Breed4Food companies Cobb, Hendrix Genetics, and Topigs Norsvin use the so-called single-step genomic Best Linear Unbiased Prediction (ssGBLUP) to predict genomic breeding values. This method uses a combination of the genomic and pedigree relationships to estimate genomic breeding values. Current research at Wageningen University & Research, Animal Breeding and Genomics focuses on the feasibility of the ssGBLUP in the context of crossbreeding schemes, and on the development of tools for its routine implementation.
The ssGBLUP jointly uses genotypes, pedigree and phenotypes in one analysis to predict breeding values for all genotyped and non-genotyped animals. Therefore, ssGBLUP is more generalizable than the multi-step approaches, and also avoids many issues of multi-step approaches.
The genomic and pedigree relationship matrices which are used to account for relationships among animals, are also the origin of two main issues. First, ssGBLUP could become infeasible with more than 150,000 genotyped animals. The computation of the inverse of the genomic relationship matrix requires large amounts of memory and time. Second, the combination of genomic and pedigree relationship matrices requires that they are compatible. This compatibility is not straightforward, especially when genotyped purebred and crossbred animals are involved in the same genomic evaluation.
Within the research program “Bright ideas for innovations in animal breeding”, researchers at WUR Animal Breeding and Genomics aimed to tackle both issues. Solutions they are working on, are the implementation of an algorithm for a fast and efficient inversion of the genomic relationship matrix (APY), and the recent concept of metafounders in the software calc_grm for routine implementations.
Implementation and testing
Currently, the APY and use of metafounders are implemented in the software calc_grm. They are under testing and already available to the Breed4Food partners. The implementation is performed in collaboration with the development of the software for genetic and genomic evaluations, MiXBLUP2.0.
Results showed that APY achieved similar accuracies as the full genomic relationship matrix. The method of metafounders allowed to adjust the pedigree relationships to be compatible with genomic relationships. The Breed4Food partners are jointly testing the tools on field datasets similar to those used for their routine evaluations and exchanging their experiences.
Do you want more information about this research project? Please contact Jérémie Vandenplas.