A note on mate allocation for dominance handling in genomic selection

Estimation of non-additive genetic effects in animal breeding is important because ignoring these effects will produce less accurate estimates of breeding values and will have an effect on ranking breeding values. As a consequence, including these effects will produce a more accurate prediction and, therefore, more genetic response. This potential increase of genetic response is about 10% for traits with a low heritability, high proportion of dominance variance, low selection intensity and high percentage (>20%) of full-sibs [1].However, dominance effects have rarely been included in genetic evaluations. The reasons, that can be argued, are the greater computational complexity and the inaccuracy in the estimation of variance components (it is commonly believed that 20 to 100 times more data are required including a high proportion of full-sibs [2]). It has also been claimed that there is little evidence of non-additive genetic variance in the literature (see for example [3]). However, although estimates are scarce, dominance variance usually amounts to about 10% of the phenotypic variance [4]. Furthermore, in an extensive review [5], estimates of the ratio of additive to dominance variance have been reported in wild species i.e. about 1.17 for life-history traits, 1.06 for physiological traits and 0.19 for morphological traits. In the same study, the estimate of this ratio for domestic species was 0.80.Moreover, mating plans (or mating allocations) have been used in animal breeding for several reasons: a) to control inbreeding; b) in situations where economic merit is not linear; c) when there is an intermediate optimum (or restricted traits); d) to increase connection among herds and, finally, e) to profit from dominance genetic effects. With respect to the last point, it is well known that every methodology pretending to use non-additive effects [6-8] must contemplate two types of mating: a) matings from which the population will be propagated; b) matings to obtai