Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE)

Abstract

Based on our results, for EGBLUP, a symmetric coding {-1,1} or {-1,0,1} should be preferred, whereas a standardization using allele frequencies should be avoided. Moreover, CE can be a valuable alternative since it does not possess the undesired theoretical properties of EGBLUP. However, which model performs best will depend on characteristics of the data and available prior information. Data from previous experiments can for instance be incorporated into the marker coding of EGBLUP.