Two ways of breeding value estimation using genotype information have been implemented in MiXBLUP. The use of genotype information allows for the estimation of reliable breeding values, even at a young age or well before any traits are measured on the animal itself or its progeny. MiXBLUP is a software package jointly developed by MTT in Finland and Animal Breeding & Genomics Centre of Wageningen UR.
The first method implemented calculates genetic relationships between animals directly from genotype information instead of using pedigree relationships (G-BLUP). Specific built-in software (calc_grm) developed by scientist Mario Calus of Wageningen UR Livestock Research allows for the inclusion of genotyped as well as non-genotyped animals in the analysis. Unfortunately this method becomes rapidly demanding in terms of processing time and computer memory if the number of animals with genotype information increases.
The second method shows more perspective but only allows the inclusion of genotyped animals. It estimates breeding values from random regression on the number of copies of a SNP allele for each locus (SNP-BLUP). With this method processing time increases only linearly with the number of animals genotyped. Although preferred, since genotyped animals are still scarce in practice this method is not widely used yet.
The incorporation of genomic evaluations in MiXBLUP was financially supported by TOPIGS and Hendrix Genetics in the context of the Breed4food research programme. Therefore, they have the privilege to use the new functionality exclusively until it is implemented in the commercial version of MixBlUP.