Molecular and Quantitative Animal Genetics

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 ixManuscript reviewers xiPreface xiii1 Decoding and Encoding the “DNA” of Teaching and Learning in College Classrooms 1Michel A. WattiauxIntroduction 1Teaching and learning: definitions 1Understanding learning 2Understanding teaching 5Implications for classroom design in the twenty-first century 6Final thoughts 9References 10Review questions 11Section 1: Quantitative and Population Genetics 132 Mating Systems: Inbreeding and Inbreeding Depression 15David L. ThomasIntroduction 15Inbreeding 15Cause of inbreeding depression 18Quantifying inbreeding 20Genomics and inbreeding 23Summary 23Further reading 24References 24Review questions 243 Genomic Selection Inbreeding and Crossbreeding in Dairy Cattle 25Kent WeigelIntroduction 25Genomic selection 25Crossbreeding 28Inbreeding and genetic defects 29Summary 30References 30Review questions 314 Basic Genetic Model for Quantitative Traits 33Guilherme J. M. RosaIntroduction 33Quantitative traits 33Expected value and variance: the normal distribution 33Basic genetic model for quantitative traits 35Heritability and selection 35Predicting rate of genetic change from selection 36Further reading 37References 375 Heritability and Repeatability 39Guilherme J. M. RosaIntroduction 39Heritability 39Estimation of heritability and variance components 40Prediction of breeding values and of response to selection 41Repeatability 41References 426 Applications of Statistics in Quantitative Traits 43Hayrettin OkutPopulation and sample 43Descriptive statistics 43Graphically examining the distribution of the data 47Normal distribution 49Exploring relationships between variables 53Summary 59Appendix 6.1 62Further reading 62References 62Review questions 63Section 2: Applications of Genetics and Genomics to Livestock and Companion Animal Species 657 Genetic Improvement of Beef Cattle 67Michael D. MacNeilIntroduction 67Single trait selection 67National cattle evaluation 69Multiple trait selection 71Summary 71Further reading 71References 728 Genetic Improvement in Sheep through Selection 73David L. ThomasProducts from sheep 73Selection among breeds 73Selection within a breed or population and the Key Equation 73Adjustment for environmental effects 73Phenotypic selection 75Estimated breeding values (EBV) 75Using multiple sources of information 76Genetic correlations 76Selection intensity 78Generation interval (L) 79Predicting progress from selection 79National genetic improvement programs 80Summary 81Further reading 82References 82Review questions 829 Genetic Improvement Programs for Dairy Cattle 85Kent WeigelIntroduction 85Data collection infrastructure 85Estimation of breeding values 87Selection for increased productivity 89Selection for functional traits 91Sire selection 94Summary 94Further reading 95References 95Review questions 9610 Genetic and Genomic Improvement of Pigs 97Max F. RothschildIntroduction 97Domestication of swine and breed development 97Methods of selection and mating systems 98Traits of economic importance 99Development of molecular genetic approaches 100QTL candidate genes and genetic improvement 100Sequencing the pig genome 101Genomic selection 102Databases 103Cloning transgenics and breeding pigs as biological models 103Future applications to genetic improvement 103Acknowledgments 104Further reading 104References 104Review questions 10511 Equine Genetics 107Jennifer Minick BormannColor 107Genetic defects 110Inbreeding and relationship 113Selection and improvement 114New technologies 116Further reading 117References 119Review questions 11912 Genetics and Genomics of the Domestic Dog 121Leigh Anne Clark and Alison Starr-MossIntroduction to canine research 121The dog genome 122Uncovering the genetic basis of phenotypes 125Future challenges 127Summary 128Further reading 129References 130Review questions 13013 The Sheep Genome 131Noelle E. Cockett and Chunhua WuInvestment in sheep genome research 131Overview of the sheep genome 131Genomic resources in sheep 131Application of genomic resources 134Summary 134References 135Review questions 13614 Goat Genetics and Genomic Progress 137Mulumebet WorkuIntroduction 137Genetics and goat domestication 137Taxonomy 138Goat chromosome number and structure 138Patterns of inheritance 139Quantitative trail loci (QTL) 139Progress in goat genomics 139Biotechnologies and goat genetics 140Summary 140Further reading 140Review questions 141Section 3: Molecular Genetics of Production and Economically Important Traits 14315 Bioinformatics in Animal Genetics 145José A. Carrillo and Jiuzhou SongIntroduction 145Bioinformatics and animal genetics 145The importance of bioinformatics in genomics research 146Gene expression 148Gene regulation 150Epigenetics 151Genomic data manipulation 151Bioinformatics perspectives in animal genetics 153References 153Review questions 15416 Genome-wide Association Studies in Pedigreed Populations 155Dirk-Jan de KoningIntroduction 155Methods and tools for GWAS in pedigreed populations 159Things to remember about analysis 160What did we miss? 160Acknowledgments 162References 16217 Molecular Genetics Techniques and High Throughput Technologies 163Wen HuangCentral dogma of molecular biology 163Review of properties of nucleic acids 163Purifi cation of nucleic acids from cells 164Determining the quantity and purity of nucleic acids 165Polymerase chain reaction (PCR) 166Determining the identity of DNA 167Concept of parallelization and high throughput assays 168Next generation sequencing technology 171Summary 174Further reading 174Review questions 17418 Single Genes in Animal Breeding 177Brian W. KirkpatrickIntroduction 177Mapping and identifying single genes 177What types of DNA sequence alterations create single gene effects? 180Examples of single genes in animal breeding 181Summary 185References 185Review questions 18619 Molecular Genetics of Coat Color: It is more than Just Skin Deep 187Samantha BrooksIntroduction 187Pathways of melanocyte migration and differentiation from the neural crest 187Melanocyte signaling and regulation 188Melanin production and transport 190Conclusions 192Summary 192Key terms 192References 193Review questions 19520 Molecular Genetics-Nutrition Interactions in Ruminant Fatty Acid Metabolism and Meat Quality 197Aduli E.O. Malau-Aduli and Benjamin W.B. HolmanIntroduction 197Genetics-nutrition interactions in ruminants 197Educating Australian undergraduate students in molecular genetics-nutrition interactions in ruminants 198Review of fatty acids and their manipulation metabolism, and effect on quality in ruminants 200Concluding remarks 205Appendix 20.1: Fats and beef quality laboratory practicals 206Appendix 20.2: Sensory evaluation of meat quality in grain-fed versus grass-fed beef 206Appendix 20.3: Total lipid extraction from a beef cut for fatty acid analysis 206Appendix 20.4: Molecular genetics laboratory practical 207 References 21221 Nutritional Epigenomics 215Congjun LiIntroduction 215Epigenomic machinery and gene regulation 216Nutrients and histone modification 219Nutrients and epigenetics in bovine cells: one definative example of the nutrient-epigenetic-phenotype relationship 221Summary 224References 224Review questions 225Section 4: Genetics of Embryo Development and Fertility 22722 Genomics of Sex Determination and Dosage Compensation 229Jenifer Cruickshank and Christopher H. ChandlerGenotypic sex determination (GSD) 229Environmental sex determination (ESD) 232Dosage compensation in mammals: X chromosome inactivation 232Activity patterns of sex chromosomes during gametogenesis 233Escape from X inactivation 234Abnormalities in chromosomal sex 235Sex reversal 235Summary 236Further reading 236Review questions 23723 Functional Genomics of Mammalian Gametes and Preimplantation Embryos 239Şule Doğan Aruna Govindaraju Elizabeth A. Crate, and Erdoğan MemiliIntroduction 239Gamete and embryo development 239Transcriptomics 242Proteomics 248Systems biology 251Conclusion 253Further reading 253References 25324 The Genetics of In Vitro Produced Embryos 257Ashley DriverIn vitro production: from livestock to humans 257Unlocking developmentally important genes in the pre-implantation embryo 258IVP: potential source of genetic alteration? 259PGD: genetic screening and human embryos 259Screening the embryo: to infinity and beyond? 260Embryogenetics: what’s next? 260Summary 260Key terms 260References 261Review questions 262Supplementary videos 262Section 5: Genetics of Animal Health and Biotechnology 26325 Understanding the Major Histocompatibility Complex and Immunoglobulin Genes 265Michael G. GondaIntroduction 265Overview of the immune system 265The major histocompatibility complex loci 267Immunoglobulin loci 268Summary 272Key terms 273Further reading and references 274Review questions 27426 Livestock and Companion Animal Genetics: Genetics of Infectious Disease Susceptibility 275Michael G. GondaIntroduction 275Why is studying the genetics of disease susceptibility important? 275Present applications of genetic selection tools for predicting disease susceptibility 276Current research into genetic selection for livestock health 279Challenges faced when studying the genetics of disease resistance in livestock 280Should we select for increased disease resistance? 281Summary 281Key terms 281Further reading 282Review questions 28227 Animal Genetics and Welfare 283Amin A. Fadl and Mark E. CookIntroduction 283A continued need for genetic improvements and knowledge 283Welfare 284Genetic advancement and animal welfare 284Genetic selection that adversely affects farmed animal welfare 286Summary 287References 287Review questions 28828 Animal Biotechnology: Scientific Regulatory and Public Acceptance Issues Associated with Cloned and Genetically Engineered Animals 289Alison L. Van EenennaamWhat is animal biotechnology? 289Cloning 290Genetic engineering 293Ethical moral and animal welfare concerns 297Summary 299Further reading 300References 300Review questions 30129 Intellectual Property Rights and Animal Genetic Resources 303Jennifer Long and Max F. RothschildIntroduction 303Old M/cDonald’s Farm meets Dolly (and her lawyer) 303What is intellectual property? 303Forms of intellectual property 303Here a patent there (not) a patent 304Forms of payment or remuneration 305Case studies 306E-I-E-I-O: The alphabet soup of domestic and international issues 307Public sector research and IP – domestic and international 307Access to animal genetic resources 307Summary 308Further reading 308References 308Review questions 309Index 311