Molecular and Quantitative Animal Genetics

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