Whole-Genome Regression and Prediction Methods Applied to Plant and Animal Breeding
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An overview of available methods for implementing parametric WGR models is provided, selected topics that emerge in applications are discussed, and a general discussion of lessons learned from simulation and empirical data analysis in the last decade are presented.Abstract:
Genomic-enabled prediction is becoming increasingly important in animal and plant breeding and is also receiving attention in human genetics. Deriving accurate predictions of complex traits requires implementing whole-genome regression (WGR) models where phenotypes are regressed on thousands of markers concurrently. Methods exist that allow implementing these large-p with small-n regressions, and genome-enabled selection (GS) is being implemented in several plant and animal breeding programs. The list of available methods is long, and the relationships between them have not been fully addressed. In this article we provide an overview of available methods for implementing parametric WGR models, discuss selected topics that emerge in applications, and present a general discussion of lessons learned from simulation and empirical data analysis in the last decade.read more
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References
More filters
Journal ArticleDOI
Maximum likelihood from incomplete data via the EM algorithm
Journal ArticleDOI
Regression Shrinkage and Selection via the Lasso
TL;DR: A new method for estimation in linear models called the lasso, which minimizes the residual sum of squares subject to the sum of the absolute value of the coefficients being less than a constant, is proposed.
Book
The Elements of Statistical Learning: Data Mining, Inference, and Prediction
TL;DR: In this paper, the authors describe the important ideas in these areas in a common conceptual framework, and the emphasis is on concepts rather than mathematics, with a liberal use of color graphics.
Journal ArticleDOI
Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images
Stuart Geman,Donald Geman +1 more
TL;DR: The analogy between images and statistical mechanics systems is made and the analogous operation under the posterior distribution yields the maximum a posteriori (MAP) estimate of the image given the degraded observations, creating a highly parallel ``relaxation'' algorithm for MAP estimation.