Title Details

Hasan Khatib is an Associate Professor in the Department of Dairy Science at the University of Wisconsin-Madison. Dr. Khatib has taught a variety of undergraduate and graduate courses on animal breeding and genetics. He is also the lead editor of Livestock Epigenetics published by Wiley in 2012.

Contributors ix

Manuscript reviewers xi

Preface xiii

1 Decoding and Encoding the “DNA” of Teaching and Learning in College Classrooms 1
Michel A. Wattiaux

Introduction 1

Teaching and learning: definitions 1

Understanding learning 2

Understanding teaching 5

Implications for classroom design in the twenty-first century 6

Final thoughts 9

References 10

Review questions 11

Section 1: Quantitative and Population Genetics 13

2 Mating Systems: Inbreeding and Inbreeding Depression 15
David L. Thomas

Introduction 15

Inbreeding 15

Cause of inbreeding depression 18

Quantifying inbreeding 20

Genomics and inbreeding 23

Summary 23

Further reading 24

References 24

Review questions 24

3 Genomic Selection Inbreeding and Crossbreeding in Dairy Cattle 25
Kent Weigel

Introduction 25

Genomic selection 25

Crossbreeding 28

Inbreeding and genetic defects 29

Summary 30

References 30

Review questions 31

4 Basic Genetic Model for Quantitative Traits 33
Guilherme J. M. Rosa

Introduction 33

Quantitative traits 33

Expected value and variance: the normal distribution 33

Basic genetic model for quantitative traits 35

Heritability and selection 35

Predicting rate of genetic change from selection 36

Further reading 37

References 37

5 Heritability and Repeatability 39
Guilherme J. M. Rosa

Introduction 39

Heritability 39

Estimation of heritability and variance components 40

Prediction of breeding values and of response to selection 41

Repeatability 41

References 42

6 Applications of Statistics in Quantitative Traits 43
Hayrettin Okut

Population and sample 43

Descriptive statistics 43

Graphically examining the distribution of the data 47

Normal distribution 49

Exploring relationships between variables 53

Summary 59

Appendix 6.1 62

Further reading 62

References 62

Review questions 63

Section 2: Applications of Genetics and Genomics to Livestock and Companion Animal Species 65

7 Genetic Improvement of Beef Cattle 67
Michael D. MacNeil

Introduction 67

Single trait selection 67

National cattle evaluation 69

Multiple trait selection 71

Summary 71

Further reading 71

References 72

8 Genetic Improvement in Sheep through Selection 73
David L. Thomas

Products from sheep 73

Selection among breeds 73

Selection within a breed or population and the Key Equation 73

Adjustment for environmental effects 73

Phenotypic selection 75

Estimated breeding values (EBV) 75

Using multiple sources of information 76

Genetic correlations 76

Selection intensity 78

Generation interval (L) 79

Predicting progress from selection 79

National genetic improvement programs 80

Summary 81

Further reading 82

References 82

Review questions 82

9 Genetic Improvement Programs for Dairy Cattle 85
Kent Weigel

Introduction 85

Data collection infrastructure 85

Estimation of breeding values 87

Selection for increased productivity 89

Selection for functional traits 91

Sire selection 94

Summary 94

Further reading 95

References 95

Review questions 96

10 Genetic and Genomic Improvement of Pigs 97
Max F. Rothschild

Introduction 97

Domestication of swine and breed development 97

Methods of selection and mating systems 98

Traits of economic importance 99

Development of molecular genetic approaches 100

QTL candidate genes and genetic improvement 100

Sequencing the pig genome 101

Genomic selection 102

Databases 103

Cloning transgenics and breeding pigs as biological models 103

Future applications to genetic improvement 103

Acknowledgments 104

Further reading 104

References 104

Review questions 105

11 Equine Genetics 107
Jennifer Minick Bormann

Color 107

Genetic defects 110

Inbreeding and relationship 113

Selection and improvement 114

New technologies 116

Further reading 117

References 119

Review questions 119

12 Genetics and Genomics of the Domestic Dog 121
Leigh Anne Clark and Alison Starr-Moss

Introduction to canine research 121

The dog genome 122

Uncovering the genetic basis of phenotypes 125

Future challenges 127

Summary 128

Further reading 129

References 130

Review questions 130

13 The Sheep Genome 131
Noelle E. Cockett and Chunhua Wu

Investment in sheep genome research 131

Overview of the sheep genome 131

Genomic resources in sheep 131

Application of genomic resources 134

Summary 134

References 135

Review questions 136

14 Goat Genetics and Genomic Progress 137
Mulumebet Worku

Introduction 137

Genetics and goat domestication 137

Taxonomy 138

Goat chromosome number and structure 138

Patterns of inheritance 139

Quantitative trail loci (QTL) 139

Progress in goat genomics 139

Biotechnologies and goat genetics 140

Summary 140

Further reading 140

Review questions 141

Section 3: Molecular Genetics of Production and Economically Important Traits 143

15 Bioinformatics in Animal Genetics 145
José A. Carrillo and Jiuzhou Song

Introduction 145

Bioinformatics and animal genetics 145

The importance of bioinformatics in genomics research 146

Gene expression 148

Gene regulation 150

Epigenetics 151

Genomic data manipulation 151

Bioinformatics perspectives in animal genetics 153

References 153

Review questions 154

16 Genome-wide Association Studies in Pedigreed Populations 155
Dirk-Jan de Koning

Introduction 155

Methods and tools for GWAS in pedigreed populations 159

Things to remember about analysis 160

What did we miss? 160

Acknowledgments 162

References 162

17 Molecular Genetics Techniques and High Throughput Technologies 163
Wen Huang

Central dogma of molecular biology 163

Review of properties of nucleic acids 163

Purifi cation of nucleic acids from cells 164

Determining the quantity and purity of nucleic acids 165

Polymerase chain reaction (PCR) 166

Determining the identity of DNA 167

Concept of parallelization and high throughput assays 168

Next generation sequencing technology 171

Summary 174

Further reading 174

Review questions 174

18 Single Genes in Animal Breeding 177
Brian W. Kirkpatrick

Introduction 177

Mapping and identifying single genes 177

What types of DNA sequence alterations create single gene effects? 180

Examples of single genes in animal breeding 181

Summary 185

References 185

Review questions 186

19 Molecular Genetics of Coat Color: It is more than Just Skin Deep 187
Samantha Brooks

Introduction 187

Pathways of melanocyte migration and differentiation from the neural crest 187

Melanocyte signaling and regulation 188

Melanin production and transport 190

Conclusions 192

Summary 192

Key terms 192

References 193

Review questions 195

20 Molecular Genetics-Nutrition Interactions in Ruminant Fatty Acid Metabolism and Meat Quality 197
Aduli E.O. Malau-Aduli and Benjamin W.B. Holman

Introduction 197

Genetics-nutrition interactions in ruminants 197

Educating Australian undergraduate students in molecular genetics-nutrition interactions in ruminants 198

Review of fatty acids and their manipulation metabolism, and effect on quality in ruminants 200

Concluding remarks 205

Appendix 20.1: Fats and beef quality laboratory practicals 206

Appendix 20.2: Sensory evaluation of meat quality in grain-fed versus grass-fed beef 206

Appendix 20.3: Total lipid extraction from a beef cut for fatty acid analysis 206

Appendix 20.4: Molecular genetics laboratory practical 207 References 212

21 Nutritional Epigenomics 215
Congjun Li

Introduction 215

Epigenomic machinery and gene regulation 216

Nutrients and histone modification 219

Nutrients and epigenetics in bovine cells: one definative example of the nutrient-epigenetic-phenotype relationship 221

Summary 224

References 224

Review questions 225

Section 4: Genetics of Embryo Development and Fertility 227

22 Genomics of Sex Determination and Dosage Compensation 229
Jenifer Cruickshank and Christopher H. Chandler

Genotypic sex determination (GSD) 229

Environmental sex determination (ESD) 232

Dosage compensation in mammals: X chromosome inactivation 232

Activity patterns of sex chromosomes during gametogenesis 233

Escape from X inactivation 234

Abnormalities in chromosomal sex 235

Sex reversal 235

Summary 236

Further reading 236

Review questions 237

23 Functional Genomics of Mammalian Gametes and Preimplantation Embryos 239
Şule Doğan Aruna Govindaraju Elizabeth A. Crate, and Erdoğan Memili

Introduction 239

Gamete and embryo development 239

Transcriptomics 242

Proteomics 248

Systems biology 251

Conclusion 253

Further reading 253

References 253

24 The Genetics of In Vitro Produced Embryos 257
Ashley Driver

In vitro production: from livestock to humans 257

Unlocking developmentally important genes in the pre-implantation embryo 258

IVP: potential source of genetic alteration? 259

PGD: genetic screening and human embryos 259

Screening the embryo: to infinity and beyond? 260

Embryogenetics: what’s next? 260

Summary 260

Key terms 260

References 261

Review questions 262

Supplementary videos 262

Section 5: Genetics of Animal Health and Biotechnology 263

25 Understanding the Major Histocompatibility Complex and Immunoglobulin Genes 265
Michael G. Gonda

Introduction 265

Overview of the immune system 265

The major histocompatibility complex loci 267

Immunoglobulin loci 268

Summary 272

Key terms 273

Further reading and references 274

Review questions 274

26 Livestock and Companion Animal Genetics: Genetics of Infectious Disease Susceptibility 275
Michael G. Gonda

Introduction 275

Why is studying the genetics of disease susceptibility important? 275

Present applications of genetic selection tools for predicting disease susceptibility 276

Current research into genetic selection for livestock health 279

Challenges faced when studying the genetics of disease resistance in livestock 280

Should we select for increased disease resistance? 281

Summary 281

Key terms 281

Further reading 282

Review questions 282

27 Animal Genetics and Welfare 283
Amin A. Fadl and Mark E. Cook

Introduction 283

A continued need for genetic improvements and knowledge 283

Welfare 284

Genetic advancement and animal welfare 284

Genetic selection that adversely affects farmed animal welfare 286

Summary 287

References 287

Review questions 288

28 Animal Biotechnology: Scientific Regulatory and Public Acceptance Issues Associated with Cloned and Genetically Engineered Animals 289
Alison L. Van Eenennaam

What is animal biotechnology? 289

Cloning 290

Genetic engineering 293

Ethical moral and animal welfare concerns 297

Summary 299

Further reading 300

References 300

Review questions 301

29 Intellectual Property Rights and Animal Genetic Resources 303
Jennifer Long and Max F. Rothschild

Introduction 303

Old M/cDonald’s Farm meets Dolly (and her lawyer) 303

What is intellectual property? 303

Forms of intellectual property 303

Here a patent there (not) a patent 304

Forms of payment or remuneration 305

Case studies 306

E-I-E-I-O: The alphabet soup of domestic and international issues 307

Public sector research and IP – domestic and international 307

Access to animal genetic resources 307

Summary 308

Further reading 308

References 308

Review questions 309

Index 311