Exploring major gene-marker phase-typing strategies in marker-assisted selection schemes

Major gene-marker phase is generally assumed to be family specific. This has the consequence in relation to marker-assisted selection (MAS) that phase information about each family may need to be collected through progeny testing, which could represent a substantial cost. This paper examines the effect of different policies in relation to major gene-marker phase-typing on response to MAS. The different policies considered varied in the criteria by which individuals were selected for phasetyping, the number of individuals phase-typed, and the frequency of establishing phase. Stochastic simulation of a closed breeding nucleus, with either high or low levels of inbreeding and undergoing selection for two traits, was utilized. Total response under MAS was lower than that under genotypic assisted selection (GAS) for all phase-typing policies. For example, additional gains of ~70% under GAS, achieved in year 1 and in comparison with non-MAS, corresponded to additional gains of 43% and 15% under MAS for linkage distances of 1 cM and 20 cM, respectively. The different phasetyping policies examined in relation to MAS did not have any effect on total response, although there were small effects on major gene response. For breeding nuclei with either level of inbreeding, higher major gene response was achieved when phase-typed sires were selected on the basis of high ranking for genetic merit rather than connectivity to the other selection candidates. Further, increasing the number of males phase-typed within any year did not increase the rate of major gene response, although phase-typing in more years was favourable for the large linkage distance. An overall conclusion of this study is that additional gain could be achieved under MAS within a closed nucleus when progeny testing to determine major gene-marker phase was limited to from one to a few individuals.