Study of the Optimum Haplotype Length to Build Genomic Relationship Matrices

As genomic data becomes more abundant, genomic prediction is more routinely used to estimate breeding values. In genomic prediction, the relationship matrix (\({\mathbf{A}}\)), which is traditionally used in genetic evaluations is replaced by the genomic relationship matrix (\({\mathbf{G}}\)). This paper considers alternative ways of building relationship matrices either using single markers or haplotypes of different lengths. We compared the prediction accuracies and log-likelihoods when using these alternative relationship matrices and the traditional \({\mathbf{G}}\) matrix, for real and simulated data.