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|Title:||Different models of genetic variation and their effect on genomic evaluation||Contributor(s):||Clark, Sam A (author) ; Hickey, John (author); Van Der Werf, Julius H (author)||Publication Date:||2011||Open Access:||Yes||DOI:||10.1186/1297-9686-43-18||Handle Link:||https://hdl.handle.net/1959.11/10098||Abstract:||Background: The theory of genomic selection is based on the prediction of the effects of quantitative trait loci (QTL) in linkage disequilibrium (LD) with markers. However, there is increasing evidence that genomic selection also relies on "relationships" between individuals to accurately predict genetic values. Therefore, a better understanding of what genomic selection actually predicts is relevant so that appropriate methods of analysis are used in genomic evaluations. Methods: Simulation was used to compare the performance of estimates of breeding values based on pedigree relationships (Best Linear Unbiased Prediction, BLUP), genomic relationships (gBLUP), and based on a Bayesian variable selection model (Bayes B) to estimate breeding values under a range of different underlying models of genetic variation. The effects of different marker densities and varying animal relationships were also examined. Results: This study shows that genomic selection methods can predict a proportion of the additive genetic value when genetic variation is controlled by common quantitative trait loci (QTL model), rare loci (rare variant model), all loci (infinitesimal model) and a random association (a polygenic model). The Bayes B method was able to estimate breeding values more accurately than gBLUP under the QTL and rare variant models, for the alternative marker densities and reference populations. The Bayes B and gBLUP methods had similar accuracies under the infinitesimal model. Conclusions: Our results suggest that Bayes B is superior to gBLUP to estimate breeding values from genomic data. The underlying model of genetic variation greatly affects the predictive ability of genomic selection methods, and the superiority of Bayes B over gBLUP is highly dependent on the presence of large QTL effects. The use of SNP sequence data will outperform the less dense marker panels. However, the size and distribution of QTL effects and the size of reference populations still greatly influence the effectiveness of using sequence data for genomic prediction.||Publication Type:||Journal Article||Source of Publication:||Genetics Selection Evolution, 43(May), p. 1-9||Publisher:||BioMed Central Ltd||Place of Publication:||London, United Kingdom||ISSN:||1297-9686
|Field of Research (FOR):||060408 Genomics||Peer Reviewed:||Yes||HERDC Category Description:||C1 Refereed Article in a Scholarly Journal||Statistics to Oct 2018:||Visitors: 161
|Appears in Collections:||Journal Article|
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