Improvement of livestock has focused on the selective breeding of individuals
with superior phenotypes. With the development of increasingly advanced
statistical methods that maximise selection for genetic gain, this simple
approach has been extremely successful in increasing the quantity of
agricultural output. However, information now available on the organisation and
functioning of the genome could be used in breeding programmes to improve a
range of traits. Many traits are under the control of several genetic loci, each of
which contribute to the variation in the trait and hence are called quantitative
trait loci (QTL). While genetic markers for QTL that are linked to the trait gene
could be used to choose animals for selective breeding programmes, the most
effective markers are the functional mutations within the trait genes. Strategies
to identify markers for traits and the application of these markers are described
by reference to examples of loci that control a range of different traits.