Equine Genomics

Equine Genomics

Equine genetics has long been studied as a means of improving traits such as performance capabilities and coat color in horses. Dramatic advances in genomics and high-throughput DNA analysis technologies have significantly increased our understanding of the molecular biology of growth, development, and disease. Equine Genomics focuses on the significant advances in genome-mapping and genomic technologies and their application to the improvement of equine traits of economic significance.

Equine Genomics provides broad-ranging coverage of advances in genome science as applied to horses. The opening chapters provide strong foundational information on defining the equine genome, the development of genetic linkage, physical and comparative maps, as well as whole genome sequences. The following several chapters then look at the underlying genetics of key traits, such as reproduction, coat color, performance, and a variety of key diseases impacting horses. The final chapter looks at equine mitochondrial DNA and its implication on equid evolution and genetic diversity.

A timely and vitally important resource, Equine Genomics, is an essential title for animal scientists, genomic researchers, veterinary scientists, equine breeders, and industry personnel.

Contributors ix

Preface xi

Chapter 1 Defining the equine genome: The nuclear genome and the mitochondrial genome 1
Bhanu P. Chowdhary

Chapter 2 Genetic linkage maps 11
June Swinburne and Gabriella Lindgren

Chapter 3 Physical and comparative maps 49
Terje Raudsepp and Bhanu P. Chowdhary

Chapter 4 The Y-chromosome 73
Terje Raudsepp, Nandina Paria, and Bhanu P. Chowdhary

Chapter 5 Unexpected structural features of the equine major histocompatibility complex 93
Loren C. Skow and Candice L. Brinkmeyer-Langford

Chapter 6 Assembly and analysis of the equine genome sequence 103
Claire M. Wade

Chapter 7 Genomic tools and resources: Development and applications of an equine SNP genotyping array 113
Molly McCue and Jim Mickelson

Chapter 8 Functional genomics 125
Stephen J. Coleman, Michael J. Mienaltowski, and James N. MacLeod

Chapter 9 Coat color genomics 143
Samantha A. Brooks and Rebecca R. Bellone

Chapter 10 Genomics of skin disorders 155
Amy E. Young, Stephen D. White, and Danika L. Bannasvch

Chapter 11 Genomics of muscle disorders 171
James R. Mickelson, Stephanie J. Valberg, Carrie J. Finno, and Molly E. McCue

Chapter 12 Genomics of skeletal disorders 187
Ottmar Distl

Chapter 13 Genomics of reproduction and fertility 199
Terje Raudsepp, Pranab J. Das and Bhanu P. Chowdhary

Chapter 14 Genetics of equine neurologic disease 217
Carrie J. Finno and Monica Aleman

Chapter 15 Molecular genetic testing and karyotyping in the horse 241
M. C. T. Penedo and Terje Raudsepp

Chapter 16 Genomics of laminitis 255
Jim K. Belknap

Chapter 17 Genomics of performance 265
Emmeline W. Hill, Lisa M. Katz, and David E. MacHugh

Chapter 18 Genomics of the circadian clock 285
Barbara A. Murphy

Chapter 19 Mitochondrial genome: Clues about the evolution of extant equids and genomic diversity of horse breeds 311
Cynthia C. Steiner, Kateryna D. Makova, and Oliver A. Ryder

Index 323

Bhanu P. Chowdhary is Professor, Faculty Fellow, and Associate Dean for Research and Graduate Studies in the Department of Veterinary Medicine and Biomedical Sciences at Texas A&M University, College Station, Texas.