Single-step genomic BLUP with genetic groups and automatic adjustment for allele coding

Background Genomic estimated breeding values (GEBV) by single-step genomic BLUP (ssGBLUP) are affected by the centering of marker information used. The use of a fixed effect called J factor will lead to GEBV that are unaffected by the centering used. We extended the use of a single J factor to a group of J factors. Results J factor(s) are usually included in mixed model equations (MME) as regression effects but a transformation similar to that regularly used for genetic groups can be applied to obtain a simpler MME, which is sparser than the original MME and does not need computation of the J factors. When the J factor is based on the same structure as the genetic groups, then MME can be transformed such that coefficients for the genetic groups no longer include information from the genomic relationship matrix. We illustrate the use of J factors in the analysis of a Red dairy cattle data set for fertility. Conclusions The GEBV from these analyses confirmed the theoretical derivations that show that the resulting GEBV are allele coding independent when a J factor is used. Transformed MME led to faster computing time than the original regression-based MME.