Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

Many important traits in plant and animal breeding are polygenic and therefore recalcitrant to traditional marker-assisted selection.  Genomic selection addresses this complexity by including all markers in the prediction model.  A key method for the genomic prediction of breeding values is ridge regression (RR), which is equivalent to BLUP when the genetic covariance between lines is proportional to their similarity in genotype space.  This additive model can be broadened to include epistatic effects by using other kernels, such as the Gaussian, which represent inner products in a complex feature space.  To facilitate the use of RR and non-additive kernels by breeders, a new software package for R called rrBLUP has been developed.  At its core is a fast maximum-likelihood algorithm for mixed models with a single variance component besides the residual error, which allows for efficient prediction with unreplicated training data.  Use of the rrBLUP software is demonstrated through several examples, including the identification of optimal crosses based on superior progeny value.  In cross-validation tests, the prediction accuracy with non-additive kernels was significantly higher than RR for wheat grain yield but equivalent for several maize traits.