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Genomic-enabled prediction based on molecular markers and pedigree using the Bayesian linear regression package in R

By: Contributor(s): Material type: ArticleArticleLanguage: English Publication details: Madison, WI (USA) : CSSA : Wiley, 2010.ISSN:
  • 0011-183X
  • 1940-3372 (Online)
Subject(s): Online resources: In: Plant Genome v. 3, no. 2, p. 106-116Summary: 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 hyperparameters, are also addressed.
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Item type Current library Collection Call number Status Date due Barcode Item holds
Article CIMMYT Knowledge Center: John Woolston Library CIMMYT Staff Publications Collection CIS-6069 (Browse shelf(Opens below)) Available
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Peer-review: Yes - Open Access: Yes|http://science.thomsonreuters.com/cgi-bin/jrnlst/jlresults.cgi?PC=MASTER&ISSN=1940-3372

Peer review

Open Access

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 hyperparameters, are also addressed.

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Text in English

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CIMMYT Staff Publications Collection

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