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Introduction XIII Michèle 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 François 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 Cécile 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 Michèle 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 Jérôme 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, François SABOT and Alain GHESQUIÈRE
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 Cécile 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
Michèle TIXIER-BOICHARD1 and Georges PELLETIER2,3
1GABI, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
2Académie des sciences, Paris, France
3Académie d'agriculture de France, Paris, France
Domestic, in the first sense, means belonging to the house, in Latin "domus". Thus, for a living being, it means living in a home, in the broadest sense, of man, being raised and fed there. The domestication of animals, plants and microorganisms is therefore a process of adapting individuals, then their descendants, to an environment that is modified by human groups. This adaptation is associated with hereditary transformations that are conducive to their exploitation, which are expressed, for example, in an animal's docile nature or the limitation of the spontaneous dispersal of cereal grains. In some cases, the species disappears in the wild and is only represented by domesticated types. Domestication can thus be seen as evolutionary pressure. A generic definition of domestication has been proposed by the Convention on Biological Diversity1 as follows: "'Domesticated or cultivated species' means species in which the evolutionary process has been influenced by humans to meet their needs".
The transition from the wild to the domesticated state is just a starting point, because as human needs continue to evolve, so does the adaptation and management of domesticated species. Domestication can thus be seen as a process of accumulating heritable modifications to the characteristics of a group of individuals, enabling them to better meet the needs of our species, not only for survival, but also for pleasure, or for cultural or symbolic reasons. These genetic transformations of the species we have chosen, and the history of their exploitation for a variety of needs, have led to a diversification of animal breeds and plant varieties, in addition to strains of microorganisms involved in the manufacture of many fermented foods, such as beer, wine, bread, cheese and more. The history of their domestication has become increasingly well documented since the advent of modern DNA analysis technologies, revealing a plethora of strains and species whose ability to evolve and exchange genes contributes to the quality of these products.
When and where did domestication begin? How did it happen?
The history of domestication is intimately linked to human history or, more accurately, to the history of different human groups scattered across the planet. Archaeological digs enable us to reconstruct the past of certain species by uncovering their remains and using all the technical resources of archaeobotany and archaeozoology,2 from morphological description to various types of analysis. These include, for example, carbon isotope content for dating, or DNA sequences that can be extracted to reveal their relationship with today's domesticated species.
In terms of the evolution of modern man, whose emergence can be traced back some 300,000 years to Africa, before migrating to the Eurasian continent and later to Australia and the Americas, the first domestications only appeared very late, in the last two tens of thousands of years before us: dog, man's oldest companion, is thought to have been domesticated for at least 25,000 years. Over the last 12,000 years, plant species have undergone new types of genetic selection, corresponding to the needs of populations and leading to the emergence of agricultural societies in various parts of the world (Purruganan and Fuller 2009). Up until then, man had already been using plant and animal resources through gathering and hunting. Thus, the use of selectively harvested wild cereals, which spontaneously seeded and invaded areas occupied by populations, shows a first stage of co-evolution between man and a species used to make food. Evidence of this can be found in the Paleolithic period, like the case of millet in northern China 28,000 years ago, or barley and wheat, with potential signs of cultivation 23,000 years ago by hunter-gatherers who set up sedentary sites in the Middle East. The beginnings of bread-making are confirmed to have started 14,600 years ago, well before the domestication of wheat. The satisfaction of these needs led to new economic activity involving work in the fields, and the storage and processing of harvests. The seasonal nature of cereals led to the construction of storage facilities. The granaries that precede the emergence of domestication by at least 1,000 years represent a critical change in the relationship between humans and plant foods, with new social organizations of sedentary communities and the emergence of agriculture (Willcox and Stordeur 2012; Vigne 2015).
Different species have been involved in different regions on all continents, identified as hotbeds of domestication. Examples include the Fertile Crescent in the Middle East (wheat, barley, lentils, peas, chickpeas, ruminants, pigeon, cat and cochineal), China and Southeast Asia (rice, millet, soy, pig, chicken and duck), sub-Saharan Africa (sorghum, rice, millet and faba bean), Mesoamerica (corn, bean, pumpkin and turkey) and the Andes (potato, bean, quinoa and llama). Domestication initiated in one region is generally followed by a migration phase, as human populations travel with their seeds and animals. For example, many plant species were consumed by hunter-gatherers in the Amazon basin. Once domesticated, these species were gradually spread to other regions of the world, following human migrations or, more recently, following the discovery of America, leading to the exploitation in Europe of sunflowers, squash, pumpkins, corn, manioc, taro, potatoes, tomatoes, sweet potatoes, beans, cotton plants and so on.
The motivations behind domestication are certainly diverse. The controlled availability of cereals (and legumes) that could be stored, as well as the possibility of cooking particular foods (wheat bread) or alcoholic beverages (fermented barley) could be, more than a quest for calories, determining factors in the choice of these two main cereals cultivated in the Middle East, whose characteristics are not found in other wild grasses. Participating in the provisioning of social feasts in a region where, at the outset, there was no evidence of demographic pressure, and where fruits and nuts were abundant, a growing cultural interest in these species would have been a determining factor. In the case of animals, three modalities have been proposed to describe domestication (Larson and Fuller 2014). The commensal pathway corresponds to the case of an animal species living in the vicinity of humans with mutual benefit and involves no human intention. The other two pathways involve human intention, with either the predatory pathway, motivated by the need to obtain supplementary food resources (as a possible reaction to over-hunting), or the directed pathway, for any other intention, such as transport or distraction. However, these three pathways are not mutually exclusive: it is likely that domestication first followed a commensal or predatory path before humans acquired the intention of influencing or modifying an animal species for their own benefit.
The processes of domestication and selection have created ever-closer links between agriculture and society, accompanied by changes in human society. Increased yields have made agricultural production systems more dependent on continuous investment in labor, leading to a form of servitude. The domestication of the horse had a major impact on the mobility of human populations, while that of cattle had a major impact on work capacity in the fields.
Which species have been domesticated? How can we identify wild ancestors? What specific morphological or physiological properties characterize it? What genes and gene modifications are involved? Have domesticated organisms been particularly isolated or have they maintained genetic exchanges with their wild ancestor (Hunter 2018)?
Analysis of the phylogeny of animal and plant species does not show a random distribution of domesticated species. This is particularly clear in the case of animals, where it can be seen that domesticated mammals, known as "cash crops", are derived from only a small fraction of the phylogenetic and phenotypic diversity of mammals, with an over-representation of the order Artiodactyla (Bovidae: cattle, goats, sheep; Suidae: pigs, etc.), and a few species from the orders Rodentia (guinea pig), Lagomorpha (rabbit) and Perissodactyla (horse, donkey). The other domestic species are essentially from the order Carnivora, phylogenetically close to Artiodactyla and Perissodactyla (in the Ferungulata group). Some authors have jointly analyzed the phylogenetic position and biological or ecological particularities of domesticated species, whether they be animal or plant, and have concluded that certain species are predisposed to others (Milla et al. 2018). The domestication of different cereals (wheat, barley, rice, corn, sorghum and millet), characterized by the loss of spontaneous grain dispersal and dormancy, as well as an increase in grain size, has given rise to the concept of a "domestication syndrome": common characteristics based on a limited number of mutations, but not implying an identity of these mutations. This concept is only...
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