Conservation genetics of UK livestock: from molecules to management

Analysis of molecular genetic diversity in livestock potentially allows for rational management of genetic resources experiencing the serious pressures now facing the livestock sector. The potentially damaging effects of genetic erosion are an ongoing threat, both through loss of breeding stock during the 2001 FMD crisis and potentially as a result of the ongoing National Scrapie Plan. These factors and an increasing focus through the Food and Agriculture Organisation of the United Nations (FAO) on the conservation of animal genetic resources force us to consider seriously how to measure, monitor and conserve diversity throughout the genomes of livestock. Currently debated ways to optimally conserve livestock diversity, particularly the 'Weitzman Approach', may fail to take into account the significance of within-breed genetic diversity and its structuring, and apply relatively simplistic models to predict the probability of extinction for breeds over defined periods of time under certain management scenarios. In this paper I argue, using examples from our work and that of others, that within-breed diversity, in particular, should not be ignored when conserving livestock diversity, since breeds may be genetically structured at a variety of scales and there is little evidence for a convincing relationship between effective population size and genetic diversity within rare UK breeds. Furthermore, until we understand the population genetic forces that shape diversify in breeds in more detail, using raw indices of genetic variation or distances to rank or prioritise breeds in terms of some notional threat of extinction has questionable conservation value.