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This article is part of the supplement: Proceedings of the 14th European workshop on QTL mapping and marker assisted selection (QTL-MAS)

Open Access Proceedings

Pre-selection of markers for genomic selection

Torben Schulz-Streeck, Joseph O Ogutu and Hans-Peter Piepho*

Author Affiliations

Bioinformatics Unit, Institute of Crop Science, University of Hohenheim, Fruwirthstrasse 23, 70599 Stuttgart, Germany

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BMC Proceedings 2011, 5(Suppl 3):S12  doi:10.1186/1753-6561-5-S3-S12

Published: 27 May 2011

Abstract

Background

Accurate prediction of genomic breeding values (GEBVs) requires numerous markers. However, predictive accuracy can be enhanced by excluding markers with no effects or with inconsistent effects among crosses that can adversely affect the prediction of GEBVs.

Methods

We present three different approaches for pre-selecting markers prior to predicting GEBVs using four different BLUP methods, including ridge regression and three spatial models. Performances of the models were evaluated using 5-fold cross-validation.

Results and conclusions

Ridge regression and the spatial models gave essentially similar fits. Pre-selecting markers was evidently beneficial since excluding markers with inconsistent effects among crosses increased the correlation between GEBVs and true breeding values of the non-phenotyped individuals from 0.607 (using all markers) to 0.625 (using pre-selected markers). Moreover, extension of the ridge regression model to allow for heterogeneous variances between the most significant subset and the complementary subset of pre-selected markers increased predictive accuracy (from 0.625 to 0.648) for the simulated dataset for the QTL-MAS 2010 workshop.