Genetics of Domestications

Introduction XIII
Michè le TIXIER-BOICHARD and Georges PELLETIER
Chapter 1 Thousands of Years of Relationship between Man and Dog Revealed by Genomics 1
Morgane OLLIVIER
1. 1 The history of dog domestication, the subject of much debate 2
1. 1. 1 The dog: domesticated since the Paleolithic period 2
1. 1. 2 The process behind dog domestication 3
1. 1. 3 The number and location of domestication events: contextualization and the contribution of archaeological and genomic data 5
1. 2 Paleogenomics: an essential tool for understanding the evolutionary history of the dog 7
1. 2. 1 Eurasian origins and diffusion 7
1. 2. 2 The uniqueness of the Iberian Peninsula 8
1. 2. 3 Origins of the dog in America 9
1. 3 From commensalism to modern breeds: identifying the genomic foundations behind the intensification of the human-dog relationship 11
1. 3. 1 Selection and domestication markers 12
1. 3. 2 Genetic variation and adaptation to a starch-rich diet 13
1. 3. 3 The evolution of coat color 14
1. 3. 4 The question of human-dog co-evolution 15
1. 4 Selection of modern breeds, evolution in an anthropic context 16
1. 4. 1 Origins and timing of selections 16
1. 4. 2 Phenotypic and genetic variability 17
1. 4. 3 Harmful effects and genetic diseases 18
1. 5 References 19
Chapter 2 Imprints of Domestication in the Sheep Genome 21
Charlotte HER and Franç ois POMPANON
2. 1 The cradle of domestication in the Middle East 21
2. 1. 1 The beginnings of domestication 21
2. 1. 2 Genes involved in domestication 24
2. 2 Conquering the West 27
2. 2. 1 Primitive sheep versus more productive breeds 28
2. 2. 2 The mouflons of the Mediterranean islands, relics of the first wave of domestication 29
2. 2. 3 Southern Europe, diversity and global influence 30
2. 3 Africa 31
2. 3. 1 Diffusion 31
2. 3. 2 North Africa, the impact of the race for productivity 34
2. 4 Asia 35
2. 4. 1 Genetic signatures of origin, expansion and mixes 35
2. 5 Conclusion 38
2. 6 References 38
Chapter 3 Humans and Pigs: Over Ten Thousand Years of Shared Evolution 41
Laurent FRANTZ
3. 1 The evolution of Sus scrofa over the last 2 million years 41
3. 2 The genomics of adaptation in Sus scrofa 44
3. 3 The processes of pig domestication 46
3. 4 Using archaeology and genomics to trace the history of pig domestication 47
3. 4. 1 Archaeology and history of pig domestication 47
3. 4. 2 Genomics and the history of pig domestication 49
3. 4. 3 The first study of mitochondrial DNA 49
3. 5 The 19th century and the advent of the out stud-book 52
3. 6 Before domestication: human-initiated movements of wild and domesticated pigs 53
3. 7 Conclusion 54
3. 8 References 54
Chapter 4 The Domestication of the Wild Rabbit: Genetic and Genomic Elements 59
Hervé GARREAU and Cé cile CALLOU
4. 1 Phylogenetic context of the species 60
4. 1. 1 Taxonomy 60
4. 1. 2 Recent genomics tools 62
4. 2 Origin and spread of the wild rabbit 63
4. 2. 1 Hispanic ancestors 63
4. 2. 2 Crossing the Pyrenees 63
4. 3 A recent domestication 64
4. 3. 1 From leporaria to hutches 64
4. 3. 2 The molecular marks of domestication 65
4. 3. 3 Creation of breeds and genes linked to domestication 67
4. 4 Back to the wild: an invasive species 70
4. 5 Conclusion 72
4. 6 References 72
Chapter 5 Domesticated Poultry: A History Illuminated by Genomics 75
Michè le TIXIER-BOICHARD, Xavier ROGNON and Bertrand BED'HOM
5. 1 Introduction 75
5. 2 Domestic birds and their phylogenetic context 76
5. 3 Domestication scenarios 81
5. 3. 1 The chicken 82
5. 3. 2 Guinea-fowl 84
5. 3. 3 Turkey 85
5. 3. 4 Quail 85
5. 3. 5 Common duck 86
5. 3. 6 Pigeon 86
5. 4 Genetic mechanisms involved in domestication 87
5. 4. 1 Setups integrating phenotypic data 87
5. 4. 2 A priori molecular signature detection 90
5. 4. 3 Integrating approaches 93
5. 5 Conclusion 98
5. 6 References 98
Chapter 6 Genetics of Fish Domestication in Aquaculture 101
Fabrice TELETCHEA
6. 1 Introduction 101
6. 2 Diverse, complex and poorly understood domestication histories 103
6. 3 Significant performance improvements for domesticated species 106
6. 4 A success story: Atlantic salmon 108
6. 5 Conclusion 110
6. 6 References 110
Chapter 7 The Domestication of Yeast 113
Jean-Luc LEGRAS, Thibault NIDELET, Virginie GALEOTE and Delphine SICARD
7. 1 The history of fermented products and the domestication of microorganisms 113
7. 2 Yeast diversity and the evolutionary origins of fermentation 116
7. 3 Population structure of yeast isolated from anthropic niches 118
7. 3. 1 No genetic structure 118
7. 3. 2 Genetic structure associated with anthropic niches 119
7. 4 Genetic basis for the evolutionary history of domesticated populations 120
7. 4. 1 Hybridization and ploidy 120
7. 4. 2 Horizontal transfers and introgressions 121
7. 4. 3 Chromosomal rearrangement 123
7. 4. 4 Duplication 124
7. 4. 5 SNP: selection signature a priori 125
7. 5 Conclusion 125
7. 6 References 127
Chapter 8 The Domestication of Oenococcus oeni: A Bacterium Crafted for Wine Production 131
Jana RUDOLF, Marguerite DOLS-LAFARGUE, Claire LE HENAFF-LE MARREC and Patrick LUCAS
8. 1 Introduction 131
8. 2 Oenococcus oeni, a wine bacterium for MLF 133
8. 2. 1 A lactic acid bacterium 133
8. 2. 2 The wine bacterium 133
8. 2. 3 The MLF bacterium 134
8. 2. 4 Description of the species O oeni 134
8. 3 Genetic characteristics of O oeni domestication 136
8. 3. 1 Characteristic traits of domesticated microorganisms 136
8. 3. 2 Identification of domesticated O oeni genetic lines 137
8. 3. 3 Genetic mechanisms that contribute to the domestication of O oeni 139
8. 3. 4 Genetic signatures of domestication 142
8. 4 Conclusion 147
8. 5 References 149
Chapter 9 Tracing the Origins of Wheat Cultivation 151
Caroline PONT and Jé rô me SALSE
9. 1 The different types of wheat, one of the most widely consumed cereals in the world 151
9. 2 A species with ancient origins resulting from multiple hybridizations 152
9. 3 Archaeological evidence of its origins: archaeobotany 154
9. 3. 1 First traces 154
9. 3. 2 Domestication center(s) 155
9. 3. 3 Domestication traits 157
9. 4 Genetic evidence of wheat origins: paleogenomics 160
9. 4. 1 Modern diversity 160
9. 4. 2 Ancient DNA 162
9. 5 Perspectives: studying the origins and spread of wheat cultivation to support the selection of modern varieties 163
9. 6 Acknowledgments 165
9. 7 References 165
Chapter 10 A History of Cultivated Rice Genomics 169
Philippe CUBRY, Mathias LORIEUX, Franç ois SABOT and Alain GHESQUIÈ RE
10. 1 The history of rice: wild rice and cultivated rice 169
10. 1. 1 The genus Oryza 169
10. 1. 2 Characteristics of cultivated rice 172
10. 2 The beginnings of genomics and the pan-genomic revolution 173
10. 2. 1 The first genomic sequence 173
10. 2. 2 Complementary sequencing and 3, 000 genomes 173
10. 2. 3 New reference genomes and the appearance of rice pan-genomes 174
10. 2. 4 Other rice species 175
10. 3 Genomics' contribution to the study of rice domestication 176
10. 3. 1 Genomics as a tool for studying domestication traits 176
10. 3. 2 Genomics as a tool for a better understanding of domestication history 178
10. 3. 3 Domestication of Asian rice 179
10. 3. 4 Domestication of African rice 180
10. 4 Conclusion: the "continuity" of domestication 181
10. 5 References 182
Chapter 11 Grapevine Domestication and Selection 185
Patrice THIS, Thierry LACOMBE and Cé cile MARCHAL
11. 1 Introduction 185
11. 2 Vitis vinifera L. , the main species of the genus Vitis used for the production of table grapes and wine 186
11. 2. 1 Vitis vinifera L. : biology and genetic diversity 187
11. 3 Origin and domestication of Vitis vinifera L 191
11. 3. 1 Phylogenetics and biogeography of the genus Vitis 191
11. 3. 2 Grapevine domestication centers 192
11. 4 The main traits that evolved during grapevine domestication 193
11. 4. 1 Domestication syndrome 193
11. 4. 2 The presence of male and female organs, a distinctive trait of the wild and cultivated compartments 194
11. 4. 3 Genetic determinism of flower gender in grapevines 195
11. 4. 4 Berry color in grapevines: the importance of anthocyanins 196
11. 5 From domestication to the present day 198
11. 5. 1 Ancient grape varieties 198
11. 5. 2 Relationships between grape varieties 199
11. 5. 3 Table grapes, wine grapes 200
11. 5. 4 The phylloxera crisis and its consequences 201
11. 6 The grapevine of tomorrow 202
11. 7 References 203
Chapter 12 Tomato Domestication and Breeding: A Major Contribution from Wild Species 207
Mathilde CAUSSE
12. 1 Introduction 207
12. 1. 1 Botanical and agronomic description 208
12. 1. 2 Etymology and systematics 208
12. 2 Origin of the cultivated tomato: wild ancestors and centers of domestication 209
12. 2. 1 Indications provided by botany 211
12. 2. 2 Archaeological and historical evidence 212
12. 2. 3 Indications provided by linguistics 212
12. 3 The origins of cultivated tomatoes: genetic data 213
12. 3. 1 Indications provided by genetic diversity 213
12. 3. 2 Genomics and its contribution 214
12. 3. 3 Some of the genes responsible for fruit shape diversity 216
12. 4 Post-domestication of the tomato after global expansion 219
12. 4. 1 Introduction and distribution in Europe and worldwide 219
12. 4. 2 Tomato breeding in modern times 222
12. 4. 3 Using South American resources for multiple breeding objectives 223
12. 5 Conclusion 225
12. 6 References 225
Chapter 13 Mutagenesis and Accelerated Domestication 227
Georges PELLETIER
13. 1 Random mutagenesis and neo-domestication 228
13. 1. 1 Random mutagenesis 228
13. 1. 2 The example of Vigna stipulacea 229
13. 2 Genome editing and domestication 229
13. 2. 1 Genome editing 229
13. 2. 2 De novo tomato domestication 231
13. 2. 3 Domestication of Physalis pruinosa 232
13. 2. 4 Domestication of Oryza alta 234
13. 2. 5 Other candidate species for accelerated domestication 235
13. 3 Limits and constraints of neo-domestication 236
13. 3. 1 In practical terms 236
13. 3. 2 In terms of health and environmental safety 237
13. 3. 3 In legal terms 238
13. 3. 4 In regulatory terms 238
13. 4 Conclusion 239
13. 5 References 239
Glossary 243
List of Authors 249
Index 253