Textbook Animal Breeding and Genetics

312 Pages·2016·16.23 MB·English

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