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

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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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Title: EXTENT OF LINKAGE DISEQUILIBRIUM, CONSISTENCY OF GAMETIC PHASE AND IMPUTATION ACCURACY WITHIN AND ACROSS CANADIAN DAIRY BREEDS
Author: Larmer, Steven
Department: Department of Animal and Poultry Science
Program: Animal and Poultry Science
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.
URI: http://hdl.handle.net/10214/3843
Date: 2012-08-09


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