Bovine Genomics ebook

Contents

Cover

Title Page

Copyright

Dedication

List of Contributors

Foreword

Chapter 1: The Origins of Cattle

Archeology and Domestication

Bovine Mitochondrial DNA Diversity and Cattle Origins

MtDNA Diversity Within B. taurus

Archeology and Domestication in the Near East

The Origins of B. indicus

Modeling Cattle Demographic History from Autosomal Sequence Variation

References

Chapter 2: Mendelian Inheritance in Cattle

Introduction

A Classic Mendelian Cattle Trait: Presence/Absence of Horns

Bovine Mendelian Traits Characterized at the DNA Level

A (Mostly) Morbid Map of the Bovine Genome

Other Bovine Mendelian Traits

Conclusion

References

Chapter 3: Genetics of Coat Color in Cattle

Introduction

Basic Coat Colors

Shades

White Markings

Unsolved Colors and Patterns

References

Chapter 4: From Quantitative Genetics to Quantitative Genomics: A Personal Odyssey

Acknowledgment

References

Chapter 5: Cartography of the Bovine Genome

Introduction

Somatic Cell Mapping

Radiation Hybrid Mapping

Linkage Mapping

Physical Mapping

Cattle Genome Sequencing

References

Chapter 6: History of Linkage Mapping the Bovine Genome

Introduction

The First Genome-wide Maps

Second-Generation Maps

Third-Generation Maps

Single Chromosome Maps

Conclusion

References

Chapter 7: Bovine X and Y Chromosomes

Cytogenetic Analysis of Bovine Sex Chromosomes

X and Y Chromosome Genetic and Physical Maps

The Pseudoautosomal Region

Pseudoautosomal Boundary

The MSY Region

Bovine Y-Chromosome Phylogeny

Sex Chromosome Abnormalities

Sex Chromosomes QTLs

References

Chapter 8: Cattle Comparative Genomics and Chromosomal Evolution

Introduction

Chromosomal Rearrangements and Genome Evolution

Chromosomal Rearrangements and Adaptation

References

Chapter 9: Sequencing the Bovine Genome

Introduction

Background on Genome Assembly

Bovine Sequencing Strategy, DNA Sources

The Different Genome Assemblies

Bovine Genome Assembly Methods

Description of the WGS-Only Assembly

Description of the BAC-Based Assembly

Combining BAC and WGS Assemblies and Mapping to Chromosomes

Description of Mapping and Placement for Btau_3.1

Description of Refined Mapping and Placement for Btau_4.0

Assembly Metrics

Assembly Validation

Mapping QC

Quality Assessment of the Assembly by Linkage Analysis

Sex Chromosomes and Autosome Assemblies

Later Improvements

Data Availability

Acknowledgment

References

Chapter 10: Bovine Genome Architecture

Introduction

De Novo Repeat Identification and Annotation

Arrays, Duplications, and Correlations

Genome Territories

Conclusions

References

Chapter 11: Bovine Epigenetics and Epigenomics

Definitions of Epigenetics and Epigenomics

Mechanisms of Epigenetics

Examples of Epigenetic Regulations: Genetic Imprinting and X-Chromosome Inactivation

Epigenomics of the Early Bovine Embryos

Epigenetics of Bovine Nonimprinted Protein-coding Genes

Effect of Biotechnology on Epigenomics

Conclusion

References

Chapter 12: Mapping Quantitative Trait Loci

Introduction

DNA-Level Genetic Markers, SSRs vs. SNPs

Detecting and Mapping of QTL via Within-Family Genetic Linkage

Methods to Estimate QTL Effects and Location in Dairy Cattle

Difficulties and Biases in QTL Analysis

The Current State of QTL Detection in Dairy Cattle by Within-Family Linkage Studies

Genome Scans, Within-Family Linkage vs. Populationwide Linkage Disequilibrium

Estimation of QTL Effects from Genome Scans

Studies on the Distribution of QTL Effects

Appropriate Criteria for Evaluation of GEBV

Implementation of Methodology to Compute GEBV for Dairy Cattle

Identification of Quantitative Trait Nucleotides

Validation of Quantitative Trait Nucleotides

Application of Identified QTL in Marker-Assisted Selection

Conclusions

Acknowledgment

References

Chapter 13: Genome-Wide Association Studies and Linkage Disequilibrium in Cattle

Introduction

The Nature of LD

Design of GWAS

Statistical Analysis of GWAS

Results of Cattle GWAS

Conclusion

References

Chapter 14: Genomic Selection in Beef Cattle

Introduction

Industry Structure

Genomic Selection Theory

Methods for Genomic Selection

SNP Detection and Assay Development

Need to Positionally Clone QTL

The Future of Genomic Selection in Beef Cattle

Conclusions

References

Chapter 15: Impact of High-Throughput Genotyping and Sequencing on the Identification of Genes and Variants Underlying Phenotypic Variation in Domestic Cattle

Introduction

Empirical and Biometrical Selection: Effective Manipulation of a Black Box

Early Days in Livestock Genomics: Attempting QTL-Based Marker-Assisted Selection

Impact of High-Density SNP Genotyping on the Analysis of Monogenic Traits: Highly Effective IBD Mapping

Impact of High-Density SNP Genotyping on the Analysis of Complex Traits: Genomic Selection & QTN Identification

Impact of Next-Generation Sequencing on the Analysis of Monogenic Traits

Impact of Next-Generation Sequencing on the Analysis of Complex Traits: Imputing Genotype from Sequence Data

Conclusions

Acknowledgment

References

Index

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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 636.2′0821--dc23 2011049351

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To my mother, Barbara Sandager Nolop

List of Contributors

David L. Adelson School of Molecular and Biomedical Science The University of Adelaide Adelaide, SA 5005, Australia

Daniel G. Bradley Smurfit Institute of Genetics Trinity College Dublin Ireland

Jared E. Decker Division of Animal Sciences University of Missouri Columbia, MO 65211-5300, USA

Michel Georges Unit of Animal Genomics GIGA-R & Faculty of Veterinary Medicine University of Liège Liège, Wallonia, Belgium

Richard A. Gibbs Department of Molecular and Human Genetics Baylor College of Medicine Houston, TX 77030, USA

M. E. Goddard Department of Agriculture and Food Systems University of Melbourne Melbourne, Victoria, Australia

B. J. Hayes Biosciences Research Division, Department of Primary Industries Victoria University of Melbourne Melbourne, Victoria, Australia

Denis M. Larkin Institute of Biological, Environmental and Rural Sciences Aberystwyth University Aberystwyth, SY23 3DA, UK

Wansheng Liu Department of Dairy and Animal Science Pennsylvania State University University Park, PA 16802, USA

Stephanie D. McKay Division of Animal Sciences University of Missouri Columbia, MO 65211-5300, USA

Frank W. Nicholas Faculty of Veterinary Science University of Sydney NSW 2006 Australia

F. Abel Ponce de León Department of Animal Science University of Minnesota St. Paul, MN 55108, USA

Holly R. Ramey Division of Animal Sciences University of Missouri Columbia, MO 65211-5300, USA>

Megan M. Rolf Division of Animal Sciences University of Missouri Columbia, MO 65211-5300, USA Sheila M. Schmutz Department of Animal and Poultry Science University of Saskatchewan Saskatoon, SK S7N 5A8, Canada

Robert D. Schnabel Division of Animal Sciences University of Missouri Columbia, MO 65211-5300, USA

Morris Soller Department of Genetics The Hebrew University of Jerusalem 91904 Jerusalem, Israel

Jeremy F. Taylor Division of Animal Sciences University of Missouri Columbia, MO 65211-5300, USA

Matthew D. Teasdale Smurfit Institute of Genetics Trinity College Dublin Ireland

Xiuchun (Cindy) Tian Department of Animal Science, Center for Regenerative Biology University of Connecticut Storrs, CT 06269-4163, USA

Joel I. Weller Institute of Animal Sciences ARO, The Volcani Center Bet Dagan 50250, Israel

James E. Womack Department of Veterinary Pathobiology Texas A&M University College Station, TX 77843-4467, USA

Kim C. Worley Department of Molecular and Human Genetics Baylor College of Medicine Houston, TX 77030, USA

Foreword

Research in cattle genetics was profoundly changed in 2009 with public release of the cattle genome sequence and the publication of papers describing its content, function, and evolution. Since the development of mixed model equations by Henderson in the early 1950s, there has been no other event that has had similar impact on bovine biology and the science of dairy and beef cattle breeding. In ways foretold by the contemporary leaders in the field, of whom the editor and the authors are a part, genomics has been adopted as a foundational tool for the genetic improvement of cattle and other livestock species. One of the most gratifying stories to emerge from cattle genomics is the way that traditional animal breeding has been integrated with the new technologies and adopted by the industry, despite the doubts of many good friends along the way. Indeed, this was the vision of the earliest pioneers in animal genetics, such as Fred Hutt and Clyde Stormont, who grasped the verdant potential for genetic markers in animal breeding. We can only wonder what they would say now if they were alive to read this marvelous book!

Bovine Genomics begins with Matthew Teasdale's and Dan Bradley's updated review on the origins of domesticated cattle, providing current information on the timing of probable domestication events and an excellent summary of the archeological evidence as well as data from mitochondrial phylogeography and nuclear DNA that support the current consensus. Although the authors avoid the issue of taxonomic classification of indicine and taurine cattle (an ongoing source of confusion to students and practitioners alike!), they leave little doubt that modern cattle are the product of two or possibly more domestication events. At least for now, the Aurochsen appear as the forbearers of all cattle, but they have leapt into domesticated cattle lineages at several points in history.

Following two well-referenced reviews on Mendelian traits by Frank Nicholas and Sheila Schmutz, respectively, the reader is treated to historical perspectives from the “foundation sires” of cattle genetics, Morris Soller and Jim Womack. Coming from entirely different scientific and geographical worlds, these giants in the field provided the scientific rationale that was eventually used for sequencing the cattle genome. Soller gives a fascinating personal history of his transformation from a curious adolescent with a fascination for Morgan, to radical quantitative geneticist who envisioned and developed a theoretical framework for marker-assisted selection. This article is a must read for any serious student of animal genetics. The accounting is honest, detailed, accurate (from my perspective) and captures most of the important people and events leading up to modern, genomically driven animal breeding methods. It is incredible that Soller had it all figured out even before most of the current leaders in the field finished high school!

Next up is Womack's review of cattle gene mapping. It is hard for me to write dispassionately about Womack's contribution to the field, given that he has been a mentor and great collaborator for more nearly 20 years. Even though Womack has reviewed this subject in recent years, this time he has come up with some real gems! His quote of Frank Ruddle's response to the question “why map genes” brought a huge “LOL” (“gene mapping is good for you!”). Having mapped thousands of genes with Womack's radiation hybrid panel, I often used that same line in convincing my own students and postdocs to persevere. As Womack details throughout the article, each gene becomes a landmark on which more detailed maps are built, similar to Jan Klein's analogy between postage stamp collecting and MHC alleles (each very beautiful but with no immediately obvious value) that exploded in number after Peter Gorer's famous discovery of the mouse H-2 complex. And, as the story turned out, the high-resolution maps that were produced using radiation hybrid analysis proved to be the critical scaffold reagent for a chromosome-based assembly of the draft cattle genome sequence. The reader of this review will come away with a true historical sense of how discoveries made in apparently disparate areas of science can have a transformative effect on other disciplines. Fortunately, Womack envisioned what was possible with the tools of somatic cell genetics, and this carried the field of animal genetics for an entire generation.

Womack's article sets the stage nicely for the comprehensive review of linkage mapping by Stephanie McKay and Bob Schnabel, which is followed by a current view of the much maligned bovine sex chromosomes by Abel Ponce DeLeon and Wansheng Liu. I shall show my bias by commenting on the article by Denis Larkin, who summarized much of the work he conducted in my laboratory during the past 10 years on the subject of cattle comparative genomics and genome evolution. Larkin presents an expert technical review, and also gives us important insights into the relatively controversial interpretation that certain genome rearrangements in mammals may be adaptive. Although this idea has been floating around among evolutionary theorists and evolutionary biologists for more than half a century, there is now strong support for adaptive chromosome rearrangements gathering from work with yeast, plants, insects, and mammals. Larkin leaves us with strong anticipation that much will be learned from the multispecies comparisons of chromosome organization that will follow from the sequencing of thousands of species in the coming years.

The centerpiece of this volume is the review by Worley and Gibbs on the sequencing of “the” bovine genome. The community owes its gratitude to the Baylor group for providing the field with the critical resource on which the “new” cattle genetics is being built. Several excellent reviews follow on subjects ranging from genome architecture (Dave Adelson) to epigenetics (Cindy Tian), QTL mapping (Joel Weller), genome-wide association studies and linkage disequilibrium (Michael Goddard and Ben Hayes), and genomic selection in beef cattle (Jerry Taylor et al.). Brevity dictates that I restrain from commenting in detail on these articles, but readers will find that they match the stellar reputations of their authors.

This brings us to the final chapter by Michel Georges, one of the genetics community's truly innovative scientists. The author critically reviews many areas of importance in cattle genetics, providing strong views on the candidate gene approach for single gene defects and QTL and on marker-assisted selection. With the hindsight gained from years of experience, and the foresight of a gifted scientist, Georges leaves no doubt concerning his enthusiasm for new genomic technologies for mutation sleuthing, and backs it up with several examples from his group's work. There is much more in this excellent review for the reader to enjoy, but moreover, for the community to take as a bellwether of where cattle genetics and complex traits analysis will be going over the next few years.

While there are a few more topics that could have been covered, this edition of Bovine Genomics is a timestamp that marks the most dynamic period in the history of cattle genetics. The new resources for doing science with what was previously a very difficult animal to understand at the molecular and systems level has brought many talented young investigators to the field. I suspect that the next edition will show how much value the public investments in cattle research have brought to our understanding of biology in general, and to applications in animal agriculture at a critical time when demand for animal products is skyrocketing on a global scale. Keep your grill hot and your laptop warm!

Harris A. Lewin Vice Chancellor for Research Professor of Evolution and Ecology Robert and Rosabel Osborne Endowed Chair University of California, Davis January, 2012

Chapter 1

The Origins of Cattle and

Matthew D. Teasdale and Daniel G. Bradley

Archeology and Domestication

The transformation of early human economies from nomadic hunter–gatherers to farmers is a pivotal moment in human evolution. Starting approximately 12,000 years ago, this process is entitled the Neolithic Revolution and encompassed the domestication of a variety of plants and animals (Bar-Yosef 1998). The archeological study of domestication requires a combination of classical and molecular approaches, which include the analysis of settlement patterns, food residues, and human, animal, and plant remains.

Settlement patterns provide an excellent source of evidence for the beginnings of domestication. Firstly, they provide direct evidence of a sedentary lifestyle, which is likely a prerequisite to Neolithisation. Secondly, the production of long-term housing requires specialist builders; these skills could likely only be supported if an agricultural economy was being practiced to offset the loss of labor from hunting. The evolution of particular building technologies within Neolithic core regions can also be informative, for example, the presence of grain stores and larger houses emerge as the Neolithic lifestyle develops (Cauvin 2000). Study of the surrounding areas can provide evidence for early attempts at domestication, for example, the manipulation of the landscape to control animal migration (Vigne 2011).

The analysis of organic residues found on cooking and storage artifacts is a relatively new technique in molecular archeology, which is providing exciting results especially in the field of domestication (Dudd et al. 1999; Copley et al. 2003; Copley et al. 2005; Outram et al. 2009). For example, lipid residues found on pottery can be used to deduce milk use and have allowed for the earliest date of specialized milking to be proposed as the seventh millennium BC (Evershed et al. 2008). Molecular archeology also allows the diet of early farmers to be inferred from the stable isotopes contained within their bones, analyses that have been fruitful in distinguishing the transition into farming (Richards et al. 2003; Liden et al. 2004; Eriksson et al. 2008).

The study of animal remains, however, is still the principal analysis for identifying domestication (Vigne 2011), with the differences in morphology of domesticates compared to their wild progenitor providing clues to this process. Cattle follow the general trend of domestic breeds being smaller than their wild relatives. However, the usefulness of this factor alone to identify early signatures of domestication has recently been called into question (Zeder 2008, and references therein). More robust evidence for the beginnings of domestication may be found in the kill-off patterns of animals (age at which animals are killed) (Vigne and Helmer 2007). (Most hunters tend to target adult males to maximize the kill. In contrast, herders are thought to slaughter males young, apart from the few needed for herd propagation) (Zeder 2008). This leads to archeological remains dominated by young males and elderly females who are killed once they have passed their prime reproductive age (Vigne and Helmer 2007; Zeder 2008). The number of domesticate finds also increases through time at the proposed Neolithic sites, which allows for the time of domestication to be proposed (Bar-Yosef 1998; Vigne 2011).

Bovine Mitochondrial DNA Diversity and Cattle Origins