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Molecular tools are becoming increasingly available to investigate the genetic basis of reproductive disorders in dogs and cats. These were first successful in identifying the molecular basis of diseases inherited as simple Mendelian traits, and these are now being applied to those that are inherited as complex traits. In order to promote similar studies of reproductive disorders, we need to understand how we can play a proactive role in accumulating sufficient case material. We also need to understand these mutation discovery tools and identify collaborators who have experience with their use. The candidate gene and genomic approaches to mutation discovery in dogs are presented, including new sequencing methods and those used to confirm that a mutation has a role in disease pathology. As the final goal is to use our study results to prevent inherited disorders, we need to consider how we can promote efficiency in obtaining DNA test results and providing genetic counselling.