Andy Beaumont is based at the School of Ocean Sciences, Unioversity of Bangor, Menai, Wales, UK Pierre Boudry, based at IFREMER, France Kate Hoare, based at the School of Ocean Sciences, Menai Bridge, University of Bangor, Wales, UK

• Preface to the second edition ixAcknowledgements xiChapter 1 What is genetic variation? 1Deoxyribose nucleic acid 1Ribose nucleic acid 5What is the genetic code? 7Protein structure 7So what about chromosomes? 9How does sexual reproduction produce variation? 11Mitochondrial and chloroplast DNA 16Chapter 2 How can genetic variation be measured? 19DNA sequence variation 19DNA fragment size variation 36Protein variation 44Phenotypic variation 47Chapter 3 Genetic structure in natural populations 49What is a population? 49How are allele frequencies estimated? 51What is the relationship between alleles and genotypes? 51How do allele frequencies change over time? 53How does population structure arise? 54How are genetic markers used to study population structure? 55Levels of genetic differentiation in aquatic organisms 60Potential problems with allozymes and coding markers 61mtDNA variation 63Microsatellite variation 66Population structure in the flat oyster 68Mixed stock analysis (MSA) 73Chapter 4 Genetics of population size in conservation and aquaculture 77Genetics of small population size in the wild 78Genetic markers in conservation 82Genetics of small population size in the hatchery 85Is there evidence of loss of genetic variation in the hatchery? 87How does hatchery propagation affect heterozygosity? 89Genetic markers for identification of hatchery product 93Genetic markers for pathogen identification 94Chapter 5 Genetic variation of traits 99Qualitative traits 99Quantitative traits 105What kinds of traits are important? 106Variation of a quantitative trait 106How can we estimate narrow-sense heritability? 109Realised heritability 115Correlated traits 118What types of artificial selections are there? 118Setting up a breeding programme 122Inbreeding, cross-breeding and hybridisation 123Current status of selective breeding programmes in aquaculture 126Chapter 6 From genetics to genomics 129What is the genome? 129Genome mapping 130Whole genome sequencing: the ‘big picture’ 137QTL mapping 137Application of QTLs in aquaculture and fisheries management 138Marker-assisted selection (MAS): from QTLs to genomic selection 139Transcriptomics 139Chapter 7 Triploids and beyond: why manipulate ploidy? 145How is it done? 146Production of gynogens and androgens 148Identification of ploidy change 149Value of Triploids 151Tetraploids 155Gynogens and androgens 157Chapter 8 Genetic engineering in aquaculture 161The DNA construct 162Transgene delivery 164Transgene integration 168Detecting integration and expression of the transgene 169Results of transgenesis efforts in fish 171So much for transgenics – what about cloning? 176Genethics 176Glossary 181Index 193Colour plates appear between pages 52 and 53

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Andy Beaumont is based at the School of Ocean Sciences, Unioversity of Bangor, Menai, Wales, UK Pierre Boudry, based at IFREMER, France Kate Hoare, based at the School of Ocean Sciences, Menai Bridge, University of Bangor, Wales, UK

• Preface to the second edition ixAcknowledgements xiChapter 1 What is genetic variation? 1Deoxyribose nucleic acid 1Ribose nucleic acid 5What is the genetic code? 7Protein structure 7So what about chromosomes? 9How does sexual reproduction produce variation? 11Mitochondrial and chloroplast DNA 16Chapter 2 How can genetic variation be measured? 19DNA sequence variation 19DNA fragment size variation 36Protein variation 44Phenotypic variation 47Chapter 3 Genetic structure in natural populations 49What is a population? 49How are allele frequencies estimated? 51What is the relationship between alleles and genotypes? 51How do allele frequencies change over time? 53How does population structure arise? 54How are genetic markers used to study population structure? 55Levels of genetic differentiation in aquatic organisms 60Potential problems with allozymes and coding markers 61mtDNA variation 63Microsatellite variation 66Population structure in the flat oyster 68Mixed stock analysis (MSA) 73Chapter 4 Genetics of population size in conservation and aquaculture 77Genetics of small population size in the wild 78Genetic markers in conservation 82Genetics of small population size in the hatchery 85Is there evidence of loss of genetic variation in the hatchery? 87How does hatchery propagation affect heterozygosity? 89Genetic markers for identification of hatchery product 93Genetic markers for pathogen identification 94Chapter 5 Genetic variation of traits 99Qualitative traits 99Quantitative traits 105What kinds of traits are important? 106Variation of a quantitative trait 106How can we estimate narrow-sense heritability? 109Realised heritability 115Correlated traits 118What types of artificial selections are there? 118Setting up a breeding programme 122Inbreeding, cross-breeding and hybridisation 123Current status of selective breeding programmes in aquaculture 126Chapter 6 From genetics to genomics 129What is the genome? 129Genome mapping 130Whole genome sequencing: the ‘big picture’ 137QTL mapping 137Application of QTLs in aquaculture and fisheries management 138Marker-assisted selection (MAS): from QTLs to genomic selection 139Transcriptomics 139Chapter 7 Triploids and beyond: why manipulate ploidy? 145How is it done? 146Production of gynogens and androgens 148Identification of ploidy change 149Value of Triploids 151Tetraploids 155Gynogens and androgens 157Chapter 8 Genetic engineering in aquaculture 161The DNA construct 162Transgene delivery 164Transgene integration 168Detecting integration and expression of the transgene 169Results of transgenesis efforts in fish 171So much for transgenics – what about cloning? 176Genethics 176Glossary 181Index 193Colour plates appear between pages 52 and 53

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Andy Beaumont is based at the School of Ocean Sciences, Unioversity of Bangor, Menai, Wales, UK Pierre Boudry, based at IFREMER, France Kate Hoare, based at the School of Ocean Sciences, Menai Bridge, University of Bangor, Wales, UK

• Preface to the second edition ixAcknowledgements xiChapter 1 What is genetic variation? 1Deoxyribose nucleic acid 1Ribose nucleic acid 5What is the genetic code? 7Protein structure 7So what about chromosomes? 9How does sexual reproduction produce variation? 11Mitochondrial and chloroplast DNA 16Chapter 2 How can genetic variation be measured? 19DNA sequence variation 19DNA fragment size variation 36Protein variation 44Phenotypic variation 47Chapter 3 Genetic structure in natural populations 49What is a population? 49How are allele frequencies estimated? 51What is the relationship between alleles and genotypes? 51How do allele frequencies change over time? 53How does population structure arise? 54How are genetic markers used to study population structure? 55Levels of genetic differentiation in aquatic organisms 60Potential problems with allozymes and coding markers 61mtDNA variation 63Microsatellite variation 66Population structure in the flat oyster 68Mixed stock analysis (MSA) 73Chapter 4 Genetics of population size in conservation and aquaculture 77Genetics of small population size in the wild 78Genetic markers in conservation 82Genetics of small population size in the hatchery 85Is there evidence of loss of genetic variation in the hatchery? 87How does hatchery propagation affect heterozygosity? 89Genetic markers for identification of hatchery product 93Genetic markers for pathogen identification 94Chapter 5 Genetic variation of traits 99Qualitative traits 99Quantitative traits 105What kinds of traits are important? 106Variation of a quantitative trait 106How can we estimate narrow-sense heritability? 109Realised heritability 115Correlated traits 118What types of artificial selections are there? 118Setting up a breeding programme 122Inbreeding, cross-breeding and hybridisation 123Current status of selective breeding programmes in aquaculture 126Chapter 6 From genetics to genomics 129What is the genome? 129Genome mapping 130Whole genome sequencing: the ‘big picture’ 137QTL mapping 137Application of QTLs in aquaculture and fisheries management 138Marker-assisted selection (MAS): from QTLs to genomic selection 139Transcriptomics 139Chapter 7 Triploids and beyond: why manipulate ploidy? 145How is it done? 146Production of gynogens and androgens 148Identification of ploidy change 149Value of Triploids 151Tetraploids 155Gynogens and androgens 157Chapter 8 Genetic engineering in aquaculture 161The DNA construct 162Transgene delivery 164Transgene integration 168Detecting integration and expression of the transgene 169Results of transgenesis efforts in fish 171So much for transgenics – what about cloning? 176Genethics 176Glossary 181Index 193Colour plates appear between pages 52 and 53

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