Genomic management of animal genetic diversity

Description

Recently developed genomic tools, like SNP-genotyping and whole genome sequencing, and their analysis, offer great opportunities for the conservation and utilisation of animal genetic diversity, both among and within breeds. These genomic tools can be used to detect potentially valuable rare alleles and haplotypes. They are important parts of the genetic diversity we need to conserve now for possible utilisation in the future. This book describes the use of genomic technology to define breeds, to measure diversity and to assess important features in the history of breeds affecting the present genetic diversity. The management of genetic diversity with genomic tools is outlined both in vivo: small populations of rare breeds or large populations with small effective population sizes and in vitro: genebanks. Special attention is given to the genomic management of populations of animals with high incidences of genetic defects. This book is intended for MSc and PhD students, scientists working with small populations in animal breeding and in conservation programmes for rare breeds. Preface......Page 8 References......Page 9 Table of contents......Page 10 Summary......Page 14 1.2 What is genetic diversity?......Page 15 1.3 Definitions of breeds......Page 21 1.4 State of genetic diversity......Page 23 1.5 Relevant developments in genomics for managing genetic diversity......Page 26 1.6 Application of genomics for breeding livestock and companion animals......Page 29 1.7 Opportunities to improve the management of genetic diversity......Page 39 1.8 The threats of genomics to the genetic diversity......Page 42 1.9 Challenges for the management of genetic diversity with genomic tools......Page 45 References......Page 46 Summary......Page 50 2.2 Measuring phenotypic diversity......Page 51 2.3 Use of pedigrees......Page 54 2.4 Molecular measures of diversity......Page 56 2.5 Advantages of genomic measures......Page 57 2.6 Relationship between molecular and pedigree measures......Page 63 2.7 Partition of diversity within and between breeds......Page 65 2.8 Using diversity measures for the prioritisation of breeds......Page 67 2.9 Towards accounting for adaptive diversity in conservation decisions......Page 71 2.10 Cluster analysis......Page 72 References......Page 73 Summary......Page 78 3.2 What is domestication?......Page 79 3.3 Approaches to study the transition from wild to domesticated forms......Page 83 3.4 Domestication pathways and recruitment of wild diversity......Page 86 3.5 Domestic animals: main facts about the domestication of cattle, pigs, chicken, sheep, goat, horse and dog......Page 90 3.6 Intensifying management......Page 96 3.7 The future of domestication processes......Page 99 3.8 Conclusion......Page 101 References......Page 102 Summary......Page 108 4.2 Human-mediated modifications to population demographic past......Page 109 4.3 Domestic animals are genetically diverse......Page 111 4.4 Domesticated traits: genes under the action of domestication......Page 112 4.5 Tests for selection in domesticated species......Page 115 4.6 Remaining challenge: to relate selective sweeps to functional traits......Page 131 References......Page 132 Summary......Page 140 5.1 Introduction......Page 141 5.2 The goals of live conservation......Page 142 5.3 Genomic breeding strategies for maintaining diversity......Page 143 5.4 Management of merged populations with genomic tools......Page 145 5.5 Mating strategies for small populations......Page 146 5.6 Multiple breed genomic prediction......Page 147 5.7 Purging of deleterious mutations......Page 150 5.9 Genomic introgression......Page 151 5.10 Recovery from crossbreeding......Page 152 References......Page 154 Summary......Page 156 6.1 Introduction......Page 157 6.2 Role of cryo-conservation......Page 158 6.3 More efficient cryo-conservation with genomic tools......Page 160 6.4 How to select breeds and animals for cryo-conservation?......Page 163 6.5 How to use cryo-collections with genomic information?......Page 169 6.6 Introgression using genomic information......Page 171 6.7 Documenting cryo-collections in the genomic era......Page 173 References......Page 176 Summary......Page 180 7.1 Introduction......Page 181 7.2 What can be learned about genetic diversity during dog breed formation?......Page 182 7.3 Why are there problems with inbreeding in dog breeds?......Page 184 7.4 Why are there problems with inherited diseases in dogs?......Page 189 7.5 What are the opportunities and challenges offered by genomics?......Page 196 7.6 How may genomic information be used ‘beyond breeds’?......Page 198 7.7 Conclusion......Page 201 References......Page 202 Glossary......Page 208 Index......Page 226