A note on mate allocation for dominance handling in genomic selection

Miguel A Toro,Luis Varona

doi:10.1186/1297-9686-42-33

Abstract

Estimation of non-additive genetic effects in animal breeding is important because it increases the accuracy of breeding value prediction and the value of mate allocation procedures. With the advent of genomic selection these ideas should be revisited. The objective of this study was to quantify the efficiency of including dominance effects and practising mating allocation under a whole-genome evaluation scenario. Four strategies of selection, carried out during five generations, were compared by simulation techniques. In the first scenario (MS), individuals were selected based on their own phenotypic information. In the second (GSA), they were selected based on the prediction generated by the Bayes A method of whole-genome evaluation under an additive model. In the third (GSD), the model was expanded to include dominance effects. These three scenarios used random mating to construct future generations, whereas in the fourth one (GSD + MA), matings were optimized by simulated annealing. The advantage of GSD over GSA ranges from 9 to 14% of the expected response and, in addition, using mate allocation (GSD + MA) provides an additional response ranging from 6% to 22%. However, mate selection can improve the expected genetic response over random mating only in the first generation of selection. Furthermore, the efficiency of genomic selection is eroded after a few generations of selection, thus, a continued collection of phenotypic data and re-evaluation will be required.

Highlights

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
Response after random mating In order to gain some insight in this loss of efficiency observed in Figures 2 and 3, we studied the response when Genomic selection with dominance (GSD) and GSD + MA are carried out after 0, 1, 2 and 3 previous generations with random mating and no selection in order to evaluate the consequences of reduction of linkage disequilibrium between SNP and QTL in a no selection scenario
Introduction of dominance effects in genetic evaluation is easier to achieve in the whole-genome evaluation scenario than in the classical polygenic model, where potential parental combinations have to be defined and evaluated

Summary

Introduction

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, 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]. Dominance effects have rarely been included in genetic evaluations. It has been claimed that there is little evidence of non-additive genetic variance in the literature (see for example [3]).

Objectives

Methods

Results

Conclusion