Introduction

From the first meeting of the International Equine Gene Mapping Workshop in Lexington, Kentucky, in
October 1995 until the sequencing of the horse genome in 2007
(http://www.broadinstitute.org/mammals/horse; Wade et al., 2009), the primary activity of the equine
genetics academic research community was the development of integrated maps of the horse genome.
Together with somatic cell hybrid, radiation hybrid, and physical/cytogenetic maps based on
fluorescence in situ hybridization (FISH), the generation of genetic linkage maps was critical to achieve
this goal. The primary driving force for these endeavors was to map genetic variants that underlie
disease, reproduction, growth, and other interesting traits such as coat color. Knowing the genetic basis
for these traits would allow for informed breeding decisions to reduce the levels of disease or select for
desired characteristics. Furthermore, it would enable investigation of the population structure of horse
breeds

genetic variants that underlie disease, reproduction, growth, and other interesting traits such as coat
color. Knowing the genetic basis for these traits would allow for informed breeding decisions to reduce
the levels of disease or select for desired characteristics. Furthermore, it would enable investigation of
the population structure of horse breeds and their relationship to other equids and also contribute to
the greater understanding of the evolution of the mammalian genome. Additionally, linkage maps would
provide scaffolding for the assembly of the horse genome sequence. Even subsequent to the release of
the horse genome sequence and the development of a single nucleotide polymorphism (SNP)
microarray, the utility of the linkage maps continues. This is evidenced by recent publications about the
use of genetic linkage analysis to map various congenital disorders and diseases