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Plant Genome. 2010;3(2):106-116.

Genomic-Enabled Prediction Based on Molecular Markers and Pedigree Using the Bayesian Linear Regression Package in R.

Author information

1
P. Pérez, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México, and Colegio de Postgraduados, Km. 36.5 Carretera México, Texcoco, Montecillo, Estado de México, 56230, México; G. de los Campos, Section on Statistical Genetics, Biostatistics, Univ. of Alabama at Birmingham, 1665 University Blvd., Ryals Public Health Building 414, Birmingham, AL 35294; J. Crossa, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México D.F., México; D. Gianola, Univ. of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706.

Abstract

The availability of dense molecular markers has made possible the use of genomic selection in plant and animal breeding. However, models for genomic selection pose several computational and statistical challenges and require specialized computer programs, not always available to the end user and not implemented in standard statistical software yet. The R-package BLR (Bayesian Linear Regression) implements several statistical procedures (e.g., Bayesian Ridge Regression, Bayesian LASSO) in a unifi ed framework that allows including marker genotypes and pedigree data jointly. This article describes the classes of models implemented in the BLR package and illustrates their use through examples. Some challenges faced when applying genomic-enabled selection, such as model choice, evaluation of predictive ability through cross-validation, and choice of hyper-parameters, are also addressed.

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