Chapter 1 Defining the equine genome: The nuclear genome and the mitochondrial genome Chapter 2 Genetic linkage maps Chapter 3 Physical and comparative maps Chapter 4 The Y-chromosome Chapter 5 Unexpected structural features of the equine major histocompatibility complex Chapter 6 Assembly and analysis of the equine genome sequence Chapter 7 Genomic tools and resources: Development and applications of an equine SNP genotyping array Chapter 8 Functional genomics Chapter 9 Coat color genomics Chapter 10 Genomics of skin disorders Chapter 11 Genomics of muscle disorders Chapter 12 Genomics of skeletal disorders Chapter 13 Genomics of reproduction and fertility Chapter 14 Genetics of equine neurologic disease Chapter 15 Molecular genetic testing and karyotyping in the horse Chapter 16 Genomics of laminitis Chapter 17 Genomics of performance Chapter 18 Genomics of the circadian clock Chapter 19 Mitochondrial genome: Clues about the evolution of extant equids and genomic diversity of horse breeds