Quantitative Trait Loci (QTL) provides a way to associate segments of genome locations with quantitative traits which represent the majority of economically important phenotypes measured in livestock animals. Over the past 15 years or so, thousands of QTL have been detected in pigs, cattle, chickens, and sheep, among other species. These data allow researchers to narrow down genomic regions and identify the genetic factors that contribute to trait variations (Mehar, 2004; Hocking, 2005; Rothschild et al., 2007). However, there is a bottleneck between mapped QTL and gene discovery (Womack, 2005) which must be overcome in order for animal geneticists to use this information in the genetic improvement of livestock.