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EXTENT OF LINKAGE DISEQUILIBRIUM, CONSISTENCY OF GAMETIC PHASE AND IMPUTATION ACCURACY WITHIN AND ACROSS CANADIAN DAIRY BREEDS

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dc.contributor.author Larmer, Steven
dc.date.accessioned 2012-08-09T15:01:29Z
dc.date.available 2012-08-09T15:01:29Z
dc.date.copyright 2012-08
dc.date.created 2012-07-19
dc.date.issued 2012-08-09
dc.identifier.uri http://hdl.handle.net/10214/3843
dc.description.abstract Some dairy breeds have too few animals genotyped for within breed genomic selection to be carried out with sufficient accuracy. As such, the level of linkage disequilibrium within each breed as well as consistency of gametic phase across breeds was studied. High correlations of phase (>0.9) were found between all breed pairs at this same SNP density. The efficacy of imputing animals genotyped on lower density (6k and 50k) panels was then explored in order to increase the size of the reference population with 777k genotypes in a cost-effective manner. These results showed high accuracies (>0.92) in all imputation scenarios studies, using both a within breed and a multi-breed reference population for imputation. It was concluded that given the results of both of these studies, pooling breeds into a common reference population for genomic selection should be a viable option for accurate genomic selection in breeds with few genotyped individuals. en_US
dc.description.sponsorship NSERC, USDA, CDN, DairyGen, Ayrshire Canada, Guernsey Canada, Semex, L'Alliance Boviteq Inc. en_US
dc.language.iso en en_US
dc.subject Dairy en_US
dc.subject Genetics en_US
dc.subject Genomics en_US
dc.subject Linkage Disequilibrium en_US
dc.subject Gametic Phase en_US
dc.subject Breeds en_US
dc.subject Imputation en_US
dc.subject Accuracy en_US
dc.subject Imputation Accuracy en_US
dc.subject FImpute en_US
dc.subject Beagle en_US
dc.subject Across Breeds en_US
dc.subject Phase Consistency en_US
dc.title EXTENT OF LINKAGE DISEQUILIBRIUM, CONSISTENCY OF GAMETIC PHASE AND IMPUTATION ACCURACY WITHIN AND ACROSS CANADIAN DAIRY BREEDS en_US
dc.type Thesis en_US
dc.degree.programme Animal and Poultry Science en_US
dc.degree.name Master of Science en_US
dc.degree.department Department of Animal and Poultry Science en_US
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