Preface
The course "Animal Breeding and Genetics"
introduces how breeding programs can be
set up to genetically improve populations
and conserve genetic diversity. The course
deals with all the steps to take when setting
up a breeding program as shown in the
figure. The figure will be used throughout
the course to indicate where we are. Those
principles apply to livestock, companion,
zoo animals or populations of endangered
breeds.
The lecture notes are written by Liesbeth
van der Waaij, Kor Oldenbroek, Dieuwertje
Lont, Piter Bijma and Han Mulder. The first
version of these notes were used in the
academic year 2014-2015. The lecture notes were redesigned to teach animal breeding
from practice to theory and to show what is needed for breeding programs. These lecture
notes are based on teaching experiences accumulated across the years. We provide many
examples covering a wide range of species, and aim to update those regularly. We have
checked the notes carefully, but no doubt there will be some typographical or other errors.
Please tell us, so we can improve the lecture notes in the coming years.
We hope that these lecture notes will help you in understanding the principles of animal
breeding and getting you excited about this interesting field in animal science!!!
Mario Calus
Pascal Duenk
Wageningen, August 2025
1
,Table of Contents
Preface ................................................................................................................ 1
Chapter 1: What is animal breeding? ....................................................................... 7
Animal breeding in context .......................................................................................................9
Animal breeding: link to societal changes ................................................................................. 15
Present and future times ........................................................................................................ 18
What has been accomplished using animal breeding? ................................................................. 20
What can you expect from this course? .................................................................................... 29
References ........................................................................................................................... 30
Chapter 2: Defining breeding goal and setting up a breeding program ....................... 31
Learning outcomes ................................................................................................................ 31
Introduction ......................................................................................................................... 31
The breeding goal ................................................................................................................. 32
Breeding goals based on economic values derived from economic models ..................................... 35
Breeding goals based on non-economic values .......................................................................... 37
The remaining steps to set up a breeding program..................................................................... 39
Key issues ........................................................................................................................... 40
References ........................................................................................................................... 40
Chapter 3: Introduction in genetics and statistics .................................................... 41
Learning outcomes (assumed knowledge)................................................................................. 41
DNA as carrier of genetic information passed on to next generation .............................................. 41
DNA composition .................................................................................................................. 41
The transfer of chromosomes and genes from parent to offspring ................................................ 42
The mode of expression of genes ............................................................................................ 42
Recombination creates differences among offspring of an individual ............................................. 44
Characteristics of monogenic traits .......................................................................................... 46
Statistical measures for continuous phenotypic measurements .................................................... 47
Normal distribution of measurements....................................................................................... 49
Relationships between traits: Covariance, correlation and regression ............................................ 50
Appendix: Rules for calculations with continuous variables .......................................................... 53
Key issues ........................................................................................................................... 54
References ........................................................................................................................... 54
Chapter 4: Collection of information ...................................................................... 55
Learning outcomes ................................................................................................................ 55
The value of a pedigree in animal breeding ............................................................................... 55
A unique identification system for animals is essential ................................................................ 56
Collection of phenotypes ........................................................................................................ 56
Collection of DNA information ................................................................................................. 62
Key issues ........................................................................................................................... 67
Chapter 5: Genetic models ................................................................................... 69
2
, Learning outcomes ................................................................................................................ 69
Introduction ......................................................................................................................... 69
Phenotype and environment ................................................................................................... 70
Phenotype in a model ............................................................................................................ 72
Genetic variation .................................................................................................................. 73
Variance components ............................................................................................................ 75
Simplify the genetic model ..................................................................................................... 76
Next generation: transmission model ....................................................................................... 77
Heritability ........................................................................................................................... 78
Simple method for estimating the heritability: parent-offspring regression .................................... 80
Misconceptions about the heritability ....................................................................................... 81
Non-genetic influences: The variance due to a Common Environment ........................................... 82
Repeatability model and permanent environmental effects .......................................................... 86
Multi-trait model ................................................................................................................... 88
Key issues ........................................................................................................................... 90
Chapter 6: Genetic diversity and inbreeding ........................................................... 91
Learning outcomes ................................................................................................................ 91
What is genetic diversity? ...................................................................................................... 92
Forces that influence genetic diversity ...................................................................................... 93
Change in diversity: inbreeding ............................................................................................... 99
Why is genetic diversity important? ....................................................................................... 101
Toolbox 1: Relationships ...................................................................................................... 102
Toolbox 2: Inbreeding at population level: the rate of inbreeding ............................................... 109
Predict the rate of inbreeding................................................................................................ 112
What rate of inbreeding is acceptable? ................................................................................... 113
Key issues ......................................................................................................................... 114
References ......................................................................................................................... 114
Chapter 7: Inheritance of monogenic traits ............................................................115
Learning outcomes .............................................................................................................. 115
Inheritance of monogenic traits: coat colour as an example ...................................................... 115
Monogenic traits with desired effects ..................................................................................... 122
Breeding to change allele frequencies of monogenic traits ......................................................... 123
The value of genetic markers in testing parents for genetic disorders .......................................... 126
Homozygosity mapping as a tool to detect recessive deleterious mutation ................................... 127
Breeding strategies against monogenic disorders ..................................................................... 129
Gene editing ...................................................................................................................... 130
Key issues ......................................................................................................................... 131
References ......................................................................................................................... 131
Chapter 8: Ranking the animals ...........................................................................133
Learning outcomes .............................................................................................................. 133
Ranking the animals: an overview of methods ......................................................................... 134
3
, In more detail: breeding value estimation............................................................................... 136
The regression framework .................................................................................................... 137
Accuracy of the breeding value: the basic concept ................................................................... 139
Breeding value estimation: Mass selection .............................................................................. 139
Breeding value estimation using information of relatives ........................................................... 141
Combining information of different relatives ............................................................................ 146
BLUP and the animal model .................................................................................................. 149
Accuracy of estimated breeding values ................................................................................... 153
Genomic selection ............................................................................................................... 158
Key issues ......................................................................................................................... 163
Chapter 9: Predicting response to selection ...........................................................165
Learning outcomes .............................................................................................................. 165
Response to selection: an overview ....................................................................................... 165
Breeding is about predicting the future................................................................................... 166
Genetic response: the basic principle ..................................................................................... 167
Response to mass selection .................................................................................................. 168
Selected proportion and selection intensity ............................................................................. 169
Selection response: the generalized approach ......................................................................... 171
Generation interval ............................................................................................................. 173
Optimising genetic gain: trade-offs between elements .............................................................. 174
Selection paths ................................................................................................................... 176
Multiple selection paths........................................................................................................ 178
Selection intensity and rate of inbreeding ............................................................................... 180
Software packages which optimise genetic gain and inbreeding ......................................................... 181
Special case: indirect selection.............................................................................................. 181
Practical issues with predicting response to selection ................................................................ 183
Key issues ......................................................................................................................... 185
Appendix: from selected proportion to selection intensity .......................................................... 186
Chapter 10: Selection and mating ........................................................................187
Learning outcomes .............................................................................................................. 187
Selection criteria and mating decisions ................................................................................... 187
Relation of mate selection with inbreeding .............................................................................. 189
Long-term genetic contribution ............................................................................................. 189
Relation between genetic contributions and occurrence of recessive disorders .............................. 194
Confirmation of parenthood .................................................................................................. 195
Key issues ......................................................................................................................... 196
Chapter 11: Crossbreeding ..................................................................................197
Learning outcomes .............................................................................................................. 197
Introduction ....................................................................................................................... 197
Heterosis ........................................................................................................................... 198
The genetic background of heterosis ...................................................................................... 198
4
The course "Animal Breeding and Genetics"
introduces how breeding programs can be
set up to genetically improve populations
and conserve genetic diversity. The course
deals with all the steps to take when setting
up a breeding program as shown in the
figure. The figure will be used throughout
the course to indicate where we are. Those
principles apply to livestock, companion,
zoo animals or populations of endangered
breeds.
The lecture notes are written by Liesbeth
van der Waaij, Kor Oldenbroek, Dieuwertje
Lont, Piter Bijma and Han Mulder. The first
version of these notes were used in the
academic year 2014-2015. The lecture notes were redesigned to teach animal breeding
from practice to theory and to show what is needed for breeding programs. These lecture
notes are based on teaching experiences accumulated across the years. We provide many
examples covering a wide range of species, and aim to update those regularly. We have
checked the notes carefully, but no doubt there will be some typographical or other errors.
Please tell us, so we can improve the lecture notes in the coming years.
We hope that these lecture notes will help you in understanding the principles of animal
breeding and getting you excited about this interesting field in animal science!!!
Mario Calus
Pascal Duenk
Wageningen, August 2025
1
,Table of Contents
Preface ................................................................................................................ 1
Chapter 1: What is animal breeding? ....................................................................... 7
Animal breeding in context .......................................................................................................9
Animal breeding: link to societal changes ................................................................................. 15
Present and future times ........................................................................................................ 18
What has been accomplished using animal breeding? ................................................................. 20
What can you expect from this course? .................................................................................... 29
References ........................................................................................................................... 30
Chapter 2: Defining breeding goal and setting up a breeding program ....................... 31
Learning outcomes ................................................................................................................ 31
Introduction ......................................................................................................................... 31
The breeding goal ................................................................................................................. 32
Breeding goals based on economic values derived from economic models ..................................... 35
Breeding goals based on non-economic values .......................................................................... 37
The remaining steps to set up a breeding program..................................................................... 39
Key issues ........................................................................................................................... 40
References ........................................................................................................................... 40
Chapter 3: Introduction in genetics and statistics .................................................... 41
Learning outcomes (assumed knowledge)................................................................................. 41
DNA as carrier of genetic information passed on to next generation .............................................. 41
DNA composition .................................................................................................................. 41
The transfer of chromosomes and genes from parent to offspring ................................................ 42
The mode of expression of genes ............................................................................................ 42
Recombination creates differences among offspring of an individual ............................................. 44
Characteristics of monogenic traits .......................................................................................... 46
Statistical measures for continuous phenotypic measurements .................................................... 47
Normal distribution of measurements....................................................................................... 49
Relationships between traits: Covariance, correlation and regression ............................................ 50
Appendix: Rules for calculations with continuous variables .......................................................... 53
Key issues ........................................................................................................................... 54
References ........................................................................................................................... 54
Chapter 4: Collection of information ...................................................................... 55
Learning outcomes ................................................................................................................ 55
The value of a pedigree in animal breeding ............................................................................... 55
A unique identification system for animals is essential ................................................................ 56
Collection of phenotypes ........................................................................................................ 56
Collection of DNA information ................................................................................................. 62
Key issues ........................................................................................................................... 67
Chapter 5: Genetic models ................................................................................... 69
2
, Learning outcomes ................................................................................................................ 69
Introduction ......................................................................................................................... 69
Phenotype and environment ................................................................................................... 70
Phenotype in a model ............................................................................................................ 72
Genetic variation .................................................................................................................. 73
Variance components ............................................................................................................ 75
Simplify the genetic model ..................................................................................................... 76
Next generation: transmission model ....................................................................................... 77
Heritability ........................................................................................................................... 78
Simple method for estimating the heritability: parent-offspring regression .................................... 80
Misconceptions about the heritability ....................................................................................... 81
Non-genetic influences: The variance due to a Common Environment ........................................... 82
Repeatability model and permanent environmental effects .......................................................... 86
Multi-trait model ................................................................................................................... 88
Key issues ........................................................................................................................... 90
Chapter 6: Genetic diversity and inbreeding ........................................................... 91
Learning outcomes ................................................................................................................ 91
What is genetic diversity? ...................................................................................................... 92
Forces that influence genetic diversity ...................................................................................... 93
Change in diversity: inbreeding ............................................................................................... 99
Why is genetic diversity important? ....................................................................................... 101
Toolbox 1: Relationships ...................................................................................................... 102
Toolbox 2: Inbreeding at population level: the rate of inbreeding ............................................... 109
Predict the rate of inbreeding................................................................................................ 112
What rate of inbreeding is acceptable? ................................................................................... 113
Key issues ......................................................................................................................... 114
References ......................................................................................................................... 114
Chapter 7: Inheritance of monogenic traits ............................................................115
Learning outcomes .............................................................................................................. 115
Inheritance of monogenic traits: coat colour as an example ...................................................... 115
Monogenic traits with desired effects ..................................................................................... 122
Breeding to change allele frequencies of monogenic traits ......................................................... 123
The value of genetic markers in testing parents for genetic disorders .......................................... 126
Homozygosity mapping as a tool to detect recessive deleterious mutation ................................... 127
Breeding strategies against monogenic disorders ..................................................................... 129
Gene editing ...................................................................................................................... 130
Key issues ......................................................................................................................... 131
References ......................................................................................................................... 131
Chapter 8: Ranking the animals ...........................................................................133
Learning outcomes .............................................................................................................. 133
Ranking the animals: an overview of methods ......................................................................... 134
3
, In more detail: breeding value estimation............................................................................... 136
The regression framework .................................................................................................... 137
Accuracy of the breeding value: the basic concept ................................................................... 139
Breeding value estimation: Mass selection .............................................................................. 139
Breeding value estimation using information of relatives ........................................................... 141
Combining information of different relatives ............................................................................ 146
BLUP and the animal model .................................................................................................. 149
Accuracy of estimated breeding values ................................................................................... 153
Genomic selection ............................................................................................................... 158
Key issues ......................................................................................................................... 163
Chapter 9: Predicting response to selection ...........................................................165
Learning outcomes .............................................................................................................. 165
Response to selection: an overview ....................................................................................... 165
Breeding is about predicting the future................................................................................... 166
Genetic response: the basic principle ..................................................................................... 167
Response to mass selection .................................................................................................. 168
Selected proportion and selection intensity ............................................................................. 169
Selection response: the generalized approach ......................................................................... 171
Generation interval ............................................................................................................. 173
Optimising genetic gain: trade-offs between elements .............................................................. 174
Selection paths ................................................................................................................... 176
Multiple selection paths........................................................................................................ 178
Selection intensity and rate of inbreeding ............................................................................... 180
Software packages which optimise genetic gain and inbreeding ......................................................... 181
Special case: indirect selection.............................................................................................. 181
Practical issues with predicting response to selection ................................................................ 183
Key issues ......................................................................................................................... 185
Appendix: from selected proportion to selection intensity .......................................................... 186
Chapter 10: Selection and mating ........................................................................187
Learning outcomes .............................................................................................................. 187
Selection criteria and mating decisions ................................................................................... 187
Relation of mate selection with inbreeding .............................................................................. 189
Long-term genetic contribution ............................................................................................. 189
Relation between genetic contributions and occurrence of recessive disorders .............................. 194
Confirmation of parenthood .................................................................................................. 195
Key issues ......................................................................................................................... 196
Chapter 11: Crossbreeding ..................................................................................197
Learning outcomes .............................................................................................................. 197
Introduction ....................................................................................................................... 197
Heterosis ........................................................................................................................... 198
The genetic background of heterosis ...................................................................................... 198
4
