Breeding value prediction with maternal genetic groups.

Abstract

For models with only additive direct genetic effects, the rules of Westell combined with the Q-P transformation can be used to calculate the coefficients of mixed-model equations corresponding to the inverse elements of the numerator relationship matrix and group effects that are used to account for selection on ancestors that do not have records. Groups generally can be assigned on the basis of most recent ancestors without records. When maternal effects are in the model, most recent female ancestors without records contribute maternal effects to their progeny. If the vectors for additive direct and maternal effects do not include the same animals, numerator relationship matrices for direct and maternal effects and between direct and maternal effects are different. Even if they are the same, the Q-P transformation and Westell's rules do not lead to simplification for calculation of the coefficient matrix unless group assignment is the same for direct and maternal effects. This result can be achieved by including each female ancestor with offspring having records in both vectors and by assigning both of her parents to the same group she would have been assigned for a model including only direct effects. This strategy is equivalent to assigning group effects similarly for both direct and maternal effects and allows making use of the computational efficiency available from the Q-P transformation and Westell's rules, which are similar to Henderson's rules for calculating the inverse of the numerator relationship matrix.