Equine Genomics -- Contents -- Contributors -- Preface -- 1 Defining the equine genome: The nuclear genome and the mitochondrial genome -- Nuclear Genome of the Horse -- Chromosome number, karyotype, and schematic presentation -- Application of different banding techniques -- Chromosome aberrations - a brief overview -- Mitochondrial Genome of the Horse -- Structure, function, and utility -- Phylogenetics of Equus -- New research directions -- Acknowledgments -- References -- 2 Genetic linkage maps -- Introduction -- Genetic Linkage Maps -- Polymorphic Genetic Markers -- Reference Pedigrees -- Horse Genetic Linkage Maps -- The Uppsala map -- The International Horse Reference Family Panel (IHRFP) map -- The Newmarket map -- The International Equine Gene Mapping Workshop (IEGMW) linkage map -- the merging of contemporary linkage maps -- The Selection of Microsatellite Mapping Panels for the Dissection of Inherited Conditions in the Horse -- The Continuing Usefulness of the Equine Linkage Map -- For monogenic trait mapping -- In assembling the genome sequence -- References -- 3 Physical and comparative maps -- Introduction -- Horse Chromosomes -- Chromosome number -- Chromosome identification -- Chromosome size -- The horse karyotype -- Gene Mapping in Horses - Historical Background -- Cytogenetic Map -- Fluorescence in situ hybridization -- FISH mapping in the horse -- Multicolor and high-resolution FISH -- Physical mapping using flow-sorted and microdissected chromosomes -- FISH for mapping chromosome and genome rearrangements -- Somatic Cell Hybrid (SCH) Panels and Synteny Mapping -- Radiation Hybrid (RH) Panels and RH Mapping -- RH mapping methodology -- Horse RH panels -- RH mapping in the horse -- Comparative Map -- Zoo-FISH maps -- High-resolution comparative maps -- Concluding remarks -- References -- 4 The Y-Chromosome -- Introduction.

Cytogenetics -- Molecular Probes -- Genes -- Maps -- The Pseudoautosomal Region (PAR) -- Disorders -- Male infertility -- The PAR and sex chromosome aneuploidies -- Sex reversal syndrome -- Polymorphism and Population Studies -- Y chromosome in Other Equids and Perissodactyls -- Cytogenetics -- Genes and mapping -- Polymorphism -- Concluding Remarks -- Acknowledgments -- References -- 5 Unexpected structural features of the equine major histocompatibility complex -- Organization and Gene Content of the Model MHC -- Some MHC Genes Are Highly Polymorphic -- The Molecular Map of the Equine Leucocyte Antigen Complex -- RT-PCR -- Chromatin Modifications Associated with Transcription -- Summary -- References -- 6 Assembly and analysis of the equine genome sequence -- Introduction -- Sequencing a Genome -- Features of the Equine Genome Assembly -- Comparison with Genetic Maps -- Repetitive Elements -- Synteny with Humans -- Special Centromeres -- Genes -- A Single Nucleotide Polymorphism Map -- Genomic Attributes of Equine Breeds -- Summary -- Acknowledgments -- References -- 7 Genomic tools and resources: Development and applications of an equine SNP genotyping array -- Introduction -- Development of an Equine SNP Genotyping Array -- Equine SNP50 Beadchip Design and Validation in the Domestic Horse -- Utility of the Equine SNP50 Beadchip for Genome-Wide Mapping Strategies -- Utility of the Beadchip for Mapping Simple Traits within Breeds -- Use of the Equine SNP50 Beadchip for Mapping of Complex Traits in the Horse -- Mapping across Breeds -- Utility of the Equine SNP50 Beadchip for Population Genetic Analysis in the Horse -- Utility of the Equine SNP50 Beadchip in Extant Perissodactyla -- Design of a Second-Generation Equine SNP Genotyping Array -- References -- 8 Functional genomics -- Introduction: From Genotype to Phenotype.

Functional Impact of the Genome -- Functional elements of the encoded genome -- Genetic interactions -- Epigenetics/epigenomics -- The Transcriptome -- Profiling the equine mRNA transcriptome -- The non-coding RNA transcriptome -- The Proteome -- Networks -- Capturing Biological Understanding from Functional Genomics -- Conclusion -- References -- 9 Coat color genomics -- Introduction -- Base Colors (Black, Chestnut, Bay, and Seal Brown) -- Dilutions (Cream, Pearl, Champagne, Silver, Dun, and Lavender Foal) -- White Spotting and Depigmentation Patterns (Frame, Tobiano, Sabino, Dominant White, Leopard Complex, Gray, Roan, and White face and leg markings) -- References -- 10 Genomics of skin disorders -- Introduction -- Skin Diseases with Identified Mutations -- Hereditary equine regional dermal asthenia -- Junctional epidermolysis bullosa -- Skin Diseases with Suspected Heritable Basis -- Insect bite dermal hypersensitivity -- Chronic progressive lymphedema/Chronic pastern dermatitis -- Linear keratosis -- Skin/Hair Color Phenotypes -- Gray/melanoma -- Albinism -- Lethal white foal syndrome (LWFS) -- Lavender foal syndrome (LFS) -- Arabian fading syndrome (AFS)/pinky Arab syndrome -- Foal immunodeficiency syndrome (FIS) -- Hair Phenotypes -- Hypotrichosis/mane and tail dystrophy/follicular dysplasia -- Curly coat syndrome -- Linear alopecia -- Alopecia areata -- Conclusion -- References -- 11 Genomics of muscle disorders -- Introduction -- Hyperkalemic Periodic Paralysis -- Malignant Hyperthermia -- Glycogen Branching Enzyme Deficiency -- Polysaccharide Storage Myopathy Type 1 -- Polysaccharide Storage Myopathy Type 2 -- Recurrent Exertional Rhabdomyolysis -- Conclusions and Future Directions -- References -- 12 Genomics of skeletal disorders -- Osteochondrosis -- Introduction -- Heritability of OC, genetic correlations, and selection response.

Quantitative trait loci (QTL) for OC -- Gene expression analyses and candidate genes -- Navicular Disease -- Conclusions -- References -- 13 Genomics of reproduction and fertility -- Introduction -- Cytogenetics of Reproduction -- Sex chromosomes -- Autosomes -- Sex reversal, intersexuality, and hermaphroditism -- Cytogenetics of gametes and embryos -- Molecular Genetics of Reproduction -- Genetics of mare fertility -- Genetics of stallion fertility -- Functional Genomics of Reproduction -- Gene expression studies in the mare -- Functional genomics of the stallion -- Summary and Future Prospects -- Acknowledgments -- References -- 14 Genetics of equine neurologic disease -- Introduction -- Neurologic Disorders with Known Mutations -- Ileocolonic aganglionosis (lethal white foal syndrome) -- Lavender foal syndrome -- Cerebellar abiotrophy -- Neurologic Disorders with Ongoing Mapping Efforts -- Neuroaxonal dystrophy/Equine degenerative myeloencephalopathy -- Shivers -- Cervical vertebral malformation and malarticulation -- Sensorineural deafness in American Paint horses -- Equine inherited myoclonus -- Juvenile idiopathic epilepsy -- Occipitoatlantoaxial malformation -- Narcolepsy -- Recurrent laryngeal neuropathy -- Photic headshaking -- Conclusion -- References -- 15 Molecular genetic testing and karyotyping in the horse -- Introduction -- Genetic Tests for Individual Identification and Parentage Analysis -- Horse racing and forensic analysis -- Genetic Tests for Genetic Diseases -- Genetic Tests for Phenotypic Traits -- Future Developments in Molecular Genetic Testing -- Karyotyping Services Available for the Horse -- The basic chromosome analysis -- Molecular cytogenetic analysis -- Equine clinical cytogenetics in perspective -- Molecular Genetic Testing and Equine Cytogenetic Resources -- References -- 16 Genomics of laminitis -- Introduction.

Functional Genomics of Laminitis -- Whole Genome Transcriptional Profiling -- Contribution of Genomics to the Therapy of Laminitis -- References -- 17 Genomics of performance -- Introduction -- Heritability of Athletic Performance -- Athletic Performance Genes Encoded by the Nuclear Genome -- Mitochondrial DNA and Athletic Performance in Thoroughbreds -- Detection of Genomic Regions under Selection in the Thoroughbred Genome -- DNA Sequence Variation and Athletic Performance Traits in the Thoroughbred -- Identification of the Myostatin Gene (MSTN) - the "Speed" Gene - as a Major Locus Affecting Race Distance Aptitude -- A Genome-Wide Association Study (GWAS) for Optimum Race Distance in the Thoroughbred -- Functional Genomics and Proteomics -- Global Gene Expression Changes: Microarrays and Other Highly Parallel Gene Expression Approaches -- Genetic Testing for Thoroughbred Performance Potential -- Acknowledgments -- References -- 18 Genomics of the circadian clock -- Introduction -- Introduction to Circadian Biology -- The Mammalian Clockwork Mechanism -- Hierarchy of Master and Peripheral Clocks -- Equine Peripheral Clocks -- Circadian Regulation of Performance -- Immune-Circadian Interaction -- Circadian Desynchrony -- Discussion -- Bibliography -- 19 Mitochondrial genome: Clues about the evolution of extant equids and genomic diversity of horse breeds -- Introduction -- Evolution of the Family Equidae -- Przewalski's Horse and Horse Domestication -- History of Horse Breeds -- Adaptation in Horse Breeds -- References -- Index -- Supplemental Images.