Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 408155
Title The Impact of Genetic Architecture on Genome-Wide Evaluation Methods
Author(s) Daetwyler, H.D.; Pong-Wong, R.; Villanueva, B.; Woolliams, J.A.
Source Genetics 185 (2010)3. - ISSN 0016-6731 - p. 1021 - 1031.
Department(s) Animal Breeding and Genetics
Publication type Refereed Article in a scientific journal
Publication year 2010
Keyword(s) breeding values - linkage disequilibrium - selection - prediction - accuracy - information - algorithm - variance - models - lasso
Abstract The rapid increase in high-throughput single-nucleotide polymorphism data has led to a great interest in applying genome-wide evaluation methods to identify an individual's genetic merit. Genome-wide evaluation combines statistical methods with genomic data to predict genetic values for complex traits. Considerable uncertainty currently exists in determining which genome-wide evaluation method is the most appropriate. We hypothesize that genome-wide methods deal differently with the genetic architecture of quantitative traits and genomes. A genomic linear method (GBLUP), and a genomic nonlinear Bayesian variable selection method (BayesB) are compared using stochastic simulation across three effective population sizes and a wide range of numbers of quantitative trait loci (N-QTL). GBLUP had a constant accuracy, for a given heritability and sample size, regardless of NQTL. BayesB had a higher accuracy than GBLUP when N-QTL was low, but this advantage diminished as N-QTL increased and when N-QTL became large, GBLUP slightly outperformed BayesB. In addition, deterministic equations are extended to predict the accuracy of both methods and to estimate the number of independent chromosome segments (Me) and N-QTL. The predictions of accuracy and estimates of Me and N-QTL were generally in good agreement with results from simulated data. We conclude that the relative accuracy of GBLUP and BayesB for a given number of records and heritability are highly dependent on Me, which is a property of the target genome, as well as the architecture of the trait (N-QTL).
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