Evaluation of an Atlantic salmon SNP chip as a genomic tool for the application in a Tasmanian Atlantic salmon (Salmo salar) breeding population

Aquaculture

Volumn 308, Issue SUPPL.1, 2010, Pages

  Dominik, Sonja ^a   Henshall, John M ^a   Kube, Peter D ^a   King, Harry ^b   Lien, Sigbjorn ^c   Kent, Matthew P ^c   Elliott, Nicolas G ^a  

^a CSIRO   (Australia)

^b Salmon Entpr of Tasmania Pty Ltd   (Australia)

^c NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

Author keywords

Amoebic gill disease; Linkage disequilibrium; Salmo salar; Single nucleotide polymorphism

Indexed keywords

BIOASSAY; BREEDING POPULATION; DISEASE INCIDENCE; GENETIC ANALYSIS; GENOME; GENOTYPE; SALMONID;

SALMO SALAR;

EID: 77957367388     PISSN: 00448486     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.aquaculture.2010.05.038     Document Type: Article

References (30)

1. ABARE Australian Fisheries Statistics 2007. Australian Bureau of Agriculture and Resource Economics 2008, Canberra, Australia, http://www.abareconomics.com/publications_html/fisheries/fisheries_08/08_fishstats.pdf (last accessed February 2010).
2. Calus M.P.L., Meuwissen T.H.E., de Roos A.P.W., Veerkamp R.F. Accuracy of genomic selection using different methods to define haplotypes. Genetics 2008, 178:553-561.
3. Dekkers J.C.M., Van der Werf J.H.J. Marker-assisted selection - current status and future perspectives in crops, livestock, forestry and aquaculture. Section III marker-assisted selection in livestock - case studies. Chapter 10: Strategies, limitations, and opportunities for marker-assisted selection in livestock 2007, FAO, Rome. E.P. Guimarães, J. Ruane, B.D. Scherf, A. Sonnino, J.D. Dargie (Eds.).
4. Dominik S., Henshall J.M., Kube P., King H., Lien S., Kent M., Elliott N. Assessment of the level of heterozygosity in the Tasmanian Atlantic salmon (Salmo salar) population using single nucleotide polymorphism markers. 18th Proceedings of the Association for Advancement in Animal Breeding Genetics, 27 September-2 October, 2009 2009, Barossa Valley, SA, Australia, http://www.aaabg.org/proceedings18/files/dominik354.pdf (last accessed February 2010).
5. Dominik S., Hunt P.W., McNally J., Murrell A., Hall A., Purvis I.W. Detection of quantitative trait loci for internal parasite resistance in sheep. I. Linkage analysis in a Romney x Merino sheep backcross population. Parasitology 2010, 137(8):1275-1282.
6. Elliott N.G., Kube P.D. Development and early results of the Tasmanian Atlantic salmon breeding program. 18th Proceedings of the Association for Advancement in Animal Breeding Genetics, 27 September-2 October, 2009 2009, Barossa Valley, South Australia, Australia, www.aaabg.org/proceedings18/files/elliott362.pdf (last accessed February 2010).
7. Falconer D.S., Mackay T.F.C. Genetic constitution of a population, Hardy-Weinberg Equilibrium. Introduction to Quantitative Genetics 1996, 5-18. Addison Wesley Longman Limited, Essex, England. 4th edition.
8. Fredman D., White S.J., Potter S., Eichler S.E., Den Dunnen J.T., Brookes A.J. Complex SNP-related sequence variation in segmental genome duplications. Nat. Genet. 2004, 36:861-866.
9. Genome British Columbia Genome BC collaborates with Chile and Norway to sequence salmon genome. Press release, December 7, 2009 (last accessed February 2010). http://www.genomebc.ca/whatnew_press/press_releases/2009_press/120709_salmon.htm.
10. Haley C.S., Knott S.A. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 1992, 69:315-324.
11. Hartley S.E., Horne M.T. Chromosome polymorphism and constitutive heterochromatin in the Atlantic salmon, Salmo salar. Chromosoma 1984, 89:377-380.
12. Hayes B.J. Whole genome association and selection methods. Workshop Notes, Armidale Summer Breeding Course, 2008 2008, Armidale, NSW, Australia, http://www-personal.une.edu.au/~jvanderw/aabc_materials2008.htm (last accessed February 2010).
13. Hayes B.J., Bowman P.J., Chamberlain A.J., Goddard M.E. Invited review: genomic selection in dairy cattle: progress and challenges. J. Dairy Sci. 2009, 92:433-443.
14. Huang Q. EM estimation of haplotype frequencies and LD calculations (last accessed February 2010). http://epi.mdanderson.org/~qhuang/Software/EMLD/.
15. Illumina Infinium Multi Sample Assay - Assay Guide 11230143 Rev A 2006.
16. Illumina Illumina Beadstudio Genotyping Module Userguide 2007, Doc#1120766 Rev C, February 2007.
17. Illumina Infinium Genotyping Data Analysis. Technical Note: Illumina DNA Analysis 2010, Publication Number 970-2007-005, January 2010.
18. Innes B.H., Elliott N.G. Genetic diversity in a Tasmanian hatchery population of Atlantic salmon (Salmo salar L.) compared with its Canadian progenitor population. Aquacult. Res. 2006, 37:563-569.
19. Kent M.P., Hayes B., Xiang Q., Berg P.R., Gibbs R.A., Lien S. Development of 16.5K SNP chip for Atlantic Salmon. Proceedings of the 17th Plant and Animal Genome Conference, January 10-14, 2009 2009, San Diego, CA. http://www.intl-pag.org/ (last accessed February 2010).
20. McCaskie P.A., Carter K.W., McCaskie S.R., Paler L.J. The effect of missing data on linkage disequilibrium mapping and haplotype association analysis in the GAW14 simulated datasets. BMC Genet. 2005, 6(Supp 1):S151-S156.
21. Meuwissen T.H.E., Hayes B.J., Goddard M.E. Prediction of total genetic value using genome-wide dense marker maps. Genetics 2001, 157:1819-1829.
22. Nielsen H.M., Sonesson A.K., Yazdi H., Meuwissen T.H.E. Comparison of accuracy of genome-wide and BLUP breeding value estimates in sib based aquaculture breeding schemes. Aquaculture 2009, 289:259-264.
23. Oliphant A., Barker D.L., Stuelpnagel J.R., Chee M.S. BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques 2002, 32:S56-S61.
24. Phillips R.B., Keatley K.A., Morasch M.R., Ventura A.B., Lubienniecki K.P., Koop B.F., Danzmann R.G., Davidson W.S. Assignment of Atlantic salmon (Salmo salar) linkage groups to specific chromosomes: Conversation of large syntenic blocks corresponding to whole chromsome arms in rainbow trout (Oncorhynchus mykiss). BMC Genetics 2009, 10:46-57.
25. Purcell S. PLINK 1.04 (last accessed February 2010). http://pngu.mgh.harvard.edu/purcell/plink/.
26. Schaeffer L.R. Strategy for applying genome-wide selection in dairy cattle. J. Anim. Breed. Genet. 2006, 123:218-223.
27. Sonesson A.K., Meuwissen T.H.E. Testing strategies for genomic selection in aquaculture breeding programs. Genet. Select. Evol. 2009, 41:37.
28. Spelman R.J., Huisman A.E., Singireddy S.R., Coppieters W., ARranz J., Georges M., Garrick D.J. Short communication: quantitative trait loci analysis on 17 nonproduction traits in the New Zealand dairy population. J. Dairy Sci. 1999, 82:2514-2516.
29. Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls. Nature 2007, 447:661-678.
30. Wigginton J.E., Cutler D.J., Abacasis G.R. A note on exact tests of Hardy-Weinberg equilibrium. Am. J. Hum. Genet. 2005, 76:887-893.