BAC-based upgrading and physical integration of a genetic SNP map in Atlantic salmon

Animal Genetics

Volumn 41, Issue 1, 2010, Pages 48-54

  Lorenz, S ^a   Brenna Hansen, S ^a   Moen, T ^a,b   Roseth, A ^a   Davidson, W S ^c   Omholt, S W ^a   Lien, S ^a  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b Norwegian University of Life Science ^*  (Norway)

^c SIMON FRASER UNIVERSITY   (Canada)

Author keywords

Atlantic salmon; Bacterial artificial chromosome; Physical integration; Single nucleotide polymorphism

Indexed keywords

ANIMAL; ARTICLE; ATLANTIC SALMON; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME MAP; EXPRESSED SEQUENCE TAG; FEMALE; GENETICS; MALE; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; EXPRESSED SEQUENCE TAGS; FEMALE; MALE; PHYSICAL CHROMOSOME MAPPING; POLYMORPHISM, SINGLE NUCLEOTIDE; SALMO SALAR;

BACTERIA (MICROORGANISMS); SALMO SALAR;

EID: 73849088359     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2009.01963.x     Document Type: Article

References (25)

1. Allendorf F.W. Thorgaard G.H. (1984) Evolutionary Genetics of Fishes, pp. 1 46. Plenum Press, New York.
2. de Boer J.G., Yazawa R., Davidson W.S. Koop B.F. (2007) Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids. BMC Genomics 8, 422.
3. Chowdhary B.P. Raudsepp T. (2008) The horse genome derby: racing from map to whole genome sequence. Chromosome Research 16, 109 127.
4. Danzmann R.G., Davidson E.A., Ferguson M.M. et al. (2008) Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (rainbow trout and Atlantic salmon). BMC Genomics 9, 557.
5. Emara M.G. Kim H. (2003) Genetic markers and their application in poultry breeding. Poultry Science 82, 952 957.
6. Fredman D., White S.J., Potter S., Eichler E.E., Den Dunnen J.T. Brookes A.J. (2004) Complex SNP-related sequence variation in segmental genome duplications. Nature Genetics 36, 861 866.
7. Gilbey J., Verspoor E., McLay A. Houlihan D. (2004) A microsatellite linkage map for Atlantic salmon (Salmo salar). Animal Genetics 35, 98 105.
8. Green P., Falls K. Crooks S. (1990) Documentation for crimap Version 2.4. Washington University School of Medicine, St Louis, MO.
9. Hayes B., Laerdahl J.K., Lien S., Moen T., Berg P., Hindar K., Davidson W.S., Koop B.F., Azuhubei A. Høyheim B. (2007) An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences. Aquaculture 265, 82 90.
10. Jorde L.B. (1995) Linkage disequilibrium as a gene-mapping tool. American Journal of Human Genetics 56, 11 4.
11. Jorde L.B. (2000) Linkage disequilibrium and the search for complex disease genes. Genome Research 10, 1435 1444.
12. Koop B.F., von Schalburg K.R., Leong J. et al. (2008) A salmonid EST genomic study: genes, puplications, phylogeny and microarrays. BMC Genomics 9, 545.
13. Leegwater P.A., van Hagen M.A. van Oost B.A. (2007) Localization of white spotting locus in Boxer dogs on CFA20 by genome-wide linkage analysis with 1500 SNPs. Journal of Heredity 98, 549 552.
14. Moen T., Hoyheim B., Munck H. Gomez-Raya L. (2004) A linkage map of Atlantic salmon (Salmo salar) reveals an uncommonly large difference in recombination rate between the sexes. Animal Genetics 35, 81 92.
15. Moen T., Hayes B., Baranski M., Berg P.R., Kjoglum S., Koop B.F., Davidson W.S., Omholt S.W. Lien S. (2008) A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics 9, 223.
16. Ng S.H.S., Artieri C.G., Bosdet I.E. et al. (2005a) A physical map of the genome of Atlantic salmon, Salmo salar. Genomics 86, 396 404.
17. Ng S.H.S., Chang A., Brown G.D., Koop B.F. Davidson W.S. (2005b) Type I microsatellite markers from Atlantic salmon (Salmo salar) expressed sequence tags. Molecular Ecology Notes 5, 762 766.
18. Quinn N.L., Levenkova N., Chow W. et al. (2008) Assessing the feasibility of GS FLX pyrosequencing for sequencing the Atlantic salmon genome. BMC Genomics 9, 404.
19. Rafalski A. (2002) Applications of single nucleotide polymorphisms in crop genetics. Current Opinion in Plant Biology 5, 94 100.
20. Sachidanandam R., Weissman D., Schmidt S.C. et al. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928 933.
21. Sherratt D.J. (1995) Mobile Genetic Elements. Oxford University Press, Oxford, UK.
22. Tang K., Fu D.J., Julien D., Braun A., Cantor C.R. Koster H. (1999) Chip-based genotyping by mass spectrometry. Proceedings of the National Academy of Sciences USA 96, 10016 10020.
23. Thorsen J., Zhu B., Frengen E., Osoegawa K., de Jong P.J., Koop B.F., Davidson W.S. Hoyheim B. (2005) A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects. BMC Genomics 6, 50.
24. Van Tassell C.P., Smith T.P.L., Matukumalli L.K., Taylor J.F., Schnabel R.D., Lawley C.T., Haudenschild C.D., Moore S.S., Warren W.C. Sonstegard T.S. (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods 5, 247 250.
25. Zhao Z., Fu Y.X., Hewett-Emmett D. Boerwinkle E. (2003) Investigating single nucleotide polymorphism (SNP) density in the human genome and its implications for molecular evolution. Gene 312, 207 213.