Incorporation of new techniques in animal breeding programmes with an emphasis on dairy cattle

Animal breeding programmes often face new challenges either from problems created by past selection strategies or the emergence of new technologies. Two such examples are the increase in inbreeding now seen in many livestock populations and the availability of molecular genetic information, which can be used to enhance genetic gain. The general objectives of this thesis were a) to determine the current levels of inbreeding in UK dairy cattle and the value of optimised selection as a method to control inbreeding and b) to evaluate certain aspects in relation to the use of molecular genetic information in animal breeding programmes.Recently, concerns have been raised over the degree of inbreeding in dairy cattle populations. A study of the inbreeding of UK Holstein cows was undertaken to assess the current levels and trends in inbreeding in this breed. Results showed that the rate of inbreeding has increased considerably since the early nineties. The annual rate from 1992 to 2003) was 0.17% while the rate from 1968 to 1991 was just 0.03%. Optimisation procedures, which have been developed to maximise the rate of genetic gain at a predefined rate of inbreeding, were applied to determine if such procedures would be useful to in a dairy cattle context. The results showed that the procedures were able to generate more genetic gain at current rates of inbreeding or alternatively to reduce the rate of inbreeding at the current rate of genetic gain.The emergence of new molecular genetic techniques has meant that many resources have been devoted to the mapping of quantitative trait loci (QTL) of economic importance in most domestic livestock species. The detection of such loci provides a new source of information that can be used in conjunction with traditional methods to enhance the selection process and increase genetic gain. In this thesis a method is described to assess the benefits of using DNA tests at the commercial herd level. This method can be used for a variety of situations and two case studies were examined to illustrate the usefulness of the method. The first study dealt with the situation in which a breeder chooses to use a sire that is a carrier for a deleterious allele. The second study dealt with the value of sires that are earners of a beneficial allele for which a premium is paid. The method would be very useful to predict the costs or benefits associated with using identified loci in commercial herds.The usefulness of QTL in breeding programs will depend on, among other things, the mode of action of a QTL on specific trait(s). An estimate of the genetic correlation equal to zero between two traits suggests that the traits in question are controlled independently. However, through stochastic simulation, it is shown that a pleiotropic QTL can result in a QTL segregating at intermediate frequencies in a population when the estimated polygenic correlation is zero. As a consequence, it is possible for a deleterious allele to remain in a population for many generations, when it might otherwise be expected to be removed via natural selection. The expected outcomes from using pleiotropic QTL in selection were also assessed. In general, the expected gain is a function of the mode of action of the QTL on traits it affects. It can lead to less gain compared to selection ignoring the QTL where the QTL has a negative effect on the fitness of the animals