Management of genetic diversity in small farm animal populations

Many local breeds of farm animals have small populations and, consequently, are highly endangered. The correct genetic management of such populations is crucial for their survival. Managing an animal population involves two steps: first, the individuals who will be permitted to leave descendants are to be chosen and the number offspring they will be permitted to produce has to be determined; second, the mating scheme has to be identified. Strategies dealing with the first step are directed towards the maximisation of effective population size and, therefore, act jointly on the reduction in the loss of genetic variation and in the increase of inbreeding. In this paper, the most relevant methods are summarised, including the so-called 'Optimum Contribution' methodology (contributions are proportional to the coancestry of each individual with the rest), which has been shown to be the best. Typically, this method is applied to pedigree information, but molecular marker data can be used to complete or replace the genealogy. When the population is subjected to explicit selection on any trait, the above methodology can be used by balancing the response to selection and the increase in coancestry/inbreeding. Different mating strategies also exist. Some of the mating schemes try to reduce the level of inbreeding in the short term by preventing mating between relatives. Others involve regular (circular) schemes that imply higher levels of inbreeding within populations in the short term, but demonstrate better performance in the long term. In addition, other tools such as cryopreservation and reproductive techniques aid in the management of small populations. In the future, genomic marker panels may replace the pedigree information in measuring the coancestry. The paper also includes the results of several experiments and field studies on the effectiveness and on the consequences of the use of the different strategies.