title: Pre-selection of markers for genomic selection.
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.
  
  
  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.
authors.affiliation: Bioinformatics Unit, Institute of Crop Science, University of Hohenheim, Fruwirthstrasse 23, 70599 Stuttgart, Germany. piepho@uni-hohenheim.de.
authors.forename: Torben
authors.initials: T
authors.lastname: Schulz-Streeck
authors.forename: Joseph O
authors.initials: JO
authors.lastname: Ogutu
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Piepho