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Bovine Genomics Bovine Genomics Edited by James E. Womack he genetic information being unlocked by advances in genomic and high throughput technologies is rapidly revolutionizing our understanding of Bovine T developmental processes in bovine species. This information is allowing researchers unprecedented insight into the genetic basis of key traits. Bovine Genomics is the first book to bring together and synthesize the information learned through the bovine genome sequencing project and look at its practical Genomics application to cattle and dairy production. Bovine Genomics opens with foundational chapters on the domestication of Edited by James E. Womack cattle and traditional Mendelian genetics. Building on these chapters, coverage rapidly moves to quantitative genetics and the advances of whole genome technologies. Significant coverage is given to such topics as epigenetics, mapping quantitative trail loci, genome-wide association studies, and genomic selection in cattle breeding. The book is a valuable synthesis of the field written by a global team of leading researchers. Providing wide-ranging coverage of the topic, Bovine Genomic, is an essential guide to the field. The basic and applied science will be of use to researchers, breeders, and advanced students. E d i t o r James E. Womack is the W. P. Luse Endowed and Distinguished Professor of Veterinary Pathobiology at Texas A&M University and Professor of Animal Genetics and Disease, WCU Biomodulation Program, Seoul National University. r E l at E d t i t l E s Womack Systems Biology and Livestock Science Edited by Marinus F. W. te Pas, Henri Woelders, and André Bannink ISBN 9780813811741 Methods in Animal Proteomics Edited by Philip D. Whitfield, David Eckersall ISBN 9780813817910 isbn 978-0-8138-2122-1 9 780813 821221 womack_9780813821221_cover.indd 1 2/17/12 6:21 PM P1: SFK/UKS P2: SFK BLBS104-FM Womack February 27, 2012 9:35 Trim: 244mm×172mm P1: SFK/UKS P2: SFK BLBS104-FM Womack February 27, 2012 9:35 Trim: 244mm×172mm Bovine Genomics P1: SFK/UKS P2: SFK BLBS104-FM Womack February 27, 2012 9:35 Trim: 244mm×172mm P1: SFK/UKS P2: SFK BLBS104-FM Womack February 27, 2012 9:35 Trim: 244mm×172mm Bovine Genomics Edited by James E. Womack A John Wiley & Sons, Ltd., Publication P1: SFK/UKS P2: SFK BLBS104-FM Womack February 27, 2012 9:35 Trim: 244mm×172mm This edition first published 2012 C 2012 by John Wiley & Sons, Inc. Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley’s global Scientific, Technical and Medical business with Blackwell Publishing. Editorial offices: 2121 State Avenue, Ames, Iowa 50014-8300, USA The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK 9600 Garsington Road, Oxford, OX4 2DQ, UK For details of our global editorial offices, for customer services and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com/wiley-blackwell. Authorization to photocopy items for internal or personal use, or the internal or personal use of specific clients, is granted by Blackwell Publishing, provided that the base fee is paid directly to the Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923. For those organizations that have been granted a photocopy license by CCC, a separate system of payments has been arranged. The fee codes for users of the Transactional Reporting Service are ISBN-13: 978-0-8138-2122-1/2012. Designations used by companies to distinguish their products are often claimed as trademarks. All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners. The publisher is not associated with any product or vendor mentioned in this book. This publication is designed to provide accurate and authoritative information in regard to the subject matter covered. It is sold on the understanding that the publisher is not engaged in rendering professional services. If professional advice or other expert assistance is required, the services of a competent professional should be sought. Library of Congress Cataloging-in-Publication Data Bovine genomics / edited by James E. Womack. p. cm. Includes bibliographical references and index. ISBN 978-0-8138-2122-1 (hardcover : alk. paper 1. Cattle–Genome mapping. 2. Cattle–Genetics. 3. Veterinary genetics. I. Womack, James E. SF756.65B68 2012 636.20821–dc23 2011049351 A catalogue record for this book is available from the British Library. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books. Set in 10/12 pt Dutch801BT by Aptara R Inc., New Delhi, India Disclaimer The publisher and the author make no representations or warranties with respect to the accuracy or completeness of the contents of this work and specifically disclaim all warranties, including without limitation warranties of fitness for a particular purpose. No warranty may be created or extended by sales or promotional materials. The advice and strategies contained herein may not be suitable for every situation. This work is sold with the understanding that the publisher is not engaged in rendering legal, accounting, or other professional services. If professional assistance is required, the services of a competent professional person should be sought. Neither the publisher nor the author shall be liable for damages arising herefrom. The fact that an organization or Website is referred to in this work as a citation and/or a potential source of further information does not mean that the author or the publisher endorses the information the organization or Website may provide or recommendations it may make. Further, readers should be aware that Internet Websites listed in this work may have changed or disappeared between when this work was written and when it is read. 1 2012 Cover photo: L1 Dominette 01449 with calf at USDA ARS, Miles City, Montana. Photograph courtesy of Dr. Mike MacNeil, Research Geneticist. Reprinted with permission. P1: SFK/UKS P2: SFK BLBS104-FM Womack February 27, 2012 9:35 Trim: 244mm×172mm Contents List of Contributors vii Foreword ix Chapter 1. The Origins of Cattle 1 Matthew D. Teasdale and Daniel G. Bradley Chapter 2. Mendelian Inheritance in Cattle 11 Frank W. Nicholas Chapter 3. Genetics of Coat Color in Cattle 20 Sheila M. Schmutz Chapter 4. From Quantitative Genetics to Quantitative Genomics: A Personal Odyssey 34 Morris Soller Chapter 5. Cartography of the Bovine Genome 51 James E. Womack Chapter 6. History of Linkage Mapping the Bovine Genome 63 Stephanie D. McKay and Robert D. Schnabel Chapter 7. Bovine X and Y Chromosomes 75 F. Abel Ponce de Leon´ and Wansheng Liu Chapter 8. Cattle Comparative Genomics and Chromosomal Evolution 101 Denis M. Larkin Chapter 9. Sequencing the Bovine Genome 109 Kim C. Worley and Richard A. Gibbs Chapter 10. Bovine Genome Architecture 123 David L. Adelson Chapter 11. Bovine Epigenetics and Epigenomics 144 Xiuchun (Cindy) Tian Chapter 12. Mapping Quantitative Trait Loci 169 Joel I. Weller Chapter 13. Genome-Wide Association Studies and Linkage Disequilibrium in Cattle 192 M. E. Goddard and B. J. Hayes Chapter 14. Genomic Selection in Beef Cattle 211 Jeremy F. Taylor, Stephanie D. McKay, Megan M. Rolf, Holly R. Ramey, Jared E. Decker, and Robert D. Schnabel v P1: SFK/UKS P2: SFK BLBS104-FM Womack February 27, 2012 9:35 Trim: 244mm×172mm vi Contents Chapter 15. Impact of High-Throughput Genotyping and Sequencing on the Identification of Genes and Variants Underlying Phenotypic Variation in Domestic Cattle 234 Michel Georges Index 259 P1: SFK/UKS P2: SFK BLBS104-LOC Womack February 18, 2012 5:59 Trim: 244mm×172mm List of Contributors David L. Adelson Denis M. Larkin School of Molecular and Biomedical Institute of Biological, Environmental Science and Rural Sciences The University of Adelaide Aberystwyth University Adelaide, SA 5005, Australia Aberystwyth, SY23 3DA, UK Daniel G. Bradley Wansheng Liu Smurfit Institute of Genetics Department of Dairy and Animal Trinity College Dublin Science Ireland Pennsylvania State University University Park, PA 16802, USA Jared E. Decker Division of Animal Sciences Stephanie D. McKay University of Missouri Division of Animal Sciences Columbia, MO 65211-5300, USA University of Missouri Columbia, MO 65211-5300, USA Michel Georges Frank W. Nicholas Unit of Animal Genomics Faculty of Veterinary Science GIGA-R & Faculty of Veterinary University of Sydney Medicine NSW 2006 University of Li`ege Australia Li`ege, Wallonia, Belgium F. Abel Ponce de Leon´ Richard A. Gibbs Department of Animal Science Department of Molecular and Human University of Minnesota Genetics St. Paul, MN 55108, USA Baylor College of Medicine Houston, TX 77030, USA Holly R. Ramey Division of Animal Sciences M. E. Goddard University of Missouri Department of Agriculture and Food Columbia, MO 65211-5300, USA Systems University of Melbourne Megan M. Rolf Melbourne, Victoria, Australia Division of Animal Sciences University of Missouri B. J. Hayes Columbia, MO 65211-5300, USA Biosciences Research Division, Department of Primary Industries Sheila M. Schmutz Victoria Department of Animal and Poultry University of Melbourne Science Melbourne, Victoria, Australia University of Saskatchewan Saskatoon, SK S7N 5A8, Canada vii P1: SFK/UKS P2: SFK BLBS104-LOC Womack February 18, 2012 5:59 Trim: 244mm×172mm viii List of Contributors Robert D. Schnabel Xiuchun (Cindy) Tian Division of Animal Sciences Department of Animal Science, Center University of Missouri for Regenerative Biology Columbia, MO 65211-5300, USA University of Connecticut Storrs, CT 06269-4163, USA Morris Soller Department of Genetics Joel I. Weller The Hebrew University of Jerusalem Institute of Animal Sciences 91904 Jerusalem, Israel ARO, The Volcani Center Bet Dagan 50250, Israel Jeremy F. Taylor Division of Animal Sciences James E. Womack University of Missouri Department of Veterinary Pathobiology Columbia, MO 65211-5300, USA Texas A&M University College Station, TX 77843-4467, USA Matthew D.
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