Naturally occurring genetic variation is the basis for differences in performance and appearance between and within different breeds and lines of livestock. In a few instances (e.g. coat colour, polling) the genes (or loci) which control the variation between animals and breeds have a large enough effect to be individually recognisable. For many traits, however, the combined effects of many different genes act together to control quantitative differences between breeds and individuals within breeds (hence such genes are often referred to as quantitative trait loci or QTLs). Thus the dramatic successes of modern breeding result from generations of selection which has produced accumulated changes at a number of different loci. The genome contains up to 100,000 different genes and identifying those which contribute to variation in traits of interest is a difficult task. One first step is to identify regions of the genome containing loci of potential interest through their linkage to genetic markers.