Selective Breeding in Aquaculture: an Introduction (eBook)

Preface 6
Acknowledgements 8
Contents 9
1 Introduction 15
1.1 Historic Development of Aquaculture 15
1.2 Definition of a Breeding Program 17
2 Domestication and the Application of Genetic Improvement in Aquaculture 18
2.1 Domestication of Animals 18
2.2 Selective Breeding 19
2.3 Quality Traits 19
2.4 Better Utilization of Resources 20
2.5 Genetic Improvement is Accumulative 20
2.6 Genetic Improvement Produces Permanent Gains 21
2.7 Initiating a Selective Breeding Program 21
2.8 Selective Breeding Programs in Aquaculture 22
2.9 Prerequisites for a Breeding Program 24
3 The Success of Selective Breeding in Aquaculture 25
3.1 Introduction 25
3.2 Atlantic Salmon 25
3.3 Rainbow Trout 27
3.4 Coho Salmon 28
3.5 Tilapia 29
3.6 Carp 30
3.7 Channel Catfish 31
3.8 Sea Bream 31
3.9 Shrimp 32
3.10 Oysters 33
3.11 Scallops 33
3.12 Genetic Improvement in Aquatic Species Compared to Terrestrial Livestock Species 33
3.13 Summary and Conclusion 34
4 The Theoretical Basis for Breeding and Selection 36
4.1 Introduction 36
4.2 The Cell 36
4.3 Basic Genetics 37
4.3.1 Introduction 37
4.3.2 Genes 37
4.3.3 Effect of Genes 40
4.4 Variation 40
4.4.1 Introduction 40
4.4.2 Single Gene Traits 41
4.4.3 Quantitative Traits 41
4.4.4 Variation in Quantitative Traits 42
4.4.5 Variation Between Species 43
4.4.6 Variation Within Species 44
4.5 Estimation of Variation and Covariation 44
4.5.1 Mean and Standard Deviation 44
4.5.2 Variance of a Sum 46
4.5.3 Genetic Variance 47
4.5.4 Heritability 47
4.5.5 Environmental Variance 49
4.5.6 Correlations Between Traits 51
4.5.7 Regression 53
4.6 Inbreeding and Relatedness 54
4.6.1 Genetic Relationship 54
4.6.2 Inbreeding 55
4.6.3 Effective Population Size 58
4.6.4 Effect of Inbreeding on Genetic Variance 59
4.6.5 Inbreeding Depression 59
4.7 Crossbreeding 60
4.7.1 Introduction 61
4.7.2 Heterosis 61
4.8 Purebreeding 62
4.9 Selection 63
4.9.1 Introduction 63
4.9.2 Natural Selection 64
4.9.3 Artificial Selection 64
4.9.4 Predicting Selection Change 65
4.9.5 Multiple Trait Selection 67
4.9.6 Correlated Response to Selection 68
4.9.7 Effect of Selection on Genetic Variance 69
4.9.8 Methods of Selection 69
4.9.9 Selection Limits 70
5 Initiating Breeding Programs 74
5.1 Introduction 74
5.2 The Fundamental Basis of a Breeding Program 75
5.3 Establishment of a Base Population 75
5.4 Breeding Goal 77
5.4.1 Introduction 78
5.4.2 Growth Rate 79
5.4.3 Feed Conversion Ratio (FCR) and Efficiency (FCE) 80
5.4.4 Disease Resistance 81
5.4.5 Age at Sexual Maturation 85
5.4.6 Product Quality 86
5.4.7 Cold Tolerance 89
5.4.8 Fecundity 89
5.4.9 Behaviour 89
5.4.10 Recapture Frequency 90
5.4.11 Central Breeding Goals 90
5.5 Registration of Records 91
5.5.1 Introduction 91
5.5.2 Body Weight 92
5.5.3 Survival 92
5.5.4 Feed Conversion Efficiency 93
5.5.5 Product Quality 93
5.6 Adjustment of Data 94
6 Breeding Strategies 97
6.1 Introduction 97
6.2 Inbreeding 97
6.3 Crossbreeding 98
6.4 Purebreeding 100
7 Selection Methods 102
7.1 Introduction 102
7.2 Factors Affecting Allele Frequencies 102
7.2.1 Migration 102
7.2.2 Selection 102
7.2.3 Mutation 103
7.2.4 Genetic Drift 103
7.3 Choice of Selection Method 103
7.4 Pedigree Selection 104
7.5 Individual Selection 104
7.6 Family Selection 105
7.7 Within-Family Selection 107
7.8 Progeny Testing 107
7.9 Correlated Response and Indirect Selection 108
7.10 Combined Selection 109
7.11 Multiple Trait Selection and Index Selection 109
7.12 Comparing Different Selection Methods 111
8 Mating Design 113
8.1 Introduction 113
8.2 Mass Spawning 113
8.3 Single Pair Mating 114
8.4 Nested Mating Design 116
8.5 Factorial Mating 117
8.6 Connectedness 118
8.7 Conclusion 118
9 Estimation of Breeding Values 120
9.1 Introduction 120
9.2 Breeding Value of Individual Animals 121
9.3 Breeding Value of Full-Sib Families 121
9.4 Breeding Value of Half-Sib Families 122
9.5 Breeding Values for Multiple Traits Using a Selection Index 122
9.6 Scaling of Selection Indexes 123
9.7 Best Linear Unbiased Prediction (BLUP) 123
10 GenotypeEnvironment Interaction 125
10.1 Introduction 125
10.2 Estimates of GenotypeEnvironment Interactions 125
10.3 Conclusion 130
11 Measuring Response to Selection 131
11.1 Introduction 131
11.2 Control Population 132
11.3 Average Breeders 132
11.4 Repeated Matings 134
11.5 Genetic Trend Analysis 134
11.6 Conclusion 135
12 Structure of Breeding Programs 136
12.1 Introduction 136
12.2 Breeding Programs Applying Individual Selection 136
12.3 Advanced Breeding Programs 137
12.3.1 Mating and Hatching 141
12.3.2 Tagging 141
12.3.3 Recording During Grow-Out 142
12.3.4 Harvest and Pre-selection of Broodstock at Breeding Stations 142
12.3.5 Final Selection of Broodstock 143
12.3.6 Genetic Markers for Parentage Assignment 143
12.4 Test Stations 143
12.5 Production of Special Lines 144
12.6 Dissemination of Genetic Gains 145
12.6.1 Direct Dissemination from Nucleus 145
12.6.2 Dissemination from Multipliers 147
12.7 Breeding Programs for New Species 148
13 Undesirable Side Effects in Breeding Programs 150
13.1 Introduction 150
13.2 Correlated Effects 150
13.3 Breeding Goal May Change 151
13.4 Disease Prevention 152
13.5 GenotypeEnvironment Interaction 152
13.6 Increase of Inbreeding 153
13.7 Conclusion 153
14 Biotechnology in Breeding Programs 155
14.1 Introduction 155
14.1.1 DNA Markers 155
14.1.2 Microsatellites 156
14.1.3 Single Nucleotide Polymorphisms (SNPs) 156
14.2 Linkage Maps 157
14.3 Quantitative Trait Loci (QTL) 158
14.3.1 Candidate Gene Approach 160
14.3.2 QTL Mapping Approach 160
14.3.3 Linkage Analysis 161
14.3.4 Fine Mapping of QTL 161
14.3.5 LDLA Mapping 162
14.3.6 An Example of QTL Mapping to Gene Discovery 162
14.3.7 Strategies to Reduce Genotyping Requirements 163
14.4 Marker Assisted Selection 163
14.4.1 Types of Marker Assisted Selection 164
14.4.2 Gene Assisted Selection (GAS) 165
14.4.3 Linkage Disequilibrium MAS (LD-MAS) 166
14.4.4 Linkage Equilibrium MAS (LE-MAS) 166
14.4.5 Genomic Selection 166
14.5 Other Applications of Genetic Markers 167
14.5.1 Parentage Assignment and Traceability 167
14.5.2 Genetic Interactions 168
14.5.3 Genetic Variation 168
14.6 Gene Expression Data 168
14.7 Transgenics 169
14.8 Genome Sequencing and Future Technologies 171
15 Reproduction Techniques 172
15.1 Introduction 172
15.2 Gynogenesis 172
15.3 Androgenesis 174
15.4 Triploidy 174
15.5 Tetraploidy 175
15.6 Production of Single Sex, YY and XX Stocks 176
16 Economic Benefits of Breeding Programs 178
16.1 Introduction 178
16.2 Cost of Broodstock Production 178
16.3 Cost of Running a Breeding Program 179
16.4 Economic Benefit of Breeding Programs 180
16.5 Relative Contribution of Selection and Feed Regimes to Performance 181
16.6 Who Benefits from Genetic Improvements? 182
16.6.1 The Animal 182
16.6.2 The Farmer 184
16.7 Ownership of Genetically Improved Material 186
Appendix 187
Glossary 188
References 199
Index 217