A stochastic simulation model of a sheep breeding program is used to show how assortative matings can increase the number of rams sold which are homozygous favourable for a major gene. The commercial implications of such a strategy are discussed in comparison with strategies focused more on increasing gene frequency. Long term inbreeding is unaffected while the lost response to selection for polygenic merit is substantially reduced, when homozygosity is increased through assortative mating, rather than though increasing the gene frequency in the population and using random mating. Rapid advances in molecular biology, in terms of both cost, and capability of downstream technologies, mean that marker assisted selection breeding programmes are becomingincreasingly attractive to sheep breeders. However such programmes may be costly and will only deliver increased overall genetic gain if managed well, particularly as the individual quantitative trait loci (QTL) for which markers are becoming availableare often modest in their effects on total economic merit. Thus, careful and innovative consideration is required when integrating information from QTL markers into a commercial breeding programme.
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