Genetic dissection of phenotypic diversity in farm animals

Farm animals provide unique resources for studying genotype–phenotype relationships of a variety of traits due to the rich genetic diversity within and between breeds. Farm animals were domesticated from their wild ancestors 5,000–15,000 years ago. In several cases, independent domestication from two or more subspecies took place. Genome research in farm animals focuses primarily on non-pathological phenotypes. Thus, the search for mutations modifying phenotypes predominates over the search for mutations with clear pathological consequences. Genetic studies of phenotypic traits, including multifactorial traits, are facilitated by the extensive pedigrees and the long tradition of collecting phenotype information in animal breeding programmes. Furthermore, resource populations for gene mapping can be generated by intercrossing different populations of farm animals. All the basic resources for genome research are in place for the major farm animals, such as large collections of genetic markers (primarily microsatellites), large-insert libraries and radiation hybrid panels. However, the number of ESTs, as well as the number of cloned genes, are low compared with human and mouse. Comparative gene mapping has been a key activity in farm animal genomics to allow access to the more developed genetic maps in other vertebrates. Comparative gene mapping has shown that the organization of the human genome is closer to that of farm animals (including chicken) than to the mouse. The chromosomal localization of trait loci is determined by genome scans. Positional candidate cloning is the main strategy for the molecular identification of trait loci. Linkage disequilibrium mapping seems to be a promising strategy for high-resolution mapping of trait loci as linkage disequilibrium occurs more frequently in farm animal populations than in human populations. Several genes causing monogenic disorders and muscle development have already been identified. Diagnostic DNA tests for these are currently used in practical animal breeding. Genome research in farm animals will lead to important practical applications in the farm animal industry but will also give new basic knowledge of the genetic basis for a variety of phenotypic traits of agricultural, biological and medical significance.