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 137 Chapter 6.13: Rate of inbreeding and active population size 139 Chapter 6.14: Predict the rate of inbreeding 141 Chapter 6.15: What rate of inbreeding is acceptable? 143 Chapter 6.16: Key issues on genetic diversity and inbreeding 143 Chapter 7: Inheritance of monogenic traits 144 Chapter 7.1 Calculation of allele frequencies 146 Chapter 7.2 Hardy and Weinberg equilibrium 146 Chapter 7.3 Random effects in matings 148 Chapter 7.4 Breeding aspects of genes with large (positive) effects 149 Chapter 7.4.1 Colour genes in ruminants 150 Chapter 7.4.2 Colour genes in pigs 152 Chapter 7.4.3 Colour genes in horses 152 Chapter 7.4.4 Coat colours in dogs 153 Chapter 7.4.5 Colour genes in poultry 154 Chapter 7.5 Breeding aspects of monogenic traits with negative effects 154 Chapter 7.6 Testing parents for monogenic traits when no genetic markers are available 156 Chapter 7.7 The value of genetic markers in testing parents for genetic defects 156 Chapter 7.8 Elimination of recessive alleles for genetic defects with genetic markers 158 Chapter 7.9 Key issues in inheritance of monogenic traits 159 Chapter 8: Ranking the animals 160 Chapter 8.1: Ranking the animals: an overview of methods 162 Chapter 8.1.1: Mass selection 162 Chapter 8.1.2: Animal Model 163 Chapter 8.1.3: Genomic selection 163 Chapter 8.2: In more detail: breeding value estimation 164 Chapter 8.2.1: The basic statistics 166 Chapter 8.3: Optimising the phenotypic information 167 Chapter 8.4: Accuracy of the breeding value: the basic concept 168 Chapter 8.5: Breeding value estimation: Mass selection 169 Chapter 8.5.1: Special case: repeated observations on a single animal 170 Chapter 8.6: Breeding value estimation: the Animal Model 171 Chapter 8.7: Breeding value estimation: the basic situation 172 Chapter 8.7.1: Breeding value estimation: the rabbit example on mass selection 172 Chapter 8.7.2: Breeding value estimation: a sheep example with information from parents 173 Chapter 8.8: Other types of information sources 173 Chapter 8.9: Examples of estimating breeding values 175 Chapter 8.10: Best Linear Unbiased Prediction 176 Chapter 8.11: Accuracy of estimated breeding values 178 Chapter 8.11.1: Effect of additional information on the accuracy 179 Chapter 8.12: Summary of breeding value estimation 180 Chapter 8.13: Effects of number of offspring on the accuracy 181 Chapter 8.14: Go for highest EBV or highest accuracy? 182 Chapter 8.14.1: Outweighing EBV and accuracy in a dairy cattle example 183 Chapter 8.15: Genomic selection 184 Chapter 8.15.1: Principle of genomic selection 185 Chapter 8.15.2: Composition of the reference population 186 Chapter 8.15.3: Accuracy of genomic selection 187 Chapter 8.15.4: The size of the reference population 188 Chapter 8.16: Key issues on ranking the animals 189 Chapter 9: Predicting response to selection 190 Chapter 9.1: Response to selection: an overview 191 Chapter 9.2: Breeding is about predicting the future 193 Chapter 9.3: Genetic response: the basic principle 194 Chapter 9.4: Response to mass selection 196 Chapter 9.5: Selected proportion and selection intensity 197 Chapter 9.5.1: Appendix: from selected proportion to selection intensity 199 Chapter 9.6: Selection response: the generalized approach 201 Chapter 9.6.1: An example: the Arabian horse 202 Chapter 9.6.2: an example: rabbit breeding 203 Chapter 9.7: Generation interval 204 Chapter 9.8: Optimising genetic gain 205 Chapter 9.9: Selection paths 207 Chapter 9.9.1: an example: beef cattle breeding 208 Chapter 9.10: More detailed selection paths 209 Chapter 9.10.1: An example: dairy cattle breeding 210 Chapter 9.11: Selection intensity and rate of inbreeding 211 Chapter 9.11.1: Special case: indirect selection 212 Chapter 9.12: Practical issues with predicting response to selection 214 Chapter 9.13: Key issues on predicting response to selection 215 Chapter 10: Selection and mating 216 Chapter 10.1: Selection criteria and mating decisions 218 Chapter 10.2: Compensatory mating 219 Chapter 10.3: Long term genetic contribution 220 Chapter 10.3.1: Example of genetic contributions 221 Chapter 10.3.2: Relation between genetic contribution and inbreeding 222 Chapter 10.3.3: Example of the effect of a popular ram on inbreeding 222 Chapter 10.4: Breeding limitations 224 Chapter 10.5: Genetic contributions and occurrence of recessive disorders 225 Chapter 10.5.1: Heavy use of a sire for the frequency of genetic defects 227 Chapter 10.6: Confirmation of parenthood 227 Chapter 10.7: Key issues on selection and inbreeding 228 Chapter 11: Crossbreeding 229 Chapter 11.1 Definitions of a breed 231 Chapter 11.2 Heterosis 232 Chapter 11.3 The genetic background of heterosis 233 Chapter 11.4 Effects of heterosis 234 Chapter 11.5 Motivation for crossbreeding 235 Chapter 11.6 The different crossbreeding systems and their applicability 237 Chapter 11.6.1 Two-way cross (pure-breed cross) 237 Chapter 11.6.2 Three-way cross 238 Chapter 11.6.3 Four-way crosses 238 Chapter 11.6.4 Two-way rotation (crisscross) 239 Chapter 11.6.5 Three-way rotation (crisscross) 240 Chapter 11.6.6 Introgression 240 Chapter 11.6.7 Grading-up 240 Chapter 11.6.8 Creating a synthetic breed 241 Chapter 11.7 Key issues on crossbreeding 242 Chapter 12: The structure of breeding programs 242 Chapter 12.1: Genetic improvement in a breeding program 244 Chapter 12.2: Breeding programs are less or more in control 244 Chapter 12.3: Breeding programs with a flat structure 246 Chapter 12.3.1: Example of a breeding program with a flat structure: the KWPN program 247 Chapter 12.4: Breeding programs with an (open) nucleus 249 Chapter 12.4.1: Example: an open nucleus breeding program: the CRV dairy program 249 250 Chapter 12.5: Breeding programs with a pyramidal structure 255 Chapter 12.5.1: Example: breeding program with a pyramidal structure: the Topigs program 256 Chapter 12.6: Key issues on breeding programs 260 Chapter 13: Evaluation of the breeding program 260 Chapter 13.1: How to measure genetic improvement? 262 Chapter 13.2: Genetic trend 263 Chapter 13.3: What could be influencing the realised response to selection? 264 Chapter 13.4: Selection limits 266 Chapter 13.5: Practical issues influencing response to selection 267 Chapter 13.6: Genotype by Environment interaction 268 Chapter 13.6.1: Prerequisites determine the environment 269 Chapter 13.6.2: Consequences of GxE for the breeding program 271 Chapter 13.6.3: Correlated response 273 Chapter 13.6.4: Limiting resources 274 Chapter 13.6.5: Role of the environment 276 Chapter 13.6.6: Evidence for the resource allocation model 277 Chapter 13.6.7: Correlations and genotype by environment interaction 278 Chapter 13.7: Solutions to undesirable correlations 278 Chapter 13.8: Future expectations: where to go from here? 279 Chapter 13.9: Balance between progress and genetic diversity 280 Chapter 13.10: Key issues of the chapter on evaluation of the breeding program 281 Chapter 14: Maintenance of genetic diversity 281 Chapter 14.1: Genetic diversity 283 Chapter 14.1.1 Genetic diversity in dogs 283 Chapter 14.1.2 Genetic diversity in farm animals 284 Chapter 14.1.3 Importance of variation between breeds 284 Chapter 14.1.4 Origin of differences between breeds 285 Chapter 14.1.5 Origin of differences within breeds 286 Chapter 14.2: Example: FAO’s global plan for farm animal genetic resources 287 Chapter 14.2.1: An example of the use of a conserved breed for research 290 Chapter 14.2.2: An example of the use of a rare breed 291 Chapter 14.3: The conservation of breeds in The Netherlands 293 Chapter 14.3.1: Revival of the native Dutch Red and White Friesian cow 294 Chapter 14.4: The use of pedigrees for measuring genetic diversity 297 Chapter 14.5: The impact of DNA information on measuring genetic diversity 297 Chapter 14.5.1: Genome-wide patters of diversity 298 Chapter 14.5.1.1: An example of haplotypes: B-blood groups of cattle 300 Chapter 14.5.1.2: An example of introgression: Booroola allele in Texel sheep 300 Chapter 14.6: Monitoring populations 301 Chapter 14.6.1: Voluntary and constrained inbreeding 302 Chapter 14.6.1.1: An outcross is very effective to reduce inbreeding 302 Chapter 14.6.2: Population size 303 Chapter 14.6.3: The ideal population 304 Chapter 14.6.4: Monitoring the rate of inbreeding 305 Chapter 14.6.5: Relationship between the additive genetic relationship and inbreeding 306 Chapter 14.7: Prevention of inbreeding 307 Chapter 14.7.1: Expansion of the size of the population 307 Chapter 14.7.2: Restrictions in the use of parents 309 Chapter 14.7.3: Mating schemes to control and manage relationship 309 Chapter 14.8: Key issues on genetic diversity 311