q, Wang QZ, and Kong LF (2011) Genetic mapping andQTLanalysis of growth-related traits in the Pacific oyster. Marine Biotechnology, 14: 218-226.
73. Hackett PB, Clark KJ (2007) Functional genomics. In: Liu Z (ed) Aquaculture Genome Technologies. Blackwell Publishing Ltd, Oxford. 427-460. DOI: 10.1002/9780470277560.ch24.
74. Hale MC, McCormick CR, Jackson JR, Dewoody JA (2009) Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics, 10: 203.
75. Han ES,Wu YM, McCarter R, Nelson JF, Richardson A, Hilsenbeck SG (2004) Reproducibility, sources of variability, pooling, and sample size: Important considerations for the design of highdensity oligonucleotide array experiments. Journals of Gerontology Series a-Biological Sciences and Medical Sciences, 59: 306-315.
76. Hannon GJ (2002) RNA interference. Nature, 418: 244-251.
77. Hansen BG, Halkier BA, Kliebenstein DJ (2008) Identifying the molecular basis of QTLs: eQTLs add a new dimension. Trends in Plant Science, 13: 72-77.
78. Harbers M, Carninci P (2005) Tag-based approaches for transcriptome research and genome annotation. Nature Methods, 2: 495-502.
79. He K, Chen Z, Ma Y, Pan Y (2011) Identification of high-copper-responsive target pathways in Atp7b knockout mouse liver by GSEA on microarray data sets. Mammalian Genome, 22: 703-713.
80. Hegedus Z, Zakrzewska A, Agoston VC, Ordas A, Racz P, Mink M, Spaink HP, Meijer AH (2009) Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Molecular Immunology, 46: 2918-2930.
81. Heintzman ND, Stuart RK, Hon G, Fu YT, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu CX, Ching KA, Wang W, Weng ZP, Green RD, Crawford GE, Ren B (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genetics, 39: 311-318.
82. Henikoff S (2008) Nucleosome destabilization in the epigenetic regulation of gene expression. Nature Reviews Genetics, 9: 15-26.
83. Hieter P, Boguski M (1997) Functional genomics: It's all how you read it. Science, 278: 601-602.
84. Hirayama M, Ahsan MN, Mitani H, Watabe S (2008) CYR61 is a novel gene associated with temperature-dependent changes in fish metabolism as revealed by cDNA microarray analysis on a medaka Oryzias latipes cell line. Journal of Cellular Biochemistry, 104: 1297-1310.
85. HollidayR(2006) Epigenetics: a historical overview. Epigenetics, 1: 76-80.
86. Horak CE, Snyder M (2002) ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods in Enzymology, 350: 469-483.
87. HouR,Bao Z, Wang S, SuH, Li Y, DuH, Hu J, Hu X (2011) Transcriptome sequencing and de novo analysis for Yesso scallop (Patinopecten yessoensis) using 454 GS FLX. PLoS ONE, 6: e21560.
88. Houston RD, Haley CS, Hamilton A, Guy DR, Mota-Velasco JC, Gheyas AA, Tinch AE, Taggart JB, Bron JE, Starkey WG, McAndrew BJ, Verner-Jeffreys DW, Paley RK, Rimmer GSE, Tew IJ, Bishop SC (2010) The susceptibility of Atlantic salmon fry to freshwater infectious pancreatic necrosis is largely explained by a major QTL. Heredity, 105: 318-327.
89. Houston RD, Haley CS, Hamilton A, Guyt DR, Tinch AE, Taggart JB, McAndrew BJ, Bishop SC (2008) Major quantitative trait loci affect resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar). Genetics, 178: 1109-1115.
90. Hu M, Yu JD, Taylor JMG, Chinnaiyan AM, Qin ZHS (2010) On the detection and refinement of transcription factor binding sites using ChIP-Seq data. Nucleic Acids Research, 38: 2154-2167.
91. Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4: 44-57.
92. Huang WT, Hsieh JC, Chiou MJ, Chen JY, Wu JL, Kuo CM (2008) Application of RNAi technology to the inhibition of zebrafish GtH alpha, FSH beta, and LH beta expression and to functional analyses. Zoological Science, 25: 614-621.
93. Hubner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, Maciver F, Mueller M, Hummel O, Monti J, Zidek V, Musilova A, Kren V, Causton H, Game L, Born G, Schmidt S, Muller A, Cook SA, Kurtz TW, Whittaker J, Pravenec M, Aitman TJ (2005) Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nature Genetics, 37: 243-253.
94. Hurst LD, Pal C, Lercher MJ (2004) The evolutionary dynamics of eukaryotic gene order. Nature Reviews Genetics, 5: 299-310.
95. Hurt JA, Thibodeau SA, Hirsh AS, Pabo CO, Joung JK (2003) Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proceedings of the National Academy of Sciences USA, 100: 12271-12276.
96. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4: 249-264.
97. Isalan M, Choo Y, Klug A (1997) Synergy between adjacent zinc fingers in sequence-specific DNA recognition. Proceedings of the National Academy of Sciences USA, 94: 5617-5621.
98. Isalan M, Klug A, Choo Y (2001) A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter. Nature Biotechnology, 19: 656-660.
99. Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proceedings of International Conference on Intelligent Systems for Molecular Biology, pp. 138-148.
100. Jackson TR, Ferguson MM, Danzmann RG, Fishback AG, Ihssen PE, O'Connell M, Crease TJ (1998) Identification of two QTL influencing upper temperature tolerance in three rainbow trout (Oncorhynchus mykiss) half-sib families. Heredity, 80: 143-151.
101. Jansen RC, Nap JP (2001) Genetical genomics: the added value from segregation. Trends in Genetics, 17: 388-391.
102. Johansen SD, Karlsen BO, Furmanek T, Andreassen M, Jorgensen TE, Bizuayehu TT, Breines R, Emblem A, Kettunen P, Luukko K, Edvardsen RB, Nordeide JT, Coucheron DH, Moum T (2011) RNA deep sequencing of the Atlantic cod transcriptome. Comparative biochemistry and physiology. Part D, Genomics & proteomics, 6: 18-22.
103. Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316: 1497-1502.
104. Jones NC, Pevzner PA (2006) Comparative genomics reveals unusually long motifs in mammalian genomes. Bioinformatics, 22: E236-E242.
105. Jothi R, Cuddapah S, Barski A, CuiK, ZhaoK(2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Research, 36: 5221-5231.
106. Ju ZL, Wells MC, Heater SJ, Walter RB (2007) Multiple tissue gene expression analyses in Japanese medaka (Oryzias latipes) exposed to hypoxia. Comparative Biochemistry and Physiology C-Toxicology & Pharmacology, 145: 134-144.
107. Karoonuthaisiri N, Sittikankeaw K, Preechaphol R, Kalachikov S, Wongsurawat T, Uawisetwathana U, Russo JJ, Ju J, Klinbunga S, Kirtikara K (2009) ReproArray(GTS): a cDNA microarray for identification of reproduction-related genes in the giant tiger shrimp Penaeus monodon and characterization of a novel nuclear autoantigenic sperm protein (NASP) gene. Comp Biochem Physiol Part D Genomics Proteomics, 4: 90-99.
108. Kassahn KS, Caley MJ, Ward AC, Connolly AR, Stone G, Crozier RH (2007) Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish. Molecular Ecology, 16: 1749-1763.
109. Kelly A, HurlstoneAF (2011) The use of RNAi technologies for gene knockdown in zebrafish. Brief Funct Genomics, 10: 189-196.
110. Keshet I, Schlesinger Y, Farkash S, Rand E, Hecht M, Segal E, Pikarski E, Young RA, Niveleau A, Cedar H, Simon I (2006) Evidence for an instructive mechanism of de novo methylation in cancer cells. Nature Genetics, 38: 149-153.
111. Kim JY, Cha DY, Park JH, Chang JB, Lee SH, Lee WJ (2006) Genome wide identification of parturition associated genes using cDNA microarray in the placenta of pregnant women between with labor and without labor. American Journal of Obstetrics and Gynecology, 195: S101-S101.
112. Kim S, Lee MJ, KimH, Kang M, Kim JS (2011a) Preassembled zinc-finger arrays for rapid construction of ZFNs. Nature Methods, 8: 7.
113. Kim SW, Rai D, Aguiar R (2011b) Gene-set enrichment analysis unveils the mechanism for the phosphodiesterase 4B control of glucocorticoid response in B-cell lymphoma. Clinical Cancer Research, 17: 6723-6732.
114. Kim YG, Cha J, Chandrasegaran S (1996) Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. Proceedings of the National Academy of Sciences of the United States of America, 93: 1156-1160.
115. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh J (2005) Complement factor H polymorphism in age-related macular degeneration. Science, 308: 385-389.
116. KochA,HrychykA,HartmannW,WahaA,Mikeska T, Schuller U, Sorensen N, Berthold F, Goodyer CG, Wiestler OD, Birchmeier W, Behrens J, Pietsch T (2007) Mutations of the Wnt antagonist AXIN2 (Conductin) result in TCF-dependent transcription in medulloblastomas. International Journal of Cancer, 121: 284-291.
117. Kondo H, Suga R, Suda S, Nozaki R, Hirono I, Nagasaka R, Kaneko G, Ushio H, Watabe S (2011) EST analysis on adipose tissue of rainbow trout Oncorhynchus mykiss and tissue distribution of adiponectin. Gene, 485: 40-45.
118. Koop BF, von Schalburg KR, Leong J, Walker N, Lieph R, Cooper GA, Robb A, Beetz-Sargent M, Holt RA, Moore R, Brahmbhatt S, Rosner J, Rexroad CE, McGowan CR, Davidson WS. 2008. A salmonid EST genomic study: genes, duplications, phylogeny and microarrays. BMC Genomics, 9: 545.
119. Kuttner E, Moghadam HK, Skulason S, Danzmann RG, Ferguson MM (2011) Genetic architecture of body weight, condition factor and age of sexual maturation in Icelandic Arctic charr (Salvelinus alpinus). Molecular Genetics and Genomics, 286: 67-79.
120. Laird PW (2010) Principles and challenges of genomewide DNA methylation analysis. Nature Reviews Genetics, 11: 191-203.
121. Lan H, Chen M, Flowers JB, Yandell BS, Stapleton DS, Mata CM, Mui ETK, Flowers MT, Schueler KL, Manly KF, Williams RW, Kendziorski C, Attie AD (2006) Combined expression trait correlations and expression quantitative trait locus mapping. PLoS Genetics, 2: 51-61.
122. Le Bras Y, Dechamp N, Krieg F, Filangi O, Guyomard R, Boussaha M, Bovenhuis H, Pottinger TG, Prunet P, Le Roy P, Quillet E (2011) Detection ofQTLwith effects on osmoregulation capacities in the rainbow trout (Oncorhynchus mykiss). BMC Genetics, 12: 46.
123. Leder EH, Danzmann RG, Ferguson MM (2006) The candidate gene, Clock, localizes to a strong spawning time quantitative trait locus region in rainbow trout. Journal of Heredity, 97: 74-80.
124. Lee JS, Chu IS, Mikaelyan A, Calvisi DF, Heo J, Reddy JK, Thorgeirsson SS (2004) Application of comparative functional genomics to identify bestfit mouse models to study human cancer. Nature Genetics, 36: 1306-1311.
125. Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, Pe'er D, Koller D (2009) Learning a Prior on Regulatory Potential from eQTL Data. PLoS Genetics, 5: e1000358.
126. Leelatanawit R, Uawisetwathana U, Klinbunga S, Karoonuthaisiri N (2011) A cDNA microarray, UniShrimpChip, for identification of genes relevant to testicular development in the black tiger shrimp (Penaeus monodon). BMC Molecular Biology, 12: 15.
127. Lessman CA (2011) The developing zebrafish (Danio rerio): A vertebrate model for highthroughput screening of chemical libraries. Birth Defects Res C Embryo Today, 93: 268-280.
128. Lewis JM, Hori TS, Rise ML, Walsh PJ, Currie S (2010) Transcriptome responses to heat stress in the nucleated red blood cells of the rainbow trout (Oncorhynchus mykiss). Physiological Genomics, 42: 361-373.
129. Li P, Peatman E, Wang SL, Feng JN, He CB, Baoprasertkul 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 ZJ (2007) Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs. BMC Genomics, 8: 177.
130. Li RW, Waldbieser GC (2006) Production and utilization of a high-density oligonucleotide microarray in channel catfish, Ictalurus punctatus. BMC Genomics, 7: 134.
131. Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, Rando OJ (2005) Singlenucleosome mapping of histone modifications in S-cerevisiae. PLoS Biology, 3: 1753-1769.
132. Liu H, Jiravanichpaisal P, Soderhall I, Cerenius L, Soderhall K (2006) Antilipopolysaccharide factor interferes with white spot syndrome virus replication in vitro and in vivo in the crayfish Pacifastacus leniusculus. Journal of Virology, 80: 10365-10371.
133. Liu N, Caderas G, Deillon C, Hoffmann S, Klauser S, Cui T, Gutte B (2001) Fusion proteins from artificial and natural structural modules. Current Protein and Peptide Science, 2: 107-121.
134. Liu SK, Zhou ZC, Lu JG, Sun FY, Wang SL, Liu H, Jiang YL, Kucuktas H, Kaltenboeck L, Peatman E, LiuZJ (2011) Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics, 12: 53.
135. Liu XD, Liu X, Zhang GF (2007) Identification of quantitative trait loci for growth-related traits in the Pacific abalone Haliotis discus hannai Ino. Aquaculture Research, 38: 789-797.
136. Lo J, Lee SC, Xu M, Liu F, Ruan H, Eun A, He YW,MaWP, Wang WF,WenZL, Peng JR (2003) 15,000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Genome Research, 13: 455-466.
137. Loukovitis D, Sarropoulou E, Tsigenopoulos CS, Batargias C, Magoulas A, Apostolidis AP, Chatziplis D, Kotoulas G (2011) Quantitative trait loci involved in sex determination and body growth in the Gilthead sea bream (Sparus aurata L.) through targeted genome scan. PLoS ONE, 6: e16599.
138. Louro B, Passos ALS, Souche EL, Tsigenopoulos C, Beck A, Lagnel J, Bonhomme F, Cancela L, Cerda J, Clark MS, Lubzens E, Magoulas A, Planas JV, Volckaert FAM, Reinhardt R, Canario AVM(2010) Gilthead sea bream (Sparus auratus) and European sea bass (Dicentrarchus labrax) expressed sequence tags: Characterization, tissuespecific expression and gene markers. Marine Genomics, 3: 179-191.
139. Lynch M, Walsh BJ (1998) Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.
140. Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, Eichtinger M, Jiang T, Foley JE, Winfrey RJ, Townsend JA, Unger-Wallace E, Sander JD, Müller-Lerch F, Fu F, Pearlberg J, Göbel C, Dassie JP, Pruett-Miller SM, Porteus MH, Sgroi DC, Iafrate AJ, Dobbs D, McCray PB Jr, Cathomen T, Voytas DF, Joung JK (2008) Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Molecular Cell, 31: 294-301.
141. Majewski J, Pastinen T (2011) The study of eQTL variations by RNA-seq: from SNPs to phenotypes. Trends in Genetics, 27: 72-79.
142. Mandell JG, Barbas CF (2006) Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Research, 34: W516-523.
143. Marguerat S, Bahler J (2010) RNA-seq: from technology to biology. Cellular and Molecular Life Sciences, 67: 569-579.
144. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nature reviews Genetics, 12: 671-682.
145. Massault C, Hellemans B, Louro B, Batargias C, Van Houdt JKJ, Canario A, Volckaert FAM,Bovenhuis H, Haley C, de Koning DJ (2010) QTL for body weight, morphometric traits and stress response in European sea bass Dicentrarchus labrax. Animal Genetics, 41: 337-345.
146. Mathavan S, Lee SG, Mak A, Miller LD, Murthy KR, Govindarajan KR, Tong Y, Wu YL, Lam SH, Yang H, Ruan Y, Korzh V, Gong Z, Liu ET, Lufkin T (2005) Transcriptome analysis of zebrafish embryogenesis using microarrays. PLoS Genetics, 1: 260-276.
147. McClelland EK, Naish KA (2010) Quantitative trait locus analysis of hatch timing, weight, length and growth rate in coho salmon, Oncorhynchus kisutch. Heredity, 105: 562-573.
148. Mckusick VA (1989) The human-genomeorganization- history, purposes, and membership. Genomics, 5: 385-387.
149. Meijer AH, Verbeek FJ, Salas-Vidal E, Corredor-Adamez M, Bussman J, van der Sar AM, Otto GW, Geisler R, Spaink HP (2005) Transcriptome profiling of adult zebrafish at the late stage of chronic tuberculosis due to Mycobacterium marinum infection. Molecular Immunology, 42: 1185-1203.
150. Meng X, Noyes MB, Zhu LJ, Lawson ND, Wolfe SA (2008) Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases. Nature Biotechnology, 26: 695-701.
151. Mikkelsen TS, Ku MC, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie XH, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE (2007) Genomewide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448: 553-560.
152. Miller MB, Tang YW (2009) Basic concepts of microarrays and potential applications in clinical microbiology. Clinical Microbiology Reviews, 22: 611-633.
153. Min XJ, Butler G, Storms R, TsangA(2005) OrfPredictor: predicting protein-coding regions in ESTderived sequences. Nucleic Acids Research, 33: W677-W680.
154. Moen T, Baranski M, Sonesson AK, Kjoglum S (2009) Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): populationlevel associations between markers and trait.BMC Genomics, 10: 368.
155. Moen T, Sonesson AK, Hayes B, Lien S, Munck H, Meuwissen THE (2007) Mapping of a quantitative trait locus for resistance against infectious salmon anaemia in Atlantic salmon (Salmo Salar): comparing survival analysis with analysis on affected/ resistant data. BMC Genetics, 8: 53.
156. Moghadam HK, Poissant J, Fotherby H, Haidle L, Ferguson MM, Danzmann RG (2007) Quantitative trait loci for body weight, condition factor and age at sexual maturation in Arctic charr (Salvelinus alpinus): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar). Molecular Genetics and Genomics, 277: 647-661.
157. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature, 464: 773-777.
158. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, Spielman RS, Cheung VG (2004) Genetic analysis of genome-wide variation in human gene expression. Nature, 430: 743-747.
159. Morozova O, Hirst M, Marra MA (2009) Applications of new sequencing technologies for transcriptome analysis. Annual Review Genomics Human Genetics, 10: 135-151.
160. Mu Y, Ding F, Cui P, Ao J, Hu S, Chen X (2010) Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection. BMC Genomics, 11: 506.
161. Nagalakshmi U, Waern K, Snyder M (2010) RNASeq: a method for comprehensive transcriptome analysis. Current Protocol of Molecular Biology, 11: 11-13.
162. Nakaya HI, Amaral PP, Louro R, Lopes A, Fachel AA, Moreira YB, El-Jundi TA, da Silva AM, Reis EM, Verjovski-Almeida S (2007) Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biology, 8: R43.
163. Ng HH, Bird A (1999) DNA methylation and chromatin modification. Current Opinion in Genetics & Development, 9: 158-163.
164. Nichols KM, Edo AF, Wheeler PA, Thorgaard GH (2008) The genetic basis of smoltificationrelated traits in Oncorhynchus mykissi. Genetics, 179: 1559-1575.
165. Norman JD, Danzmann RG, Glebe B, Ferguson MM(2011) The genetic basis of salinity tolerance traits in Arctic charr (Salvelinus alpinus). BMC Genetics, 12: 81.
166. Nuwaysir EF, Huang W, Albert TJ, Singh J, Nuwaysir K, Pitas A, Richmond T, Gorski T, Berg JP, Ballin J, McCormick M, Norton J, Pollock T, Sumwalt T, Butcher L, Porter D, Molla M, Hall C, Blattner F, Sussman MR, Wallace RL, Cerrina F, Green RD (2002) Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Research, 12: 1749-1755.
167. Olsvik PA, Lie KK, Mykkeltvedt E, Samuelsen OB, Petersen K, Stavrum AK, Lunestad BT (2008) Pharmacokinetics and transcriptional effects of the anti-salmon lice drug emamectin benzoate in Atlantic salmon (Salmo salar L.). BMC Pharmacology, 8: 16.
168. O'Malley KG, Sakamoto T, Danzmann RG, Ferguson MM (2003) Quantitative trait loci for spawning date and body weight in rainbow trout: Testing for conserved effects across ancestrally duplicated chromosomes. Journal of Heredity, 94: 273-284.
169. Ordas A, Hegedus Z, Henkel CV, Stockhammer OW, Butler D, Jansen HJ, Racz P, Mink M, Spaink HP, Meijer AH (2011) Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection. Fish & Shellfish Immunology, 31: 716-724.
170. Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nature Reviews Genetics, 10: 669-680.
171. Peal DS, Mills RW, Lynch SN, Mosley JM, Lim E, Ellinor PT, January CT, Peterson RT, Milan DJ (2011) Novel chemical suppressors of long QT syndrome identified by an in vivo functional screen. Circulation, 123: 23-30.
172. Peatman E, Baoprasertkul P, Terhune J, Xu P, Nandi S, Kucuktas H, Li P, Wang SL, Somridhivej B, Dunham R, Liu ZJ (2007) Expression analysis of the acute phase response in channel catfish (Ictalurus punctatus) after infection with a Gram-negative bacterium. Developmental and Comparative Immunology, 31: 1183-1196.
173. Peatman E, Liu Z (2007) Microarray fundamentals: Basic principles and application in aquaculture. In: Liu Z (ed) Aquaculture Genome Technologies. Blackwell Publishing Ltd., Oxford. DOI: 10.1002/9780470277560.ch21.
174. Perry GML, Danzmann RG, Ferguson MM, Gibson JP (2001) Quantitative trait loci for upper thermal tolerance in outbred strains of rainbow trout (Oncorhynchus mykiss). Heredity, 86: 333-341.
175. PerryGML,FergusonMM,Sakamoto T, Danzmann RG (2005) Sex-linked quantitative trait loci for thermotolerance and length in the rainbow trout. Journal of Heredity, 96: 97-107.
176. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature, 464: 768-772.
177. Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, Bell GW, Walker K, Rolfe PA, Herbolsheimer E, Zeitlinger J, Lewitter F, Gifford DK, YoungRA(2005) Genome-wide map of nucleosome acetylation and methylation in yeast. Cell, 122: 517-527.
178. Pruett-Miller SM, Connelly JP, Maeder ML, Joung JK, Porteus MH. 2008. Comparison of zinc finger nucleases for use in gene targeting in mammalian cells. Molecular Therapy, 16: 707-717.
179. Purcell MK, Marjara IS, Batts W, Kurath G, Hansen JD (2011) Transcriptome analysis of rainbow trout infected with high and low virulence strains of infectious hematopoietic necrosis virus. Fish & Shellfish Immunology, 30: 84-93.
180. Rahman MA, Mak R, Ayad H, Smith A, Maclean N (1998) Expression of a novel piscine growth hormone gene results in growth enhancement in transgenic tilapia (Oreochromis niloticus). Transgenic Research, 7: 357-369.
181. Rahman MA, Ronyai A, Engidaw BZ, Jauncey K, Hwang GL, Smith A, Roderick E, Penman D, Varadi L, Maclean N (2001) Growth and nutritional trials on transgenic Nile tilapia containing an exogenous fish growth hormone gene. Journal of Fish Biology, 59: 62-78.
182. Ramirez CL, et al. (2008) Unexpected failure rates for modular assembly of engineered zinc-fingers. Nature Methods, 5: 374-375.
183. Reid DP, Szanto A, Glebe B, Danzmann RG, Ferguson MM (2005) QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus). Heredity, 94: 166-172.
184. Reinartz J, Bruyns E, Lin JZ, Burcham T, Brenner S, Bowen B, Kramer M, Woychik R (2002) Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. Brief Functional Genomics & Proteomics, 1: 95-104.
185. Ren J, Jenkins TC, Chaires JB (2000) Energetics of DNA intercalation reactions. Biochemistry, 39: 8439-8447.
186. Renaut S, Nolte AW, Bernatchez L (2010) Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Molecular Ecology, 19(Suppl 1): 115-131.
187. Reyon D, Kirkpatrick JR, Sander JD, Zhang F, Voytas DF, Joung JK, Dobbs D, Coffman CR (2011) ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms. BMC Genomics, 12: 83.
188. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao YJ, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods, 4: 651-657.
189. Robison BD, Wheeler PA, Sundin K, Sikka P, Thorgaard GH (2001) Composite interval mapping reveals a major locus influencing embryonic development rate in rainbow trout (Oncorhynchus mykiss). Journal of Heredity, 92: 16-22.
190. Robyr D, Suka Y, Xenarios I, Kurdistani SK, Wang A, Suka N, Grunstein M (2002) Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell, 109: 437-446.
191. Roh TY, Wei G, Farrell CM, Zhao K (2007) Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Genome Research, 17: 74-81.
192. Ronning CM, Stegalkina SS, Ascenzi RA, Bougri O, Hart AL, Utterbach TR, Vanaken SE, Riedmuller SB, White JA, Cho J, Pertea GM, Lee Y, Karamycheva S, Sultana R, Tsai J, Quackenbush J, Griffiths HM, Restrepo S, Smart CD, Fry WE, Van Der Hoeven R, Tanksley S, Zhang P, Jin H, Yamamoto ML, Baker BJ, Buell CR (2003) Comparative analyses of potato expressed sequence tag libraries. Plant Physiology, 131: 419-429.
193. Rosa GJ, de Leon N, Rosa AJ (2006) Review of microarray experimental design strategies for genetical genomics studies. Physiological Genomics, 28: 15-23.
194. Rosel TD, Hung LH, Medenbach J, Donde K, Starke S, Benes V, Ratsch G, Bindereif A (2011) RNASeq analysis in mutant zebrafish reveals role of U1Cprotein in alternative splicing regulation. The EMBO journal, 30: 1965-1976.
195. Rowen L, Mahairas G, Hood L (1997) Sequencing the human genome. Science, 278: 605-607.
196. Royce TE, Rozowsky JS, Gerstein MB (2007) Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics, 23: 988-997.
197. Salem M, Rexroad CE, Wang J, Thorgaard GH, Yao J (2010) Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC Genomics, 11: 564.
198. Sanchez BC, Carter B, Hammers HR, SepulvedaMS (2011) Transcriptional response of hepatic largemouth bass (Micropterus salmoides) mRNA upon exposure to environmental contaminants. Journal of Applied Toxicology, 31: 108-116.
199. Sander JD, Dahlborg EJ, Goodwin MJ, Cade L, Zhang F, Cifuentes D, Curtin SJ, Blackburn JS, Thibodeau-Beganny S, Qi Y, Pierick CJ, Hoffman E, Maeder ML, Khayter C, Reyon D, Dobbs D, Langenau DM, Stupar RM, Giraldez AJ, Voytas DF, Peterson RT, Yeh JR, Joung JK (2011). Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA). Nature Methods, 8: 67-69.
200. Sander JD, Reyon D, Maeder ML, Foley JE, Thibodeau-Beganny S, Li X, Regan MR, Dahlborg EJ, Goodwin MJ, Fu F, Voytas DF, Joung JK, Dobbs D (2010a). Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences. BMC Bioinformatics, 11: 543.
201. Sander JD, Maeder ML, Reyon D, Voytas DF, Joung JK, DobbsD(2010b). ZiFiT (zinc finger targeter): an updated zinc finger engineering tool. Nucleic Acids Research, 38: W462-W468.
202. Sander JD, Zaback P, Joung JK, Voytas DF, Dobbs D (2007) Zinc finger targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucleic Acids Research, 35: W599-W605.
203. Sauvage C, Boudry P, de Koning DJ, Haley CS, Heurtebise S, Lapegue S (2010) QTL for resistance to summer mortality and OsHV-1 load in the Pacific oyster (Crassostrea gigas). Animal Genetics, 41: 390-399.
204. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V, Ruff TG, Milligan SB, Lamb JR, Cavet G, Linsley PS, Mao M, Stoughton RB, Friend SH (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature, 422: 297-302.
205. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementaryDNAmicroarray. Science, 270: 467-470.
206. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proceedings of the National Academy of Sciences of the United States of America, 93: 10614-10619.
207. Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT (2010) Five-vertebrate ChIPseq reveals the evolutionary dynamics of transcription factor binding. Science, 328: 1036-1040.
208. Schones DE, Zhao K (2008) Genome-wide approaches to studying chromatin modifications. Nature Reviews Genetics, 9: 179-191.
209. Schubeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, van Leeuwen F, Gottschling DE, O'Neill LP, Turner BM, Delrow J, Bell SP, GroudineM(2004) The histone modification pattern of active genes revealed through genomewide chromatin analysis of a higher eukaryote. Genes & Development, 18: 1263-1271.
210. Segal DJ, Beerli RR, Blancafort P, Dreier B, Effertz K, Huber A, Koksch B, Lund CV, Magnenat L, Valente D, Barbas CF (2003) Evaluation of a modular strategy for the construction of novel polydactyl zinc finger DNA-binding proteins. Biochemistry, 42: 2137-2148.
211. Segal DJ, Barbas CF (2001) Custom DNAbinding proteins come of age: polydactyl zincfinger proteins. Current Opinion in Biotechnology, 12: 632-637.
212. Shen LL, Waterland RA (2007) Methods of DNA methylation analysis. Current Opinion in Clinical Nutrition and Metabolic Care, 10: 576-581.
213. Shirak A, Seroussi E, Cnaani A, Howe AE, Domokhovsky R, Zilberman N, Kocher TD, Hulata G, Ron M (2006) Amh and Dmrta2 genes map to tilapia (Oreochromis spp.) linkage group 23 within quantitative trait locus regions for sex determination. Genetics, 174: 1573-1581.
214. Shukla VK, Doyon Y, Miller JC, DeKelver RC, Moehle EA, Worden SE, Mitchell JC, Arnold NL, Gopalan S, Meng X, Choi VM, Rock JM, Wu YY, Katibah GE, Zhifang G, McCaskill D, Simpson MA, Blakeslee B, Greenwalt SA, Butler HJ, Hinkley SJ, Zhang L, Rebar EJ, Gregory PD, Urnov FD (2009) Precise genome modification in the crop species Zea mays using zinc-finger nucleases. Nature, 459: 437-441.
215. Sladek R, Rocheleau G, Rung J, Dina C, Shen L, Serre D, Boutin P, Vincent D, Belisle A, Hadjadj S, Balkau B, Heude B, Charpentier G, Hudson TJ, Montpetit A, Pshezhetsky AV, Prentki M, Posner BI, Balding DJ, Meyre D, Polychronakos C, Froguel P (2007) A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature, 445: 881-885.
216. Soares MB, Bonaldo MD, Jelene P, Su L, Lawton L, EfstratiadisA (1994) Construction and characterization of a normalized Cdna library. Proceedings of the National Academy of Sciences of the United States of America, 91: 9228-9232.
217. Solomon MJ, Larsen PL, Varshavsky A (1988) Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell, 53: 937-947.
218. Stockhammer OW, Rauwerda H, Wittink FR, Breit TM,Meijer AH, SpainkHP(2010) Transcriptome analysis of Traf6 function in the innate immune response of zebrafish embryos. Molecular Immunology, 48: 179-190.
219. Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nature Reviews Genetics, 9: 465-476.
220. Tate PH, Bird AP (1993) Effects of DNA methylation on DNA-binding proteins and gene expression. Current Opinion in Genetics & Development, 3: 226-231.
221. The Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls. Nature, 447: 661-678.
222. Thomas MA, Yang L, Carter BJ, Klaper RD (2011) Gene set enrichment analysis of microarray data from Pimephales promelas (Rafinesque), a nonmammalian model organism. BMC Genomics, 12: 66.
223. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, PavesiG, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology, 23: 137-144.
224. Ton C, Stamatiou D, Dzau VJ, Liew CC (2002) Construction of a zebrafish cDNA microarray: gene expression profiling of the zebrafish during development. Biochemical and Biophysical Research Communications, 296: 1134-1142.
225. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nature Methods, 5: 829-834.
226. Vasemagi A, Gross R, Palm D, Paaver T, Primmer CR(2010) Discovery and application of insertiondeletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon. BMC Genomics, 11: 156.
227. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Science, 270: 484-487.
228. Venter JC, Smith HO, Hood L (1996)Anew strategy for genome sequencing. Nature, 381: 364-366.
229. Vesterlund L, Jiao H, Unneberg P, Hovatta O, Kere J (2011) The zebrafish transcriptome during early development. BMC Developmental Biology, 11: 30.
230. Vogt G (2008) The marbled crayfish: a new model organism for research on development, epigenetics and evolutionary biology. Journal of Zoology, 276: 1-13.
231. 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.
232. Wang CM, Bai ZY, He XP, Lin G, Xia JH, Sun F, Lo LC, Feng F, Zhu ZY, Yue GH (2011) A highresolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer. BMC Genomics, 12: 174.
233. Wang CM, Lo LC, Zhu ZY, Yue GH (2006) A genome scan for quantitative trait loci affecting growth-related traits in an F1 family of Asian seabass (Lates calcarifer). BMC Genomics, 7: 174.
234. Wang J, Williams RW, Manly KF (2003) WebQTL: web-based complex trait analysis. Neuroinformatics, 1: 299-308.
235. Wang S, Peatman E, Liu H, Bushek D, Ford SE, Kucuktas H, Quilang J, Li P, Wallace R, Wang Y, Guo X, Liu Z (2010) Microarray analysis of gene expression in eastern oyster (Crassostrea virginica) reveals a novel combination of antimicrobial and oxidative stress host responses after dermo (Perkinsus marinus) challenge. Fish & Shellfish Immunology, 29: 921-929.
236. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews. Genetics, 10: 57-63.
237. Wargelius A, Ellingsen S, Fjose A (1999) DoublestrandedRNAinduces specific developmental defects in zebrafish embryos. Biochemical and Biophysical Research Communications, 263: 156-161.
238. Wayne ML, McIntyre LM (2002) Combining mapping and arraying: An approach to candidate gene identification. Proceedings of the National Academy of Sciences of the United States of America, 99: 14903-14906.
239. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schubeler D (2005) Chromosomewide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nature Genetics, 37: 853-862.
240. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, SchubelerD(2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genetics, 39: 457-466.
241. Wederell ED, Bilenky M, Cullum R, Thiessen N, Dagpinar M, Delaney A, Varhol R, Zhao YJ, Zeng T, Bernier B, Ingham M, Hirst M, Robertson G, Marra MA, Jones S, Hoodless PA (2008) Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Research, 36: 4549-4564.
242. Wongsurawat T, Leelatanawit R, Thamniemdee N, Uawisetwathana U, Karoonuthaisiri N, Menasveta P, Klinbunga S (2010) Identification of testisrelevant genes using in silico analysis from testis ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon). BMC Molecular Biology, 11: 55.
243. Wringe BF, Devlin RH, Ferguson MM, Moghadam HK, Sakhrani D, Danzmann RG (2010) Growthrelated quantitative trait loci in domestic and wild rainbow trout (Oncorhynchus mykiss). BMC Genetics, 11:63.
244. Wu CC, Huang HC, Juan HF, Chen ST (2004) GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data. Bioinformatics, 20: 3691-3693.
245. Xiang CC, Chen YD (2000) cDNA microarray technology and its applications. Biotechnology Advances, 18: 35-46.
246. Xiang LX, He D, Dong WR, Zhang YW, Shao JZ (2010) Deep sequencing-based transcriptome profiling analysis of bacteria-challenged Lateolabrax japonicus reveals insight into the immunerelevant genes in marine fish. BMC Genomics, 11: 472.
247. Xie XH, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, KellisM(2005) Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature, 434: 338-345.
248. Yu ZN, Guo XM (2006) Identification and mapping of disease-resistance QTLs in the eastern oyster, Crassostrea virginica Gmelin. Aquaculture, 254: 160-170.
249. Zhan A, Hu J, Hu X, Hui M, Wang M, Peng W, Huang X, Wang S, Lu W, Sun C, Bao Z (2009) Construction of microsatellite-based linkage maps and identification of size-related quantitative trait loci for Zhikong scallop (Chlamys farreri). Animal Genetics, 40: 821-831.
250. Zhang XY, Yazaki J, Sundaresan A, Cokus S, Chan SWL, Chen HM, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell, 126: 1189-1201.
251. Zhang Y, Xu P, Lu C, Kuang Y, Zhang X, Cao D, Li C, Chang Y, Hou N, Li H, Wang S, Sun X (2011) Genetic linkage mapping and analysis of muscle fiber-related QTLs in common carp (Cyprinus carpio L.). Marine Biotechnology (NY), 13: 376-392.
252. Zheng Q, Wang XJ (2008) GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Research, 36: W358-363.
253. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics, 39: 61-69.
254. Zou J, Maeder ML, Mali P, Pruett-Miller SM, Thibodeau-Beganny S, Chou BK, Chen G, Ye Z, Park IH, Daley GQ, Porteus MH, Joung JK, Cheng L (2009) Gene targeting of a diseaserelated gene in human induced pluripotent stem and embryonic stem cells. Cell Stem Cell, 5: 97-110.
255. Zou ZH, Zhang ZP, Wang YL, Han KH, Fu MJ, Lin P, Jia XW (2011) EST analysis on the gonad development related organs and microarray screen for differentially expressed genes in mature ovary and testis of Scylla paramamosain. Comparative Biochemistry and Physiology D-Genomics & Proteomics, 6: 150-157.