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Technical note: Derivation of equivalent computing algorithms for genomic predictions and reliabilities of animal merit

I. Strandén^*,1 and D. J. Garrick^,

^* MTT Agrifood Research Finland, FIN-31600 Jokioinen, Finland
Department of Animal Science, Iowa State University, Ames 50014
Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand

¹ Corresponding author: ismo.stranden{at}mtt.fi

Conventional prediction of dairy cattle merit involves setting up and solving linear equations with the number of unknowns being the number of animals, typically millions, multiplied by the number of traits being simultaneously assessed. The coefficient matrix has been large and sparse and iteration on data has been the method of choice, whereby the coefficient matrix is not stored but recreated as needed. In contrast, genomic prediction involves assessment of the merit of genome fragments characterized by single nucleotide polymorphism genotypes, currently some 50,000, which can then be used to predict the merit of individual animals according to the fragments they have inherited. The prediction equations for chromosome fragments typically have fewer than 100,000 unknowns, but the number of observations used to predict the fragment effects can be one-tenth the number of fragments. The coefficient matrix tends to be dense and the resulting system of equations can be ill behaved. Equivalent computing algorithms for genomic prediction were derived. The number of unknowns in the equivalent system grows with number of genotyped animals, usually bulls, rather than the number of chromosome fragment effects. In circumstances with fewer genotyped animals than single nucleotide polymorphism genotypes, these equivalent computations allow the solving of a smaller system of equations that behaves numerically better. There were 3 solving strategies compared: 1 method that formed and stored the coefficient matrix in memory and 2 methods that iterate on data. Finally, formulas for reliabilities of genomic predictions of merit were developed.

Key Words: breeding value • computing method • dairy cattle • equivalent model