Textbook animal breeding Animal breeding and genetics for BSc

311 Pages·2015·16.13 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 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 215
Chapter 10.1: Selection criteria and mating decisions 217
Chapter 10.2: Compensatory mating 218
Chapter 10.3: Long term genetic contribution 219
Chapter 10.3.1: Example of genetic contributions 220
Chapter 10.3.2: Relation between genetic contribution and inbreeding 221
Chapter 10.3.3: Example of the effect of a popular ram on inbreeding 221
Chapter 10.4: Breeding limitations 223
Chapter 10.5: Genetic contributions and occurrence of recessive disorders 224
Chapter 10.5.1: Heavy use of a sire for the frequency of genetic defects 226
Chapter 10.6: Confirmation of parenthood 226
Chapter 10.7: Key issues on selection and inbreeding 227
Chapter 11: Crossbreeding 228
Chapter 11.1 Definitions of a breed 230
Chapter 11.2 Heterosis 231
Chapter 11.3 The genetic background of heterosis 232
Chapter 11.4 Effects of heterosis 233
Chapter 11.5 Motivation for crossbreeding 234
Chapter 11.6 The different crossbreeding systems and their applicability 236
Chapter 11.6.1 Two-way cross (pure-breed cross) 236
Chapter 11.6.2 Three-way cross 237
Chapter 11.6.3 Four-way crosses 237
Chapter 11.6.4 Two-way rotation (crisscross) 238
Chapter 11.6.5 Three-way rotation (crisscross) 239
Chapter 11.6.6 Introgression 239
Chapter 11.6.7 Grading-up 239
Chapter 11.6.8 Creating a synthetic breed 240
Chapter 11.7 Key issues on crossbreeding 241
Chapter 12: The structure of breeding programs 241
Chapter 12.1: Genetic improvement in a breeding program 243
Chapter 12.2: Breeding programs are less or more in control 243
Chapter 12.3: Breeding programs with a flat structure 245
Chapter 12.3.1: Example of a breeding program with a flat structure: the KWPN program 246
Chapter 12.4: Breeding programs with an (open) nucleus 248
Chapter 12.4.1: Example: an open nucleus breeding program: the CRV dairy program 248
249
Chapter 12.5: Breeding programs with a pyramidal structure 254
Chapter 12.5.1: Example: breeding program with a pyramidal structure: the Topigs program 255
Chapter 12.6: Key issues on breeding programs 259
Chapter 13: Evaluation of the breeding program 259
Chapter 13.1: How to measure genetic improvement? 261
Chapter 13.2: Genetic trend 262
Chapter 13.3: What could be influencing the realised response to selection? 263
Chapter 13.4: Selection limits 265
Chapter 13.5: Practical issues influencing response to selection 266
Chapter 13.6: Genotype by Environment interaction 267
Chapter 13.6.1: Prerequisites determine the environment 268
Chapter 13.6.2: Consequences of GxE for the breeding program 270
Chapter 13.6.3: Correlated response 272
Chapter 13.6.4: Limiting resources 273
Chapter 13.6.5: Role of the environment 275
Chapter 13.6.6: Evidence for the resource allocation model 276
Chapter 13.6.7: Correlations and genotype by environment interaction 277
Chapter 13.7: Solutions to undesirable correlations 277
Chapter 13.8: Future expectations: where to go from here? 278
Chapter 13.9: Balance between progress and genetic diversity 279
Chapter 13.10: Key issues of the chapter on evaluation of the breeding program 280
Chapter 14: Maintenance of genetic diversity 280
Chapter 14.1: Genetic diversity 282
Chapter 14.1.1 Genetic diversity in dogs 282
Chapter 14.1.2 Genetic diversity in farm animals 283
Chapter 14.1.3 Importance of variation between breeds 283
Chapter 14.1.4 Origin of differences between breeds 284
Chapter 14.1.5 Origin of differences within breeds 285
Chapter 14.2: Example: FAO’s global plan for farm animal genetic resources 286
Chapter 14.2.1: An example of the use of a conserved breed for research 289
Chapter 14.2.2: An example of the use of a rare breed 290
Chapter 14.3: The conservation of breeds in The Netherlands 292
Chapter 14.3.1: Revival of the native Dutch Red and White Friesian cow 293
Chapter 14.4: The use of pedigrees for measuring genetic diversity 296
Chapter 14.5: The impact of DNA information on measuring genetic diversity 296
Chapter 14.5.1: Genome-wide patters of diversity 297
Chapter 14.5.1.1: An example of haplotypes: B-blood groups of cattle 299
Chapter 14.5.1.2: An example of introgression: Booroola allele in Texel sheep 299
Chapter 14.6: Monitoring populations 300
Chapter 14.6.1: Voluntary and constrained inbreeding 301
Chapter 14.6.1.1: An outcross is very effective to reduce inbreeding 301
Chapter 14.6.2: Population size 302
Chapter 14.6.3: The ideal population 303
Chapter 14.6.4: Monitoring the rate of inbreeding 304
Chapter 14.6.5: Relationship between the additive genetic relationship and inbreeding 305
Chapter 14.7: Prevention of inbreeding 306
Chapter 14.7.1: Expansion of the size of the population 306
Chapter 14.7.2: Restrictions in the use of parents 308
Chapter 14.7.3: Mating schemes to control and manage relationship 308
Chapter 14.8: Key issues on genetic diversity 310