Genetics After Twilight

•The whole genome sequence for the horse made it possible to discover genetic variants at the DNA level.•Whole genome sequencing has a routine approach to gene discovery.•Sequences of ancient DNA suggest that domestication led to an increase deleterious recessive genes.•The advances in genomics for horses make it possible to begin investigating functional genomics.•Functional genomics will provide tools relevant to all fields of equine research.

In 2006, the whole genome sequence was completed for the Thoroughbred mare, Twilight. This sequence and the tools derived from this work led to the discovery of genetic variants responsible for coat color traits, hereditary diseases, and even some performance traits. Technological advances have made whole genome sequence easier and less expensive. Whole genome sequencing derived from ancient horse DNA has provided insights into the events associated with domestication of the horse and also suggests that one of the costs of domestication has been an increase in the genetic load, specifically, autosomal recessive deleterious genes. The next step for genomic research is the development of approaches for readily investigating functional genomics. Functional genomics is a tool relevant to all fields of equine study, including immunology, nutrition, reproduction, exercise physiology, and veterinary medicine.