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Textbook Animal Breeding Animal Breeding and Genetics for Bsc Students Textbook animal breeding Animal breeding and genetics for BSc students Author: Kor Oldenbroek en Liesbeth van der Waaij, 2014. Centre for Genetic Resources and Animal Breeding and Genomics Group, Wageningen University and Research Centre, the Netherlands. Groen Kennisnet Table of Contents Chapter 1: Introduction to animal breeding 13 Chapter 1.1 The history of animal breeding: science and application 14 Chapter 1.2 Selection by nature 16 Chapter 1.3 Domestication and animal breeding 17 Chapter 1.4 Domestication continues 20 Chapter 1.5 Origin of animal breeding: a history of science 21 Chapter 1.6 Breeding in the 19-th century 23 Chapter 1.7 Animal breeding in the 20-th century 23 Chapter 1.8 Introduction of DNA in animal breeding 26 Chapter 1.9 Animal breeding: link to societal requirements 27 Chapter 1.10 Organization of breeding activities 29 Chapter 1.11 Relation society and breeding 30 Chapter 1.12 Results of animal breeding 33 Chapter 1.13 Negative effects of animal breeding 36 Chapter 1.14 Key issues in animal breeding 39 Chapter 2: Basics of animal breeding 40 Chapter 2.1 Set up of a breeding program 41 Chapter 2.2 DNA as carrier 43 Chapter 2.3 Structure and composition of chromosomes 45 Chapter 2.4 The transfer from chromosomes and genes from parent to offspring 46 Chapter 2.5 The expression of genes, of their alleles, in the phenotype 46 Chapter 2.6 Meiosis creates differences among offspring of an individual 49 Chapter 2.7 Relatives share similar DNA, they have a relationship 50 Chapter 2.8 Key issues in basics of animal breeding 51 Chapter 3: Reasons to keep animals determine the breeding goal 52 Chapter 3.1 Challenges for animal breeding 54 Chapter 3.2 Breeding goals depend on the production system 54 Chapter 3.3 The choice of the appropriate breed 55 Chapter 3.4 The breeding goal 56 Chapter 3.5 Breeding goals are directed towards the future and require tenacity 56 Chapter 3.6 Breeding goals consists of several traits 57 Chapter 3.7 Measurement of breeding goal traits 58 Chapter 3.8 The breeding goal determines which traits should be recorded. 58 Chapter 3.9 Weighing the different traits of the breeding goal 60 Chapter 3.10 Aspects of sustainability and economics in breeding goals 62 Chapter 3.11 Key issues in reasons to keep animals determine the breeding goal 63 Chapter 3.12 Example: Pig breeding goals 64 Chapter 3.13 Chapter Example: Breeding goals for horses 66 Chapter 3.14 Example: Dutch milk production index 68 Chapter 3.15 Example: Breeding methods of top breeders in dogs 70 Chapter 3.16 Example: Production objectives for village poultry in Ethiopia 71 Chapter 4: Collecting information for breeding decisions 72 Chapter 4.1 The value of a pedigree in animal breeding 73 Chapter 4.2 A unique identification system for animals is essential 76 Chapter 4.3 Collecting phenotypes, monogenic and polygenic traits 76 Chapter 4.4 Mean, variation, standard deviation and coefficient of variation 77 Chapter 4.5 Normal distribution of measurements 78 Chapter 4.6 Covariance and correlation 79 Chapter 4.7 Regression 80 Chapter 4.8 Measurement errors 81 Chapter 4.9 Frequency of measurements 82 Chapter 4.10 Measurements on the animal or on relatives? 82 Chapter 4.11 Value of indicator traits 83 Chapter 4.12 Value of information of relatives 83 Chapter 4.13 The possibilities of DNA analysis 85 Chapter 4.14 DNA markers 86 Chapter 4.14.1 Parentage control 86 Chapter 4.14.2 Marker-assisted and genomic selection 89 Chapter 4.15 Key issues in collecting information for breeding decisions 91 Chapter 5: Genetic models 92 Chapter 5.1 Phenotype and environment during life history 94 Chapter 5.1.1 Events before birth 94 Chapter 5.1.2 Events after birth 95 Chapter 5.1.3 Events after weaning 95 Chapter 5.1.4 Events after maturity 95 Chapter 5.1.5 Events after reproductive phase 96 Chapter 5.2 Phenotype in a model 96 Chapter 5.3 Monogenic genetic variation 97 Chapter 5.4 Polygenic genetic variation 98 Chapter 5.5 Variance components 100 Chapter 5.6 Simplify the genetic model 101 Chapter 5.7 Next generation: transmission model 102 Chapter 5.8 Heritability 104 Chapter 5.9 Simply estimating the heritability: parent-offspring regression 106 Chapter 5.10 Misconceptions about the heritability 107 Chapter 5.11 Non-genetic influences: The variance due to a Common Environment 109 Chapter 5.11.1 Importance of common environment 110 Chapter 5.11.2 Examples of common environmental effects 110 Chapter 5.11.3 Special case of a common environmental effect: the maternal effect 111 112 Chapter 5.11.4 A special common environmental effect: (indirect) social genetic effect 112 Chapter 5.12 Key issues of genetic models 114 Chapter 6: Genetic diversity and inbreeding 114 Chapter 6.1: What is genetic diversity? 116 Chapter 6.2: Forces that influence genetic diversity 117 Chapter 6.2.1: Loss of genetic diversity: genetic drift 118 Chapter 6.2.2: Loss of genetic diversity: selection 120 122 Chapter 6.2.3: Diversity and migration 123 Chapter 6.2.4: Increase in genetic diversity: mutation 125 Chapter 6.3: Change in diversity: inbreeding 125 Chapter 6.4: Causes of inbreeding 126 Chapter 6.5: Inevitable inbreeding 126 Chapter 6.6: Why is genetic diversity important? 127 Chapter 6.7: Toolbox:relationships 128 Chapter 6.7.1: Additive genetic relationship 129 Chapter 6.7.2: Calculation of additive relationships 130 Chapter 6.8: Additive genetic relationship using genomic information 131 Chapter 6.9: Realised additive relationship 133 Chapter 6.10: Inbreeding coefficient and relationship 133 Chapter 6.11: Additive genetic relationship when the common ancestor is inbred 134 Chapter 6.12: Inbreeding at population level: the rate of inbreeding 136 Chapter 6.13: Rate of inbreeding and active population size 138 Chapter 6.14: Predict the rate of inbreeding 140 Chapter 6.15: What rate of inbreeding is acceptable? 142 Chapter 6.16: Key issues on genetic diversity and inbreeding 142 Chapter 7: Inheritance of monogenic traits 143 Chapter 7.1 Calculation of allele frequencies 145 Chapter 7.2 Hardy and Weinberg equilibrium 145 Chapter 7.3 Random effects in matings 147 Chapter 7.4 Breeding aspects of genes with large (positive) effects 148 Chapter 7.4.1 Colour genes in ruminants 149 Chapter 7.4.2 Colour genes in pigs 151 Chapter 7.4.3 Colour genes in horses 151 Chapter 7.4.4 Coat colours in dogs 152 Chapter 7.4.5 Colour genes in poultry 153 Chapter 7.5 Breeding aspects of monogenic traits with negative effects 153 Chapter 7.6 Testing parents for monogenic traits when no genetic markers are available 155 Chapter 7.7 The value of genetic markers in testing parents for genetic defects 155 Chapter 7.8 Elimination of recessive alleles for genetic defects with genetic markers 157 Chapter 7.9 Key issues in inheritance of monogenic traits 158 Chapter 8: Ranking the animals 159 Chapter 8.1: Ranking the animals: an overview of methods 161 Chapter 8.1.1: Mass selection 161 Chapter 8.1.2: Animal Model 162 Chapter 8.1.3: Genomic selection 162 Chapter 8.2: In more detail: breeding value estimation 163 Chapter 8.2.1: The basic statistics 165 Chapter 8.3: Optimising the phenotypic information 166 Chapter 8.4: Accuracy of the breeding value: the basic concept 167 Chapter 8.5: Breeding value estimation: Mass selection 168 Chapter 8.5.1: Special case: repeated observations on a single animal 169 Chapter 8.6: Breeding value estimation: the Animal Model 170 Chapter 8.7: Breeding value estimation: the basic situation 171 Chapter 8.7.1: Breeding value estimation: the rabbit example on mass selection 171 Chapter 8.7.2: Breeding value estimation: a sheep example with information from parents 172 Chapter 8.8: Other types of information sources 172 Chapter 8.9: Examples of estimating breeding values 174 Chapter 8.10: Best Linear Unbiased Prediction 175 Chapter 8.11: Accuracy of estimated breeding values 177 Chapter 8.11.1: Effect of additional information on the accuracy 178 Chapter 8.12: Summary of breeding value estimation 179 Chapter 8.13: Effects of number of offspring on the accuracy 180 Chapter 8.14: Go for highest EBV or highest accuracy? 181 Chapter 8.14.1: Outweighing EBV and accuracy in a dairy cattle example 182 Chapter 8.15: Genomic selection 183 Chapter 8.15.1: Principle of genomic selection 184 Chapter 8.15.2: Composition of the reference population 185 Chapter 8.15.3: Accuracy of genomic selection 186 Chapter 8.15.4: The size of the reference population 187 Chapter 8.16: Key issues on ranking the animals 188 Chapter 9: Predicting response to selection 189 Chapter 9.1: Response to selection: an overview 190 Chapter 9.2: Breeding is about predicting the future 192 Chapter 9.3: Genetic response: the basic principle 193 Chapter 9.4: Response to mass selection 195 Chapter 9.5: Selected proportion and selection intensity 196 Chapter 9.5.1: Appendix: from selected proportion to selection intensity 198 Chapter 9.6: Selection response: the generalized approach 200 Chapter 9.6.1: An example: the Arabian horse 201 Chapter 9.6.2: an example: rabbit breeding 202 Chapter 9.7: Generation interval 203 Chapter 9.8: Optimising genetic gain 204 Chapter 9.9: Selection paths 206 Chapter 9.9.1: an example: beef cattle breeding 207 Chapter 9.10: More detailed selection paths 208 Chapter 9.10.1: An example: dairy cattle breeding 209 Chapter 9.11: Selection intensity and rate of inbreeding 210 Chapter 9.11.1: Special case: indirect selection 211 Chapter 9.12: Practical issues with predicting response to selection 213 Chapter 9.13: Key issues on predicting response to selection 214 Chapter 10: Selection and mating
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