Biotechnology and Genetics in Fisheries and Aquaculture

173 Pages·2005·2.02 MB·English

Biotechnology and
Genetics in Fisheries and
Aquaculture
A.R. Beaumont
K. Hoare
Blackwell Science
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Biotechnology and Genetics in
Fisheries and Aquaculture
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Biotechnology and Genetics in
Fisheries and Aquaculture
A.R. Beaumont and K. Hoare
School of Ocean Sciences
University of Wales, Bangor, UK
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Contents
List of boxes ix
Preface xi
1 What is Genetic Variation? 1
Deoxyribose nucleic acid: DNA 1
Ribose nucleic acid: RNA 5
What is the genetic code? 6
Protein structure 7
So what about chromosomes? 8
How does sexual reproduction produce variation? 11
Mitochondrial DNA 16
Further reading 18
2 How Can Genetic Variation be Measured? 19
DNA sequence variation 19
DNA fragment size variation 32
Restriction fragment length polymorphisms (RFLPs) 32
Variable number tandem repeats (VNTR) 34
DNA fingerprinting 38
Random amplified polymorphic DNA (RAPD) 38
Amplified fragment length polymorphism (AFLP) 39
Protein variation 41
Phenotypic variation 45
Further reading 46
3 Genetic Structure in Natural Populations 47
What is a stock? 47
How are allele frequencies estimated? 48
What is the relationship between alleles and genotypes? 49
How do allele frequencies change over time? 51
How does population structure arise? 52
How are genetic markers used to define population structure? 53
Levels of genetic differentiation in aquatic organisms 56
Mixed stock analysis (MSA) 68
Conservation genetics 70
Further reading 71
4 Genetic Considerations in the Hatchery 73
Is there evidence of loss of genetic variation in the hatchery? 75
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vi Contents
How do hatcheries affect heterozygosity? 77
How can we use genetic markers to identify hatchery-produced individuals? 81
Identification to family level 81
Identification to population level 81
Genome mapping 82
How is a genome mapped? 83
How do we carry out linkage analysis? 85
The SALMAP project 88
Identification of diseases 88
Further reading 89
5 Artificial Selection in the Hatchery 91
Qualitative traits 91
Quantitative traits 95
What kinds of traits are important? 96
Variance of a trait 97
How can we estimate narrow-sense heritability? 99
Correlated traits 104
What types of artificial selection are there? 105
What about realised heritabilities? 108
Setting up a breeding programme 108
Inbreeding, cross-breeding and hybridisation 110
Further reading 113
6 Triploids and Beyond: Why Manipulate Ploidy? 114
How is it done? 115
Production of gynogens and androgens 117
Identification of ploidy change 118
Triploids 119
Tetraploids 123
Gynogens and androgens 123
Further reading 125
7 Genetic Engineering in Aquaculture 127
The DNA construct 127
The transgene 127
The promoter 128
Transgene delivery 130
Microinjection 130
Electroporation 132
Sperm-mediated transfer 132
Biolistics 133
Viral vectors 133
Lipofection 133
Transgene integration 133
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Contents vii
Detecting integration and expression of the transgene 134
So much for transgenics – what about cloning? 138
Genethics 138
Further reading 140
Glossary 141
Index 155
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List of boxes
Box 1.1 Genetic variation at the level of the chromosomes 10
Box 2.1 Cloning 19
Box 2.2 The polymerase chain reaction (PCR) 24
Box 2.3 Electrophoresis. 27
Box 2.4 DNA sequencing 30
Box 2.5 Restriction fragment length polymorphism (RFLP) 33
Box 2.6 Mitochondrial DNA extraction and analysis 35
Box 2.7 Variable number tandem repeats (VNTR): microsatellites 35
Box 2.8 Random amplified polymorphic DNA (RAPD) 39
Box 2.9 Amplified fragment length polymorphism (AFLP) 40
Box 2.10 Allozymes 42
Box 2.11 Immunological identification of proteins 44
Box 3.1 The Hardy–Weinberg model and causes of deviation from it 50
Box 3.2 F-statistics 54
Box 3.3 Genetic distance measures based on allele frequencies 57
Box 3.4 Genetic distance measures based on DNA restriction
fragments or DNA sequences 64
Box 3.5 Statistical problems associated with population genetic analyses 66
Box 4.1 Inbreeding 74
Box 4.2 The relationship between allele frequencies and heterozygosity 78
Box 4.3 The correlation between multiple-locus heterozygosity
(MLH) and physiological parameters 79
Box 4.4 Fluorescent in situhybridisation (FISH) 86
Box 5.1 Estimation of narrow-sense heritability 100
Box 5.2 Cryopreservation 102
Box 5.3 Response to selection and realised heritability 106