title: Modeling Epistasis in Genomic Selection.
abstract: Modeling epistasis in genomic selection is impeded by a high computational load. The extended genomic best linear unbiased prediction (EG-BLUP) with an epistatic relationship matrix and the reproducing kernel Hilbert space regression (RKHS) are two attractive approaches that reduce the computational load. In this study, we proved the equivalence of EG-BLUP and genomic selection approaches, explicitly modeling epistatic effects. Moreover, we have shown why the RKHS model based on a Gaussian kernel captures epistatic effects among markers. Using experimental data sets in wheat and maize, we compared different genomic selection approaches and concluded that prediction accuracy can be improved by modeling epistasis for selfing species but may not for outcrossing species.
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Stadt Seeland, Germany.
authors.forename: Yong
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Stadt Seeland, Germany reif@ipk-gatersleben.de.
authors.forename: Jochen C
authors.initials: JC
authors.lastname: Reif
mesh_terms: D001947:Breeding; D004843:Epistasis, Genetic; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics; D008957:Models, Genetic; D008962:Models, Theoretical; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D014908:Triticum / Q000235:genetics; D003313:Zea mays / Q000235:genetics
keywords: GenPred; epistasis; extended G-BLUP (EG-BLUP); genomic best linear unbiased prediction (G-BLUP); genomic selection; reproducing kernel Hilbert space regression (RKHS); shared data resource