A first generation BAC-based physical map of the rainbow trout genome

BMC Genomics

Volumn 10, Issue , 2009, Pages 462-

  Palti, Yniv ^a   Luo, Ming Cheng ^b   Hu, Yuqin ^b   Genet, Carine ^c   You, Frank M ^b   Vallejo, Roger L ^a   Thorgaard, Gary H ^d   Wheeler, Paul A ^d   Rexroad III, Caird E ^a  

^a NATIONAL CENTER FOR COOL AND COLD WATER AQUACULTURE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UMR1313 GÉNÉTIQUE ANIMALE ET BIOLOGIE INTÉGRATIVE   (France)

^d WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; DNA;

AQUACULTURE; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BREEDING METHOD; COMPARATIVE GENE MAPPING; CONSENSUS SEQUENCE; CONTROLLED STUDY; DNA FINGERPRINTING; FRESHWATER FISH; GENE MAPPING; GENE SEQUENCE; GENETIC LINKAGE; GENETIC SELECTION; GENETIC TRAIT; LIFE HISTORY TRAIT; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; QUANTITATIVE TRAIT LOCUS; QUANTITATIVE TRAIT LOCUS MAPPING; RAINBOW TROUT;

ANIMALS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CONTIG MAPPING; DNA FINGERPRINTING; GENETIC MARKERS; GENOME; GENOTYPE; MICROSATELLITE REPEATS; ONCORHYNCHUS MYKISS; QUANTITATIVE TRAIT LOCI; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS); ONCORHYNCHUS MYKISS;

EID: 70449513697     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-462     Document Type: Article

References (66)

1. Thorgaard GH, Bailey GS, Williams D, Buhler DR, Kaattari SL, Ristow SS, Hansen JD, Winton JR, Bartholomew JL, Nagler JJ. Status and opportunities for genomics research with rainbow trout. Comp Biochem Physiol B Biochem Mol Biol 2002, 133:609-646. 10.1016/S1096-4959(02)00167-7, 12470823.
2. Ng SH, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJ. A physical map of the genome of Atlantic salmon, Salmo salar. Genomics 2005, 86:396-404. 10.1016/j.ygeno.2005.06.001, 16026963.
3. Young WP, Wheeler PA, Coryell VH, Keim P, Thorgaard GH. A detailed linkage map of rainbow trout produced using doubled haploids. Genetics 1998, 148:839-850. 1459819, 9504929.
4. Allendorf FW, Thorgaard GH. Tetraploidy and the evolution of salmonid fishes. Evolutionary Genetics of Fishes 1984, 1-46. New York: Plenum Press, Turner BJ.
5. Palti Y, Gahr SA, Hansen JD, Rexroad CE. Characterization of a new BAC library for rainbow trout: evidence for multi-locus duplication. Anim Genet 2004, 35:130-133. 10.1111/j.1365-2052.2004.01112.x, 15025574.
6. Phillips RB, Nichols KM, DeKoning JJ, Morasch MR, Keatley KA, Rexroad C, Gahr SA, Danzmann RG, Drew RE, Thorgaard GH. Assignment of rainbow trout linkage groups to specific chromosomes. Genetics 2006, 174:1661-1670. 10.1534/genetics.105.055269, 1667062, 16951085.
7. Katagiri T, Asakawa S, Minagawa S, Shimizu N, Hirono I, Aoki T. Construction and characterization of BAC libraries for three fish species; rainbow trout, carp and tilapia. Anim Genet 2001, 32:200-204. 10.1046/j.1365-2052.2001.00764.x, 11531698.
8. Robison BD, Wheeler PA, Sundin K, Sikka P, Thorgaard GH. Composite interval mapping reveals a major locus influencing embryonic development rate in rainbow trout (Oncorhynchus mykiss). J Hered 2001, 92:16-22. 10.1093/jhered/92.1.16, 11336224.
9. Robison BD, Wheeler PA, Thorgaard GH. Variation in development rate among clonal lines of rainbow trout (Oncorhynchus mykiss). Aquaculture 1999, 173:131-141.
10. Young WP, Wheeler PA, Fields RD, Thorgaard GH. DNA fingerprinting confirms isogenicity of androgenetically derived rainbow trout lines. J Hered 1996, 87:77-80.
11. Quillet E, Dorson M, Le Guillou S, Benmansour A, Boudinot P. Wide range of susceptibility to rhabdoviruses in homozygous clones of rainbow trout. Fish & Shellfish Immunology 2007, 22:510-519.
12. Guyomard R, Mauger S, Tabet-Canale K, Martineau S, Genet C, Krieg F, Quillet E. A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms. BMC Genomics 2006, 7:302. 1698487, 17137492.
13. Nichols KM, Young WP, Danzmann RG, Robison BD, Rexroad C, Noakes M, Phillips RB, Bentzen P, Spies I, Knudsen K. A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Anim Genet 2003, 34:102-115.
14. Sakamoto T, Danzmann RG, Gharbi K, Howard P, Ozaki A, Khoo SK, Woram RA, Okamoto N, Ferguson MM, Holm L-E. A Microsatellite Linkage Map of Rainbow Trout (Oncorhynchus mykiss) Characterized by Large Sex-Specific Differences in Recombination Rates. Genetics 2000, 155:1331-1345. 1461176, 10880492.
15. Rexroad CE, Palti Y, Gahr SA, Vallejo RL. A second generation genetic map for rainbow trout (Oncorhynchus mykiss). BMC Genet 2008, 9:74. 2605456, 19019240.
16. Rexroad CE, Lee Y, Keele JW, Karamycheva S, Brown G, Koop B, Gahr SA, Palti Y, Quackenbush J. Sequence analysis of a rainbow trout cDNA library and creation of a gene index. Cytogenet Genome Res 2003, 102:347-354.
17. Govoroun M, Le Gac F, Guiguen Y. Generation of a large scale repertoire of Expressed Sequence Tags (ESTs) from normalised rainbow trout cDNA libraries. BMC Genomics 2006, 7:196. 1564016, 16887034.
18. Rise ML, von Schalburg KR, Brown GD, Mawer MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR. Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics. Genome Res 2004, 14:478-490. 353236, 14962987.
19. Salem M, Kenney B, Rexroad CE, Yao J. Development of a 37 k high-density oligonucleotide microarray: a new tool for functional genome research in rainbow trout. Journal of Fish Biology 2008, 72:2187-2206.
20. Coulibaly I, Danzmann RG, Palti Y, Vallejo R, Gahr SA, Yao J, Rexroad CE. Mapping of genes in a region associated with upper temperature tolerance in rainbow trout. Animal Genetics 2006, 37:598-599.
21. Coulibaly I, Gahr SA, Palti Y, Yao J, Rexroad CE. Genomic structure and expression of uncoupling protein 2 genes in rainbow trout (Oncorhynchus mykiss). BMC Genomics 2006, 7:203. 1559616, 16899121.
22. Gahr SA, Palti Y, Rexroad CE. Genomic characterization of a novel pair of ID genes in the rainbow trout (Oncorhynchus mykiss). Anim Genet 2004, 35:317-320.
23. Palti Y, Rodriguez MF, Gahr SA, Hansen JD. Evolutionary history of the ABCB2 genomic region in teleosts. Developmental & Comparative Immunology 2007, 31:483-498.
24. Palti Y, Rodriguez MF, Vallejo RL, Rexroad CE. Mapping of Toll-like receptor genes in rainbow trout. Anim Genet 2006, 37:597-598.
25. Phillips RB, Zimmerman A, Noakes MA, Palti Y, Morasch MR, Eiben L, Ristow SS, Thorgaard GH, Hansen JD. Physical and genetic mapping of the rainbow trout major histocompatibility regions: evidence for duplication of the class I region. Immunogenetics 2003, 55:561-569.
26. Rodriguez M, Wiens G, Purcell M, Palti Y. Characterization of Toll-like receptor 3 gene in rainbow trout (Oncorhynchus mykiss). Immunogenetics 2005, 57:510-519.
27. Rodriguez MF, Gahr SA, Rexroad CE, Palti Y. A polymerase chain reaction screening method for rapid detection of microsatellites in bacterial artificial chromosomes. Mar Biotechnol (NY) 2006, 8:346-350.
28. Thorgaard GH. Chromosomal differences among rainbow trout populations. Copeia 1983, 1983:650-662.
29. Phillips RB, Morasch MR, Wheeler PA, Thorgaard GH, Quattro JM. Rainbow Trout (Oncorhynchus mykiss) of Idaho and Alaskan Origin (2n = 58) Share a Chromosome Fusion Relative to Trout of California Origin (2n = 60). Copeia 2005, 2005:661-664.
30. Danzmann R, Davidson E, Ferguson M, Gharbi K, Koop B, Hoyheim B, Lien S, Lubieniecki K, Moghadam H, Park J. Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon). BMC Genomics 2008, 9:557. 2632648, 19032764.
31. Danzmann RG, Cairney M, Davidson WS, Ferguson MM, Gharbi K, Guyomard R, Holm LE, Leder E, Okamoto N, Ozaki A. A comparative analysis of the rainbow trout genome with 2 other species of fish (Arctic char and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae). Genome 2005, 48:1037-1051.
32. Nichols KM, Bartholomew J, Thorgaard GH. Mapping multiple genetic loci associated with Ceratomyxa shasta resistance in Oncorhynchus mykiss. Dis Aquat Organ 2003, 56:145-154.
33. Barroso RM, Wheeler PA, LaPatra SE, Drew RE, Thorgaard GH. QTL for IHNV resistance and growth identified in a rainbow (Oncorhynchus mykiss)xYellowstone cutthroat (Oncorhynchus. Aquaculture 2008, 277:156-163.
34. Rodriguez MF, LaPatra S, Williams S, Famula T, May B. Genetic markers associated with resistance to infectious hematopoietic necrosis in rainbow and steelhead trout. Aquaculture 2004, 241:93-115.
35. Ozaki A, Sakamoto T, Khoo S, Nakamura K, Coimbra MR, Akutsu T, Okamoto N. Quantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss). Mol Genet Genomics 2001, 265:23-31.
36. Zimmerman A, Evenhuis J, Thorgaard G, Ristow S. A single major chromosomal region controls natural killer cell-like activity in rainbow trout. Immunogenetics 2004, 55:825-835.
37. Perry GM, Danzmann RG, Ferguson MM, Gibson JP. Quantitative trait loci for upper thermal tolerance in outbred strains of rainbow trout (Oncorhynchus mykiss). Heredity 2001, 86:333-341.
38. Perry GM, Ferguson MM, Sakamoto T, Danzmann RG. Sex-linked quantitative trait loci for thermotolerance and length in the rainbow trout. J Hered 2005, 96:97-107.
39. Nichols KM, Broman KW, Sundin K, Young JM, Wheeler PA, Thorgaard GH. Quantitative trait loci × maternal cytoplasmic environment interaction for development rate in Oncorhynchus mykiss. Genetics 2007, 175:335-347. 1774986, 17057232.
40. Sundin K, Brown KH, Drew RE, Nichols KM, Wheeler PA, Thorgaard GH. Genetic analysis of a development rate QTL in backcrosses of clonal rainbow trout, Oncorhynchus mykiss. Aquaculture 2005, 247:75-83.
41. O'Malley KG, Sakamoto T, Danzmann RG, Ferguson MM. Quantitative trait Loci for spawning date and body weight in rainbow trout: testing for conserved effects across ancestrally duplicated chromosomes. J Hered 2003, 94:273-284.
42. Sakamoto T, Danzmann RG, Okamoto N, Ferguson MM, Ihssen PE. Linkage analysis of quantitative trait loci associated with spawning time in rainbow trout (Oncorhynchus mykiss). Aquaculture 1999, 173:33-43.
43. Drew RE, Schwabl H, Wheeler PA, Thorgaard GH. Detection of QTL influencing cortisol levels in rainbow trout (Oncorhynchus mykiss). Aquaculture 2007, 272:S183-S194.
44. Haidle L, Janssen J, Gharbi K, Moghadam H, Ferguson M, Danzmann R. Determination of Quantitative Trait Loci (QTL) for Early Maturation in Rainbow Trout (Oncorhynchus mykiss). Marine Biotechnology 2008, 10:579-592. 2516301, 18491191.
45. Nichols KM, Edo AF, Wheeler PA, Thorgaard GH. The Genetic Basis of Smoltification-Related Traits in Oncorhynchus mykiss. Genetics 2008, 179:1559-1575. 2475755, 18562654.
46. Johnson NA, Vallejo RL, Silverstein JT, Welch TJ, Wiens GD, Hallerman EM, Palti Y. Suggestive Association of Major Histocompatibility IB Genetic Markers with Resistance to Bacterial Cold Water Disease in Rainbow Trout (Oncorhynchus mykiss). Mar Biotechnol 2008, 10:429-437.
47. Katagiri T, Kidd C, Tomasino E, Davis JT, Wishon C, Stern JE, Carleton KL, Howe AE, Kocher TD. A BAC-based physical map of the Nile tilapia genome. BMC Genomics 2005, 6:89. 1180826, 15946383.
48. Quiniou S, Waldbieser G, Duke M. A first generation BAC-based physical map of the channel catfish genome. BMC Genomics 2007, 8:40. 1800894, 17284319.
49. Xu P, Wang S, Liu L, Thorsen J, Kucuktas H, Liu Z. A BAC-based physical map of the channel catfish genome. Genomics 2007, 90:380-388.
50. Luo M-C, Thomas C, You FM, Hsiao J, Ouyang S, Buell CR, Malandro M, McGuire PE, Anderson OD, Dvorak J. High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 2003, 82:378-389.
51. Nievergelt CM, Smith DW, Kohlenberg JB, Schork NJ. Large-Scale Integration of Human Genetic and Physical Maps. Genome Research 2004, 14:1199-1205. 419799, 15140834.
52. Nelson WM, Bharti AK, Butler E, Wei F, Fuks G, Kim H, Wing RA, Messing J, Soderlund C. Whole-Genome Validation of High-Information-Content Fingerprinting. Plant Physiol 2005, 139:27-38. 1203355, 16166258.
53. Frenkel Z, Paux E, Mester D, Feuillet C, Korol A. Improving The Efficiency Of Contig Assembly For Physical Mapping. Plant & Animal Genome XVII, the international conference on the status of plant and animal genome research 2009, W282.
54. Nelson W, Soderlund C. Integrating sequence with FPC fingerprint maps. Nucl Acids Res 2009, 37:e36. 2655663, 19181701.
55. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186-194.
56. Kim UJ, Birren BW, Slepak T, Mancino V, Boysen C, Kang HL, Simon MI, Shizuya H. Construction and characterization of a human bacterial artificial chromosome library. Genomics 1996, 34:213-218.
57. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999, 27:573-580. 148217, 9862982.
58. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-386.
59. Boutin-Ganache I, Raposo M, Raymond M, Deschepper CF. M13-tailed primers improve the readability and usability of microsatellite analyses performed with two different allele-sizing methods. Biotechniques 2001, 31:24-26.
60. Kongchum P, CE Rexroad I, Hallerman EM, David L, Palti Y. Single nucleotide polymorphism identification, genetic mapping and tissue expression of the rainbow trout TLR9 gene. Animal Genetics 2009,
61. Lathrop GM, Lalouel JM, Julier C, Ott J. Strategies for multilocus linkage analysis in humans. Proc Natl Acad Sci USA 1984, 81:3443-3446. 345524, 6587361.
62. O'Connell JR, Weeks DE. PedCheck: a program for identification of genotype incompatibilities in linkage analysis. Am J Hum Genet 1998, 63:259-266. 1377228, 9634505.
63. O'Connell JR, Weeks DE. The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance. Nat Genet 1995, 11:402-408.
64. LNKTOCRI++. , http://www.filewatcher.com/b/ftp/ftp.ebi.ac.uk/pub/software/linkage_and_ mapping/MULTIMA/lnktocri/C%2B%2B.0.0.html
65. Lander ES, Green P. Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci USA 1987, 84:2363-2367. 304651, 3470801.
66. Matise TC, Perlin M, Chakravarti A. Automated construction of genetic linkage maps using an expert system (MultiMap): a human genome linkage map. Nat Genet 1994, 6:384-390.