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198 results on '"DOMESTICATION DES PLANTES"'

1. An allometry perspective on crops

Author: Westgeest, Adrianus J., Vasseur, François, Enquist, Brian, Milla, Rubén, Gómez-Fernández, Alicia, Pot, David, Vile, Denis, Violle, Cyrille, Westgeest, Adrianus J., Vasseur, François, Enquist, Brian, Milla, Rubén, Gómez-Fernández, Alicia, Pot, David, Vile, Denis, and Violle, Cyrille
Abstract: Understanding trait–trait coordination is essential for successful plant breeding and crop modeling. Notably, plant size drives variation in morphological, physiological, and performance-related traits, as described by allometric laws in ecology. Yet, as allometric relationships have been limitedly studied in crops, how they influence and possibly limit crop performance remains unknown. Here, we review how an allometry perspective on crops gains insights into the phenotypic evolution during crop domestication, the breeding of varieties adapted to novel conditions, and the prediction of crop yields. As allometry is an active field of research, modeling and manipulating crop allometric relationships can help to develop more resilient and productive agricultural systems to face future challenges.
Published: 2024

2. Crop domestication in the Asia Pacific Region: A review

Author: Okemo, Pauline, Wijesundra, Upendra, Nakandala, Upuli, Dillon, Natalie, Chandora, Rahul, Campbell, Bradley, Smith, Millicent, Hardner, Craig, Cadorna, Charles A., Martin, Guillaume, Yahiaoui, Nabila, Garsmeur, Olivier, Pompidor, Nicolas, D'Hont, Angélique, Henry, Robert, Okemo, Pauline, Wijesundra, Upendra, Nakandala, Upuli, Dillon, Natalie, Chandora, Rahul, Campbell, Bradley, Smith, Millicent, Hardner, Craig, Cadorna, Charles A., Martin, Guillaume, Yahiaoui, Nabila, Garsmeur, Olivier, Pompidor, Nicolas, D'Hont, Angélique, and Henry, Robert
Abstract: Understanding crop domestication provides a basis for ongoing genetic improvement of crops, especially in the utilization of wild crop relatives as a source of new variation and may guide the domestication of new crops. The Asia Pacific region is home to most of the world's human population and is a region in which many important crops were domesticated. Here we review the domestication of banana, citrus, coconut, macadamia, mango, millet, mungbean, rice, sugarcane and taro in the Asia Pacific region. These examples illustrate the importance of this region in the development of agriculture. The challenges of conservation of the genetic resources for these crops are exacerbated by the large human population and rapid economic development in the region. Advances in genetic technologies provide an opportunity for accelerated genetic improvement of these crops and the domestication of new crops.
Published: 2024

3. Chorematic modeling to represent dynamics in the quinoa agroecosystems in Peru

Author: Fagandini Ruiz, Francesca, Villanueva, Antonio, Bazile, Didier, Fagandini Ruiz, Francesca, Villanueva, Antonio, and Bazile, Didier
Abstract: Our research occurred in the Andean region, one of the eight global centers of domestication of plant species grown for agriculture. The shores of Lake Titicaca (located between Peru and Bolivia), at 3800 meters above sea level, are recognized as the center of origin of quinoa (Chenopodium quinoa Willd.). In this region, complex societies have emerged, thanks to the development of water and soil management technologies. They have managed to overcome high mountain territories' extreme and variable climatic conditions. These societies have traditionally protected and preserved quinoa as food for present and future generations through their long-standing knowledge and cultivation practices. The fieldwork occurred in the context of Andean family farming, and our study analyzes nature-society dynamics with a chorematic approach and interviews with local communities. The interest of this work is the transformation of the landscape at the scale of the mountain agroecosystem to understand better the impacts of rural development policies. Chorematic modeling was applied to two periods, before and after 1970, a pivotal year in Peru for agriculture, to show how socio-spatial dynamics in the Andean environment are changing, particularly concerning the evolution of quinoa cultivation. The results show that wild quinoa relatives' distribution is strongly linked to the socio-spatial organization of the agroecosystem. Different species of wild quinoa relatives are maintained by villagers for their multiple foods, medicinal and cultural uses in natural areas, grazed areas, on edge, and also within cultivated fields. However, this management is changing under the pressure of global issues related to the international quinoa market, whose requirements imply reducing the presence of wild relatives in cultivated fields.
Published: 2024

4. Evolution of the cotton genus, Gossypium, and its domestication in the Americas

Author: Viot, Christopher, Wendel, Jonathan F., Viot, Christopher, and Wendel, Jonathan F.
Abstract: Gossypium, the cotton genus, includes ∼50 species distributed in tropical and sub-tropical regions of all continents except Europe. Here we provide a synopsis of the evolutionary history of Gossypium and domestication of the American allopolyploid species, integrating data from fundamental taxonomic investigations, biogeography, molecular genetics, phylogenetic analysis, and archaeology. These diverse sources of information provide a temporal and phylogenetic perspective on diversification among the diploids and on polyploid formation, uncover multiple previously cryptic interspecific hybridizations, clarify and contribute to the taxonomy of the genus, and offer a firm foundation for understanding parallel domestications in Mesoamerica and South America, which led to the globally important cotton crop species G. barbadense and G. hirsutum. Gossypium thus offers a testimonial example of the importance and utility of fundamental botanical discovery combined with modern technological capabilities to generate genomic insights into evolutionary history. We also review the current state of our knowledge regarding the archaeological history of cotton domestication and diffusion in the Americas, a seemingly unlikely story entailing parallel domestication origins and parallel directional selection tracing to 8,000 (G. barbadense) and 5,500 (G. hirsutum) years ago, transforming two geographically isolated wild short-day perennial shrubs having small capsules and seeds covered by short, tan-colored epidermal trichomes into modern daylength-neutral annuals bearing abundant, fine, strong white fibers. This dual domestication was followed several millennia later by unintentional and more recently intentional interspecific introgression, as the two species came into contact following their initial domestication in different hemispheres. Thus, the cycle of species divergence and biological reunion was reiterated, this time at the allopolyploid level. Understanding this evolutionary
Published: 2023

5. African army ants at the forefront of virome surveillance in a remote tropical forest

Author: Fritz, Matthieu, Reggiardo, Bérénice, Filloux, Denis, Claude, Lisa, Fernandez, Emmanuel, Mahe, Frédéric, Kraberger, Simona, Custer, Joy M., Becquart, Pierre, Mebaley, Telsta Ndong, Kombila, Linda Bohou, Lenguiya, Léadisaelle H., Boundenga, Larson, Mombo, Illich M., Maganga, Gaël Darren, Niama, Fabien R., Koumba, Jean-Sylvain, Ogliastro, Mylène, Yvon, Michel, Martin, Darren Patrick, Blanc, Stéphane, Varsani, Arvind, Leroy, Eric M., Roumagnac, Philippe, Fritz, Matthieu, Reggiardo, Bérénice, Filloux, Denis, Claude, Lisa, Fernandez, Emmanuel, Mahe, Frédéric, Kraberger, Simona, Custer, Joy M., Becquart, Pierre, Mebaley, Telsta Ndong, Kombila, Linda Bohou, Lenguiya, Léadisaelle H., Boundenga, Larson, Mombo, Illich M., Maganga, Gaël Darren, Niama, Fabien R., Koumba, Jean-Sylvain, Ogliastro, Mylène, Yvon, Michel, Martin, Darren Patrick, Blanc, Stéphane, Varsani, Arvind, Leroy, Eric M., and Roumagnac, Philippe
Abstract: In this study, we used a predator-enabled metagenomics strategy to sample the virome of a remote and difficult-to-access densely forested African tropical region. Specifically, we focused our study on the use of army ants of the genus Dorylus that are obligate collective foragers and group predators that attack and overwhelm a broad array of animal prey. Using 209 army ant samples collected from 29 colonies and the virion-associated nucleic acid-based metagenomics approach, we showed that a broad diversity of bacterial, plant, invertebrate and vertebrate viral sequences were accumulated by army ants: including sequences from 157 different viral genera in 56 viral families. This suggests that using predators and scavengers such as army ants to sample broad swathes of tropical forest viromes can shed light on the composition and the structure of viral populations of these complex and inaccessible ecosystems.
Published: 2023

6. Domestication provides durum wheat with protection from locust herbivory

Author: Chapuis, Marie-Pierre, Leménager, Nicolas, Piou, Cyril, Roumet, Pierre, Marche, Héloïse, Centanni, Julia, Estienne, Christophe, Ecarnot, Martin, Vasseur, François, Violle, Cyrille, Kazakou, Elena, Chapuis, Marie-Pierre, Leménager, Nicolas, Piou, Cyril, Roumet, Pierre, Marche, Héloïse, Centanni, Julia, Estienne, Christophe, Ecarnot, Martin, Vasseur, François, Violle, Cyrille, and Kazakou, Elena
Abstract: Lower plant resistance to herbivores following domestication has been suggested as the main cause for higher feeding damage in crops than in wild progenitors. While herbivore compensatory feeding has also been proposed as a possible mechanism for raised damage in crops with low nutritional quality, predictions regarding the effects of plant domestication on nutritional quality for herbivores remain unclear. In particular, data on primary metabolites, even major macronutrients, measured in the organs consumed by herbivores, are scarce. In this study, we used a collection of 10 accessions of wild ancestors and 10 accessions of modern progenies of Triticum turgidum to examine whether feeding damage and selectivity by nymphs of Locusta migratoria primarily depended on five leaf traits related to structural resistance or nutrient profiles. Our results unexpectedly showed that locusts favored wild ancestors over domesticated accessions and that leaf toughness and nitrogen and soluble protein contents increased with the domestication process. Furthermore, the quantitative relationship between soluble protein and digestible carbohydrates was found to poorly meet the specific requirements of the herbivore, in all wheat accessions, both wild and modern. The increase in leaf structural resistance to herbivores in domesticated tetraploid wheat accessions suggested that resource allocation trade-offs between growth and herbivory resistance may have been disrupted by domestication in the vegetative organs of this species. Since domestication did not result in a loss of nutritional quality in the leaves of the tetraploid wheat, our results rather provides evidence for a role of the content of plants in nonnutritive nitrogenous secondary compounds, possibly deterrent or toxic, at least for grasshopper herbivores.
Published: 2023

7. Interspecific introgression patterns reveal the origins of worldwide cultivated bananas in New Guinea

Author: Martin, Guillaume, Cottin, Aurélien, Baurens, Franc-Christophe, Labadie, Karine, Hervouet, Catherine, Salmon, Frédéric, Paulo De La Reberdière, Nilda, Van Den Houwe, Ines, Sardos, Julie, Aury, Jean-Marc, D'Hont, Angélique, Yahiaoui, Nabila, Martin, Guillaume, Cottin, Aurélien, Baurens, Franc-Christophe, Labadie, Karine, Hervouet, Catherine, Salmon, Frédéric, Paulo De La Reberdière, Nilda, Van Den Houwe, Ines, Sardos, Julie, Aury, Jean-Marc, D'Hont, Angélique, and Yahiaoui, Nabila
Abstract: Hybridizations between Musa species and subspecies, enabled by their transport via human migration, were proposed to have played an important role in banana domestication. We exploited sequencing data of 226 Musaceae accessions, including wild and cultivated accessions, to characterize the inter(sub)specific hybridization pattern that gave rise to cultivated bananas. We identified 11 genetic pools that contributed to cultivars, including two contributors of unknown origin. Informative alleles for each of these genetic pools were pinpointed and used to obtain genome ancestry mosaics of accessions. Diploid and triploid cultivars had genome mosaics involving three up to possibly seven contributors. The simplest mosaics were found for some diploid cultivars from New Guinea, combining three contributors, i.e., banksii and zebrina representing Musa acuminata subspecies and, more unexpectedly, the New Guinean species Musa schizocarpa. Breakpoints of M. schizocarpa introgressions were found to be conserved between New Guinea cultivars and the other analyzed diploid and triploid cultivars. This suggests that plants bearing these M. schizocarpa introgressions were transported from New Guinea and gave rise to currently cultivated bananas. Many cultivars showed contrasted mosaics with predominant ancestry from their geographical origin across Southeast Asia to New Guinea. This revealed that further diversification occurred in different Southeast Asian regions through hybridization with other Musa (sub)species, including two unknown ancestors that we propose to be M. acuminata ssp. halabanensis and a yet to be characterized M. acuminata subspecies. These results highlighted a dynamic crop formation process that was initiated in New Guinea, with subsequent diversification throughout Southeast Asia.
Published: 2023

8. Evolution of the cotton genus, Gossypium, and its domestication in the Americas

Author: Christopher R. Viot and Jonathan F. Wendel
Subjects: Gossypium, Phylogénie, F40 - Écologie végétale, Domestication des plantes, Hybridation, Gossypium hirsutum, Évolution, Plant Science, F30 - Génétique et amélioration des plantes, génomique, Gossypium barbadense, Histoire, F01 - Culture des plantes, Hybridation interspécifique
Abstract: Gossypium, the cotton genus, includes ∼50 species distributed in tropical and sub-tropical regions of all continents except Europe. Here we provide a synopsis of the evolutionary history of Gossypium and domestication of the American allopolyploid species, integrating data from fundamental taxonomic investigations, biogeography, molecular genetics, phylogenetic analysis, and archaeology. These diverse sources of information provide a temporal and phylogenetic perspective on diversification among the diploids and on polyploid formation, uncover multiple previously cryptic interspecific hybridizations, clarify and contribute to the taxonomy of the genus, and offer a firm foundation for understanding parallel domestications in Mesoamerica and South America, which led to the globally important cotton crop species G. barbadense and G. hirsutum. Gossypium thus offers a testimonial example of the importance and utility of fundamental botanical discovery combined with modern technological capabilities to generate genomic insights into evolutionary history. We also review the current state of our knowledge regarding the archaeological history of cotton domestication and diffusion in the Americas, a seemingly unlikely story entailing parallel domestication origins and parallel directional selection tracing to 8,000 (G. barbadense) and 5,500 (G. hirsutum) years ago, transforming two geographically isolated wild short-day perennial shrubs having small capsules and seeds covered by short, tan-colored epidermal trichomes into modern daylength-neutral annuals bearing abundant, fine, strong white fibers. This dual domestication was followed several millennia later by unintentional and more recently intentional interspecific introgression, as the two species came into contact following their initial domestication in different hemispheres. Thus, the cycle of species divergence and biological reunion was reiterated, this time at the allopolyploid level. Understanding this evolutionary history is vitally important to our understanding of the genomic architecture of the world's most important fiber plant and contributes substantially to our understanding of general biological principles.
Published: 2023

9. Interspecific introgression patterns reveal the origins of worldwide cultivated bananas in New Guinea

Author: Guillaume Martin, Aurélien Cottin, Franc‐Christophe Baurens, Karine Labadie, Catherine Hervouet, Frédéric Salmon, Nilda Paulo‐de‐la‐Reberdiere, Ines Van den Houwe, Julie Sardos, Jean‐Marc Aury, Angélique D'Hont, Nabila Yahiaoui, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT) [Rome] (Alliance), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: Introgression, [SDV]Life Sciences [q-bio], Plant Science, F30 - Génétique et amélioration des plantes, domestication, Variation génétique, F01 - Culture des plantes, Genetics, hybridization, Musa spp, Diversité génétique (comme ressource), Domestication des plantes, phytogénétique, Musa, Cell Biology, genetic diversity, Hybridation interspécifique, genome ancestry
Abstract: International audience; Hybridizations between Musa species and subspecies, enabled by their transport via human migration, were proposed to have played an important role in banana domestication. We exploited sequencing data of 226 Musaceae accessions, including wild and cultivated accessions, to characterize the inter(sub)specific hybridization pattern that gave rise to cultivated bananas. We identified 11 genetic pools that contributed to cultivars, including two contributors of unknown origin. Informative alleles for each of these genetic pools were pinpointed and used to obtain genome ancestry mosaics of accessions. Diploid and triploid cultivars had genome mosaics involving three up to possibly seven contributors. The simplest mosaics were found for some diploid cultivars from New Guinea, combining three contributors, i.e., banksii and zebrina representing Musa acuminata subspecies and, more unexpectedly, the New Guinean species Musa schizocarpa. Breakpoints of M. schizocarpa introgressions were found to be conserved between New Guinea cultivars and the other analyzed diploid and triploid cultivars. This suggests that plants bearing these M. schizocarpa introgressions were transported from New Guinea and gave rise to currently cultivated bananas. Many cultivars showed contrasted mosaics with predominant ancestry from their geographical origin across Southeast Asia to New Guinea. This revealed that further diversification occurred in different Southeast Asian regions through hybridization with other Musa (sub)species, including two unknown ancestors that we propose to be M. acuminata ssp. halabanensis and a yet to be characterized M. acuminata subspecies. These results highlighted a dynamic crop formation process that was initiated in New Guinea, with subsequent diversification throughout Southeast Asia.
Published: 2023

10. A genome-wide assessment of the genetic diversity, evolution and relationships with allied species of the clonally propagated crop Vanilla planifolia Jacks. ex Andrews

Author: Favre, Félicien, Jourda, Cyril, Grisoni, Michel, Piet, Quentin, Rivallan, Ronan, Dijoux, Jean-Bernard, Hascoat, Jérémy, Lepers-Andrzejewski, Sandra, Besse, Pascale, Charron, Carine, Favre, Félicien, Jourda, Cyril, Grisoni, Michel, Piet, Quentin, Rivallan, Ronan, Dijoux, Jean-Bernard, Hascoat, Jérémy, Lepers-Andrzejewski, Sandra, Besse, Pascale, and Charron, Carine
Abstract: The Vanilla genus is a complex taxonomic group characterized by a vegetative reproduction mode combined with intra- and inter-specific hybridizations, and polyploidy events. These factors strongly impact the diversification of the genus and complicate the delimitation of taxa. Among the hundred Vanilla species, Vanilla planifolia Jacks. ex Andrews and Vanilla × tahitensis J. W. Moore are the main cultivated aromatic species. We applied Genotyping-by-Sequencing to explore the genetic diversity of these two cultivated vanilla species, seven closely related species and nineteen interspecific hybrids. The inter- and intra-specific relationships of 133 vanilla accessions were examined based on 2004 filtered SNPs. Our results showed a strong genetic structuring between the nine species studied, with wild species showing much lower heterozygosity levels than cultivated ones. Moreover, using Bayesian clustering analyses, the kinship of several hybrids could be verified. We evidenced in particular that Vanilla sotoarenasii and Vanilla odorata C.Presl may be the parental species of V. x tahitensis. The analysis of 1129 SNPs for 84 V. planifolia accessions showed a clear genetic demarcation between the vegetatively propagated traditional vanilla cultivars compared to the accessions derived from sexual reproduction, and a higher genetic diversity and lower heterozygosity of the latter (Ho = 0.206) compared to the former (Ho = 0.362). Our data are consistent with a single-step domestication for V. planifolia in accordance with the recent history of its cultivation. It also opens avenues to breed new V. planifolia varieties adapted to biotic and abiotic constraints and to reduce mutational load induced by clonal propagation.
Published: 2022

11. Genome-wide footprints in the carob tree (Ceratonia siliqua) unveil a new domestication pattern of a fruit tree in the Mediterranean

Author: Baumel, Alex, Feliner, Gonzalo Nieto, Médail, Frédéric, La Malfa, Stefano, Di Guardo, Mario, Bou Dagher Kharrat, Magda, Lakhal-Mirleau, Fatima, Frelon, Valentine, Ouahmane, Lahcen, Diadema, Katia, Sanguin, Hervé, Viruel, Juan, Baumel, Alex, Feliner, Gonzalo Nieto, Médail, Frédéric, La Malfa, Stefano, Di Guardo, Mario, Bou Dagher Kharrat, Magda, Lakhal-Mirleau, Fatima, Frelon, Valentine, Ouahmane, Lahcen, Diadema, Katia, Sanguin, Hervé, and Viruel, Juan
Abstract: Intense research efforts over the last two decades renewed our understanding of plant phylogeography and domestication in the Mediterranean basin. We aim to investigate the evolutionary history and the origin of domestication of the carob tree (Ceratonia siliqua), which has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to delimit seven carob evolutionary units (CEUs). We investigated genome-wide diversity and evolutionary patterns of the CEUs with 3557 SNPs generated by restriction-site associated DNA sequencing (RADseq). To address the complex wild vs. cultivated status of sampled trees, we classified 56 sampled populations across the Mediterranean basin as wild, semi-natural or cultivated. Nuclear and cytoplasmic loci were identified from RADseq data and separated for analyses. Phylogenetic analyses of these genomic-wide data allowed us to resolve west-to-east expansions from a single long-term refugium likely located in the foothills of the High Atlas Mountains near the Atlantic coast. Our findings support multiple origins of domestication with a low impact on the genetic diversity at range wide level. The carob was mostly domesticated from locally selected wild genotypes and scattered long-distance westward dispersals of domesticated varieties by humans, concomitant with major historical migrations by Romans, Greeks and Arabs. Ex-situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in Southwest Morocco, South Spain and Eastern Mediterranean. Our study highlights the relevance of wild and seminatural habitats in the conservation of genetic resources for cultivated trees.
Published: 2022

12. Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas

Author: Sardos, Julie, Breton, Catherine, Perrier, Xavier, Van Den Houwe, Ines, Carpentier, Sébastien Christian, Paofa, Janet, Rouard, Mathieu, Roux, Nicolas, Sardos, Julie, Breton, Catherine, Perrier, Xavier, Van Den Houwe, Ines, Carpentier, Sébastien Christian, Paofa, Janet, Rouard, Mathieu, and Roux, Nicolas
Abstract: Hybridization and introgressions are important evolutionary forces in plants. They contribute to the domestication of many species, including understudied clonal crops. Here, we examine their role in the domestication of a clonal crop of outmost importance, banana (Musa ssp.). We used genome-wide SNPs generated for 154 diploid banana cultivars and 68 samples of the wild M. acuminata to estimate and geo-localize the contribution of the different subspecies of M. acuminata to cultivated banana. We further investigated the wild to domesticate transition in New Guinea, an important domestication center. We found high levels of admixture in many cultivars and confirmed the existence of unknown wild ancestors with unequal contributions to cultivated diploid. In New Guinea, cultivated accessions exhibited higher diversity than their direct wild ancestor, the latter recovering from a bottleneck. Introgressions, balancing selection and positive selection were identified as important mechanisms for banana domestication. Our results shed new lights on the radiation of M. acuminata subspecies and on how they shaped banana domestication. They point candidate regions of origin for two unknown ancestors and suggest another contributor in New Guinea. This work feed research on the evolution of clonal crops and has direct implications for conservation, collection, and breeding.
Published: 2022

13. Towards domestication of the endemic Malagasy pepper tsiperifery (Piper sp.): Lessons learnt from domestication and cultivation history of other peppers

Author: V. Ceccarelli, J. Queste, P. Bàrberi, Savoirs, ENvironnement et Sociétés (SENS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut de Recherche pour le Développement (IRD), Département Environnements et Sociétés (Cirad-ES), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: [SDV]Life Sciences [q-bio], F08 - Systèmes et modes de culture, Sélection, Rainforest, Agroforesterie, Horticulture, [SHS]Humanities and Social Sciences, F30 - Génétique et amélioration des plantes, F01 - Culture des plantes, Pepper, Cultivation System, Domestication, ComputingMilieux_MISCELLANEOUS, Management practices, Piper, biology, Agroforestry, Domestication des plantes, Edaphic, Understory, biology.organism_classification, culture de plantation, Système de culture, Plante de culture, Agronomy and Crop Science, Génotype, Food Science
Abstract: Introduction – Since the international popularity of tsiperifery, the Malagasy wild pepper (Piper sp.) from Madagascar started to grow, traditional low-intensity harvesting has turned into uncontrolled systematic collection, which is environmentally and socio-economically unsustainable. Domestication could be key for sustainable exploitation of tsiperifery. Here we collated information from comparable domesticated Piper species to identify pathways to accelerate the domestication of tsiperifery. Materials and methods – We conducted a literature review, upon four steps: (1) identification of the already domesticated Piper species; (2) analysis of their domestication history and cultivation methods to highlight the common critical points for domestication; (3) comparison of this information with the limited ones available on tsiperifery; and (4) provision of preliminary recommendations on a possible domestication pathway for tsiperifery. Results and discussion – We identified and analyzed 22 domesticated Piper species. We found nine critical issues, the most important being: (i) genotype selection; (ii) procedure for vegetative propagation; (iii) reproduction of the microclimatic and edaphic conditions of the rainforest understory; (iv) choice of the best supports and cultivation system; (v) reduction of the delay before entry into production; and (vi) control of plant height. For each critical issue, we suggested preliminary recommendations. Conclusion – This paper provides baseline information towards the domestication of tsiperifery. Further on-field and molecular experiments are needed to confirm these findings and identify suitable management practices.
Published: 2021

14. Redox-related gene expression and sugar accumulation patterns are altered in the edible inflorescence produced by the cultivated form of pacaya palm (Chamaedorea tepejilote)

Author: Hanene Hosni, Christine Tranchant-Dubreuil, Fabienne Morcillo, James W. Tregear, Stéphane Dussert, Felipe Castaño, Virginie Vaissayre, Abdoulaye Diallo, Juan Jose Castillo Mont, Xavier Marquínez, Fred W. Stauffer, Donald R. Hodel, Thierry Joët, Stefan Jouannic, Hélène Adam, and Myriam Collin
Subjects: 0106 biological sciences, 0301 basic medicine, Oxydoréduction, Chamaedorea, Gene Expression, Plant Science, Arecaceae, 01 natural sciences, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, Chamaedorea tepejilote, Botany, Inflorescence, Secondary metabolism, Sugar, Domestication, Variation phénotypique, biology, Domestication des plantes, phytogénétique, Original Articles, Meristem, biology.organism_classification, 030104 developmental biology, Sugars, Oxidation-Reduction, 010606 plant biology & botany
Abstract: Background and Aims The pacaya palm is a dioecious neotropical palm species that is exploited in Latin America for its male inflorescence, which is edible when immature. It is cultivated, in a non-intensive manner, in Guatemala, where a morphotype occurs that produces much larger, more highly branched inflorescences compared with wild palms. We sought to identify molecular factors underlying this phenotypic divergence, which is likely to be a product of domestication. Methods We performed RNA-seq-based studies on immature pacaya palm male inflorescences in order to identify genes that might be directly or indirectly affected in their expression in relation to domestication. We also measured the accumulation of a range of soluble sugar molecules to provide information on the biochemical status of the two different types of material. Key Results A total of 408 genes were found to display significantly different expression levels between the wild and cultivated morphotypes. Three different functional categories were found to be enriched in the gene set that was upregulated in the cultivated morphotype: redox balance; secondary metabolism; and transport. Several sugars were found to accumulate at higher levels in inflorescences of the cultivated morphotype, in particular myo-inositol, fructose and glucose. Conclusions The observed upregulation of redox-related genes in the cultivated morphotype is corroborated by the observation of higher myo-inositol accumulation, which has been shown to be associated with enhanced scavenging of reactive oxygen species in other plants and which may affect meristem activity.
Published: 2021

15. A genome-wide assessment of the genetic diversity, evolution and relationships with allied species of the clonally propagated crop Vanilla planifolia Jacks. ex Andrews

Author: Félicien Favre, Cyril Jourda, Michel Grisoni, Quentin Piet, Ronan Rivallan, Jean-Bernard Dijoux, Jérémy Hascoat, Sandra Lepers-Andrzejewski, Pascale Besse, Carine Charron, Université de La Réunion (UR), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Etablissement Vanille de Tahiti, Partenaires INRAE, and Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD)Universite de la ReunionMENRT grant from the French Ministry of Higher Education, Research and InnovationEuropean CommissionConseil General de la ReunionFORDECYT-CONACYT297484
Subjects: Vanilla × tahitensis, F40 - Écologie végétale, Diversité génétique (comme ressource), phytogénétique, Domestication des plantes, Vanilla planifolia, Plant Science, Breeding, F30 - Génétique et amélioration des plantes, Domestication, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Agronomy and Crop Science, Ecology, Evolution, Behavior and Systematics, Génotype
Abstract: The Vanilla genus is a complex taxonomic group characterized by a vegetative reproduction mode combined with intra- and inter-specific hybridizations, and polyploidy events. These factors strongly impact the diversification of the genus and complicate the delimitation of taxa. Among the hundred Vanilla species, Vanilla planifolia Jacks. ex Andrews and Vanilla × tahitensis J. W. Moore are the main cultivated aromatic species. We applied Genotyping-by-Sequencing to explore the genetic diversity of these two cultivated vanilla species, seven closely related species and nineteen interspecific hybrids. The inter- and intra-specific relationships of 133 vanilla accessions were examined based on 2004 filtered SNPs. Our results showed a strong genetic structuring between the nine species studied, with wild species showing much lower heterozygosity levels than cultivated ones. Moreover, using Bayesian clustering analyses, the kinship of several hybrids could be verified. We evidenced in particular that Vanilla sotoarenasii and Vanilla odorata C.Presl may be the parental species of V. x tahitensis. The analysis of 1129 SNPs for 84 V. planifolia accessions showed a clear genetic demarcation between the vegetatively propagated traditional vanilla cultivars compared to the accessions derived from sexual reproduction, and a higher genetic diversity and lower heterozygosity of the latter (Ho = 0.206) compared to the former (Ho = 0.362). Our data are consistent with a single-step domestication for V. planifolia in accordance with the recent history of its cultivation. It also opens avenues to breed new V. planifolia varieties adapted to biotic and abiotic constraints and to reduce mutational load induced by clonal propagation.
Published: 2022

16. Pilot assessment of locally acknowledged morphotypes of Irvingia gabonensis (Aubry-Lecomte) Baill. in southwestern Benin (West Africa).

Author: Padonou, E. A., Tovissodé, F. C., Idohou, R., Salako, V. K., Fantondji, L., Vihotogbé, R., Fandohan, B., and Assogbadjo, A. E.
Abstract: Copyright of Fruits is the property of International Society for Horticultural Science and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Published: 2017
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17. Genome-wide footprints in the carob tree (Ceratonia siliqua) unveil a new domestication pattern of a fruit tree in the Mediterranean

Author: Alex Baumel, Gonzalo Nieto Feliner, Frédéric Médail, Stefano La Malfa, Mario Di Guardo, Magda Bou Dagher Kharrat, Fatma Lakhal‐Mirleau, Valentine Frelon, Lahcen Ouahmane, Katia Diadema, Hervé Sanguin, Juan Viruel, Agence Nationale de la Recherche (France), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Real Jardín Botánico de Madrid (RJB), Spanish National Research Council (CSIC), Università degli studi di Catania = University of Catania (Unict), Université Saint-Joseph de Beyrouth (USJ), Faculté des Sciences Semlalia [Marrakech], Université Cadi Ayyad [Marrakech] (UCA), Conservatoire Botanique National Méditerranéen de Porquerolles, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Royal Botanic Gardens [Kew], ANR-14-CE02-0016,DYNAMIC,Décryptage des réseaux symbiotiques au sein des agro-écosystèmes méditerranéens à caroubier(2014), and European Project: 704464,H2020,H2020-MSCA-IF-2015,Yamnomics(2017)
Subjects: microsatellite, Biogéographie, phylogeography, Galactans, F30 - Génétique et amélioration des plantes, Domestication, Mannans, Ceratonia siliqua, Variation génétique, Ressource génétique végétale, Plant Gums, Genetics, origin, Ecology, Evolution, Behavior and Systematics, Phylogeny, biogeography, Génome, Mediterranean Region, Domestication des plantes, phytogénétique, Genetic Variation, Fabaceae, F70 - Taxonomie végétale et phytogéographie, genetic diversity, RADseq, Fruit, [SDE]Environmental Sciences
Abstract: International audience; Intense research efforts over the last two decades have renewed our understand-ing of plant phylogeography and domestication in the Mediterranean basin. Here we aim to investigate the evolutionary history and the origin of domestication of the carob tree (Ceratonia siliqua), which has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to delimit seven carob evolutionary units (CEUs). We investigated genome-wide diversity and evolutionary patterns of the CEUs with 3557 single nucleotide polymorphisms generated by restriction-site asso-ciated DNA sequencing (RADseq). To address the complex wild vs. cultivated status of sampled trees, we classified 56 sampled populations across the Mediterranean basin as wild, seminatural or cultivated. Nuclear and cytoplasmic loci were identified from RADseq data and separated for analyses. Phylogenetic analyses of these genomic- wide data allowed us to resolve west-to- east expansions from a single long-term refu-gium probably located in the foothills of the High Atlas Mountains near the Atlantic coast. Our findings support multiple origins of domestication with a low impact on the genetic diversity at range-wide level. The carob was mostly domesticated from locally selected wild genotypes and scattered long-distance westward dispersals of domesticated varieties by humans, concomitant with major historical migrations by Romans, Greeks and Arabs. Ex situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in southwest Morocco, south Spain and eastern Mediterranean. Our study highlights the relevance of wild and seminatural habitats in the conservation of genetic resources for cultivated trees
Published: 2022

18. The road to sorghum domestication: Evidence from nucleotide diversity and gene expression patterns

Author: Burgarella, Concetta, Berger, Angélique, Glemin, Sylvain, David, Jacques, Terrier, Nancy, Deu, Monique, Pot, David, Burgarella, Concetta, Berger, Angélique, Glemin, Sylvain, David, Jacques, Terrier, Nancy, Deu, Monique, and Pot, David
Abstract: Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well-understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and nine wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a global reduction of diversity during the domestication process, although several genes also showed patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyzes revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totaling 2,449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that the combined and intricated effects of the domestication and improvement processes do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome. Overall, these analyzes pave the way toward the identification of key domestication genes valuable for genetic resources c
Published: 2021

19. Stratégies paysannes de participation à la domestication du poivre sauvage de Madagascar, le Tsiperifery

Author: Rasambo, Sedera Norotiana, Queste, Jérôme, Razafiarijoana, Jules, Audouin, Sarah, Jankowski, Frédérique, Rabefarihy, Andriantsoa Tahiry, Ramananarivo, Romaine, Rasambo, Sedera Norotiana, Queste, Jérôme, Razafiarijoana, Jules, Audouin, Sarah, Jankowski, Frédérique, Rabefarihy, Andriantsoa Tahiry, and Ramananarivo, Romaine
Abstract: À Madagascar, le Tsiperifery, une espèce de poivrier sauvage endémique de l'île, est actuellement soumis à une surexploitation. Un programme participatif de domestication de cette plante a été lancé pour assurer la durabilité de son exploitation. Des techniques de culture sont co-construites par des chercheurs et des paysans sur trois sites pilotes. Cette étude s'intéresse aux facteurs influençant la propension des paysans à co-construire et expérimenter ces techniques. Les données collectées via 90 entretiens semi-dirigés ont été traitées en suivant les principes de l'approche " grounded theory ". Les principaux déterminants influençant le comportement des paysans sont (i) la logique économique, (ii) le contexte informationnel, (iii) l'accès au marché, (iv) les capacités productives de l'exploitation et (v) l'esprit de conservation de la nature. À partir de ces déterminants, nous avons pu définir cinq types de stratégies paysannes : les " homo-economicus " ; les " conservationnistes " ; les " opportunistes ", les " exclus " et les " suiveurs ". Cette meilleure compréhension des stratégies paysannes permet d'améliorer la conception et la conduite des programmes de recherche participative.
Published: 2021

20. Les bananiers en Afrique. Voyages des hommes, voyages des plantes

Author: Perrier, Xavier, Jenny, Christophe, Bakry, Frédéric, Perrier, Xavier, Jenny, Christophe, and Bakry, Frédéric
Abstract: Bananes dessert 'Cavendish' du commerce international, bananes plantains à cuire des marchés du Cameroun, du Congo… ou bananes à cuire et à bière des Pays des Grands Lacs, des millions de bananiers sont cultivés en Afrique. Pourtant, aucune de ces variétés n'est originaire de ce continent ! Toutes viennent d'Asie, centre d'origine du complexe d'espèces. C'est l'histoire de ces bananiers voyageurs que nous retraçons ici.
Published: 2021

21. Preserving local knowledge on Chenopodium Quinoa Willd. in the Andes in the context of market globalization

Author: Bazile, Didier and Bazile, Didier
Abstract: The IYQ-2013 highlighted the huge biodiversity of quinoa crop and its high nutritional value. This international recognition conferred a new status to this minor crop for food and agriculture. The rapid global spread of quinoa is not based on the biodiversity that is not easily available outside the Andes. Preserving quinoa genetic diversity may implied local actors considering their knowledge accumulated during generations of farmers. A new way of doing research may be invent for considering both genetic resources and traditional knowledge.
Published: 2021

22. Contribution à l'étude des déterminants génétiques et biochimiques des arômes de cacaos fins d'Équateur. Le Nacional, de la diversité aromatique de sa population d'origine jusqu'à sa domestication récente

Author: Colonges, Kelly and Colonges, Kelly
Abstract: Theobroma cacao est un arbre originaire des régions tropicales humides d'Amérique latine. Il est cultivé pour ses fèves qui permettent la production de chocolat. Le Nacional, originaire d'Equateur, est une variété de cacao fin connue pour ses arômes floraux et épicées, appelée saveur "Arriba". Les mécanismes de la synthèse de ses arômes restent peu connus. Les travaux de cette thèse ont porté sur l'étude des déterminants génétiques et biochimiques des arômes des cacaos fins équatoriens afin d'initier de contribuer aux connaissances dans ce domaine.Une première partie de l'étude a été réalisée à partir d'une population de cacaoyer de type Nacional moderne, qui est la variété de Nacional actuellement cultivée. Des études d'associations ont été réalisées sur l'ensemble du génome (GWAS) et ont porté sur l'analyse des composés volatils relatifs aux arôme floraux et fruités (fruits frais et fruits secs) contenus dans les fèves, avant et après torréfaction, ainsi que, sur des résultats d'analyses sensorielles de liqueurs. Cette première étude a pu montrer que les arômes floraux du Nacional étaient principalement synthétisés grâce à deux voies de biosynthèse: celle des monoterpènes et la voie de dégradation du L-phénylalanine. Les résultats relatifs aux arômes fruités ont permis de mettre en lumière cinq voies métaboliques majeures: la voie de biosynthèse des monoterpènes, les voies de dégradations du L-phénylalanine, des sucres, des acides gras et des protéines. Des gènes candidats codant pour des enzymes impliqués dans ces voies métaboliques ont été identifiés dans les zones d'associations correspondantes.La variété Nacional moderne est issue de diverses générations de croisements entre des Trinitario (hybrides Amelonado/Criollo) et le Nacional ancestral, mettant ainsi en jeu 3 ancêtres contrastés. L'effet de cette étape de domestication récente sur les arômes de la variété Nacional moderne a été étudié. Grâce aux données de génotypage des trois ancêtres de référence et a
Published: 2021

23. Fahien reconsidered: Pleistocene exploitation of wild bananas and Holocene introduction of Musa cultivars to Sri Lanka

Author: Tim Denham, Xavier Perrier, Luc Vrydaghs, Edmond De Langhe, Laboratory of Tropical Crop Improvement, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Centre de recherches en archéologie et patrimoine (CReA-Patrimoine), Université libre de Bruxelles (ULB), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), School of Archaeology and Anthropology, and Australian National University (ANU)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 010506 paleontology, triploid cultivars, Context (language use), 010502 geochemistry & geophysics, Musa acuminata, 01 natural sciences, banana domestication, Arts and Humanities (miscellaneous), F01 - Culture des plantes, Paleoethnobotany, Musa balbisiana, phytoliths, Earth and Planetary Sciences (miscellaneous), Variété, Domestication, 0105 earth and related environmental sciences, Hybrid, biology, Agroforestry, Domestication des plantes, Paleontology, F70 - Taxonomie végétale et phytogéographie, Taxonomie, diploid cultivars, biology.organism_classification, Botanique, Geography, Phytolith, Biological dispersal, archaeobotany
Abstract: International audience; A recent publication on the phytolith assemblage at Fahien rockshelter, Sri Lanka (Premathilake and Hunt) is argued to represent: the exploitation of wild Musa acuminata and M. balbisiana during the Late Pleistocene; the introduction of edible diploid cultivars from the Southeast Asia-New Guinea region during the early to mid-Holocene; the generation and cultivation of triploid banana hybrids on Sri Lanka before 6194-5994 cal bp; and the subsequent spread of derived triploid cultivars to mainland India and westward to Africa. A careful review of the archaeobotanical research presented by Premathilake and Hunt, in the context of broader multidisciplinary evidence (agronomy, archaeobotany, genetics and linguistics) for the domestication and spread of banana cultivars, indicates that three main aspects of their argument are problematic: the lack of clarity in the characterization of banana domestication in the past; the methods used to discriminate phytoliths into banana taxa; and the promotion of Sri Lanka as a source region rather than a recipient of banana cultivars. Following reconsideration, the Fahien evidence is consistent with previous interpretations for the origins of diploid and significant triploid cultivars outside of Sri Lanka and dispersal to that island.
Published: 2019

24. Genome ancestry mosaics reveal multiple and cryptic contributors to cultivated banana

Author: Martin, Guillaume, Cardi, Céline, Sarah, Gautier, Ricci, Sebastien, Jenny, Christophe, Fondi, Emmanuel, Perrier, Xavier, Glaszmann, Jean-Christophe, D'Hont, Angélique, Yahiaoui, Nabila, Martin, Guillaume, Cardi, Céline, Sarah, Gautier, Ricci, Sebastien, Jenny, Christophe, Fondi, Emmanuel, Perrier, Xavier, Glaszmann, Jean-Christophe, D'Hont, Angélique, and Yahiaoui, Nabila
Abstract: Hybridizations between closely related species commonly occur in the domestication process of many crops. Banana cultivars are derived from such hybridizations between species and subspecies of the Musa genus that have diverged in various tropical Southeast Asian regions and archipelagos. Among the diploid and triploid hybrids generated, those with seedless parthenocarpic fruits were selected by humans and thereafter dispersed through vegetative propagation. Musa acuminata subspecies contribute to most of these cultivars. We analyzed sequence data from 14 M. acuminata wild accessions and 10 M. acuminata‐based cultivars, including diploids and one triploid, to characterize the ancestral origins along their chromosomes. We used multivariate analysis and single nucleotide polymorphism clustering and identified five ancestral groups as contributors to these cultivars. Four of these corresponded to known M. acuminata subspecies. A fifth group, found only in cultivars, was defined based on the 'Pisang Madu' cultivar and represented two uncharacterized genetic pools. Diverse ancestral contributions along cultivar chromosomes were found, resulting in mosaics with at least three and up to five ancestries. The commercially important triploid Cavendish banana cultivar had contributions from at least one of the uncharacterized genetic pools and three known M. acuminata subspecies. Our results highlighted that cultivated banana origins are more complex than expected – involving multiple hybridization steps – and also that major wild banana ancestors have yet to be identified. This study revealed the extent to which admixture has framed the evolution and domestication of a crop plant.
Published: 2020

25. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Author: Abrouk, Michael, Ibrahim Ahmed, Hanin, Cubry, Philippe, Simoníková, Denisa, Cauet, Stéphane, Pailles, Yveline, Bettgenhaeuser, Jan, Gapa, Liubov, Scarcelli, Nora, Couderc, Marie, Zekraoui, Leïla, Kathiresan, Nagarajan, Cizkova, Jana, Hribova, Eva, Dolozel, Jaroslav, Arribat, Sandrine, Berges, Hélène, Wieringa, Jan J., Gueye, Mathieu, Kane, Ndjido Ardo, Leclerc, Christian, Causse, Sandrine, Vancoppenolle, Sylvie, Billot, Claire, Wicker, Thomas, Vigouroux, Yves, Barnaud, Adeline, Krattinger, Simon G., Abrouk, Michael, Ibrahim Ahmed, Hanin, Cubry, Philippe, Simoníková, Denisa, Cauet, Stéphane, Pailles, Yveline, Bettgenhaeuser, Jan, Gapa, Liubov, Scarcelli, Nora, Couderc, Marie, Zekraoui, Leïla, Kathiresan, Nagarajan, Cizkova, Jana, Hribova, Eva, Dolozel, Jaroslav, Arribat, Sandrine, Berges, Hélène, Wieringa, Jan J., Gueye, Mathieu, Kane, Ndjido Ardo, Leclerc, Christian, Causse, Sandrine, Vancoppenolle, Sylvie, Billot, Claire, Wicker, Thomas, Vigouroux, Yves, Barnaud, Adeline, and Krattinger, Simon G.
Abstract: Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.
Published: 2020

26. Enhancing germination and seedling growth in Vitex doniana Sweet for horticultural prospects and conservation of genetic resources.

Author: N’Danikou, Sognigbé, Achigan-Dako, Enoch G., Tchokponhoué, Dèdéou A., Assogba Komlan, Françoise, Gebauer, Jens, Vodouhè, Raymond S., and Ahanchédé, Adam
Abstract: Introduction. Many fruit trees with a hard seed coat exhibit seed dormancy, posing problems for their regeneration. Vitex doniana, an indigenous multipurpose but threatened fruit and vegetable tree that supports the livelihoods of many households in West Africa, is a typical example. Materials and methods. In our research, we evaluated five dormancy-breaking treatments. We tested the effects of sulphuric acid at 95% concentration (T1); 3 d sun-drying + 48 h soaking in tap water (T2); 3 d alternation of 8 h sun-drying + 1 h soaking in tap water (T3); 2 weeks sun-drying with regular watering in the daytime (T4); and physical shock (T5). These treatments were compared with two controls (T0 and Tc), with seeds from two different sources. The germination percentage, mean germination time, time to first germination and time to threshold germination (20%) were compared; the seedling height, diameter and biomass produced were monitored for 15 weeks. We used generalised linear models and correlation tests to compare the effects of the various treatments on germination and seedling growth. Results and discussion. T3 significantly enhanced seed germination in V. doniana (72% after 12 months). T4 best promoted homogeneity in germination (p < 0.01), followed by T3. The best seedling growth was obtained with T4 and T3. Alternation of sun-drying followed by soaking of seeds, a technique with almost no cost, improved seed germination in V. doniana and, in 33 d, just over 1 month, 20% germination can be achieved. Vitex doniana is a fast-growing species (at the nursery stage), in contrast to the common opinion. Conclusion. Our method should be further investigated to assess the adequate soaking and drying length so as to speed up germination and reach homogenous cohorts. [ABSTRACT FROM AUTHOR]
Published: 2014
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27. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Author: Ndjido Ardo Kane, Yves Vigouroux, Denisa Šimoníková, Leila Zekraoui, Jaroslav Dolezel, Nagarajan Kathiresan, Sandrine Causse, Michael Abrouk, Thomas Wicker, Sandrine Arribat, Claire Billot, Stéphane Cauet, Simon G. Krattinger, Jana Cizkova, Sylvie Vancoppenolle, Adeline Barnaud, E. Hribova, Hélène Bergès, Philippe Cubry, Jan Bettgenhaeuser, Mathieu Gueye, Hanin Ibrahim Ahmed, Liubov Gapa, Nora Scarcelli, Yveline Pailles, Jan J. Wieringa, Christian Leclerc, Marie Couderc, University of Zurich, Barnaud, Adeline, Krattinger, Simon G, King Abdullah University of Science and Technology (KAUST), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Naturalis Biodiversity Center [Leiden], Institut Fondamental d'Afrique Noire (IFAN), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Senegalese Agricultural Research Institute, LMI Adaptation des Plantes et microorganismes associés aux Stress Environnementaux [Dakar] (LAPSE), Institut de Recherche pour le Développement (IRD), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universität Zürich [Zürich] = University of Zurich (UZH), European Regional Development Fund OPVVV project 'Plants as a tool for sustainable development' CZ.02.1.01/0.0/0.0/16_019/0000827, ANR-16-IDEX-0006,MUSE,MUSE(2016), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Digitaria, General Physics and Astronomy, 580 Plants (Botany), 01 natural sciences, Plant breeding, F30 - Génétique et amélioration des plantes, Domestication, 0302 clinical medicine, 10126 Department of Plant and Microbial Biology, lcsh:Science, 2. Zero hunger, Molecular breeding, 0303 health sciences, Multidisciplinary, Diversité génétique (comme ressource), Agroforestry, Domestication des plantes, phytogénétique, food and beverages, Agriculture, 3100 General Physics and Astronomy, Genome, Plant, Agricultural genetics, Plant domestication, Science, Climate Change, Context (language use), 1600 General Chemistry, Genetics and Molecular Biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, génomique, Evolution, Molecular, 03 medical and health sciences, Ressource génétique végétale, Variation génétique, Species Specificity, 1300 General Biochemistry, Genetics and Molecular Biology, 10211 Zurich-Basel Plant Science Center, Selection, Genetic, 030304 developmental biology, Changement climatique, Genetic diversity, business.industry, Genetic Variation, Molecular Sequence Annotation, Digitaria exilis, General Chemistry, 15. Life on land, biology.organism_classification, Amélioration des plantes, 030104 developmental biology, Crop diversity, 13. Climate action, General Biochemistry, Africa, lcsh:Q, business, Edible Grain, 030217 neurology & neurosurgery, 010606 plant biology & botany
Abstract: Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments., Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.
Published: 2020

28. Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat

Author: Denis Vile, Agathe Roucou, Marie-Christine Breuil, Aymé Spor, Cyrille Violle, Pierre Roumet, Laurent Philippot, David Bru, Florian Fort, Arnaud Mounier, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), European Research Council (ERC) Starting Grant Project 'Ecophysiological and biophysical constraints on domestication in crop plants' (Grant ERC-StG-2014-639706-CONSTRAINTS), INRAE Pari Scientifique (IDIOME-Ble)., European Project: 639706,H2020,ERC-2014-STG,CONSTRAINTS(2015), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro
Subjects: 0301 basic medicine, Genotype, Science, 030106 microbiology, Introgression, Microbial communities, Triticum turgidum, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Plant Roots, Article, Domestication, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Ophiostomataceae, Abundance (ecology), Mycorrhizae, Botany, Relative species abundance, Soil Microbiology, Triticum, 2. Zero hunger, Rhizosphere, Multidisciplinary, Bacteria, Ecology, biology, Obligate, Microbiota, Domestication des plantes, fungi, food and beverages, 15. Life on land, biology.organism_classification, Rhizobiales, Tetraploidy, Phenotype, 030104 developmental biology, Medicine, Mycobiome
Abstract: International audience; Despite the large morphological and physiological changes that plants have undergone through domestication, little is known about their impact on their microbiome. Here we characterized rhizospheric bacterial and fungal communities as well as the abundance of N-cycling microbial guilds across thirty-nine accessions of tetraploid wheat, Triticum turgidum, from four domestication groups ranging from the wild subspecies to the semi dwarf elite cultivars. We identified several microbial phylotypes displaying significant variation in their relative abundance depending on the wheat domestication group with a stronger impact of domestication on fungi. The relative abundance of potential fungal plant pathogens belonging to the Sordariomycetes class decreased in domesticated compared to wild emmer while the opposite was found for members of the Glomeromycetes, which are obligate plant symbionts. The depletion of nitrifiers and of arbuscular mycorrhizal fungi in elite wheat cultivars compared to primitive domesticated forms suggests that the Green Revolution has decreased the coupling between plant and rhizosphere microbes that are potentially important for plant nutrient availability. Both plant diameter and fine root percentage exhibited the highest number of associations with microbial taxa, highlighting their putative role in shaping the rhizosphere microbiota during domestication. Aside from domestication, significant variation of bacterial and fungal community composition was found among accessions within each domestication group. In particular, the relative abundances of Ophiostomataceae and of Rhizobiales were strongly dependent on the host accession, with heritability estimates of ~ 27% and ~ 25%, indicating that there might be room for genetic improvement via introgression of ancestral plant rhizosphere-beneficial microbe associations. Crop domestication events led to spectacular modifications of plant traits increasing their suitability to human requirements. Cereals and especially wheat have been domesticated in the Middle East 1. Domestication process led to dramatic phenotypic changes in cultivated species in relation to cultivation conditions and human needs. The Domestication syndrome 2 refers to the whole set of phenotypic changes occurred during this process, including: loss of dormancy, increasing seed size, modifying seed dispersal mode and apical dominance as well photoperiod sensitivity. open
Published: 2020
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29. Domestication and varietal diversification of Old World cultivated cottons ( Gossypium sp.) in the Antiquity

Author: Viot, Christopher and Viot, Christopher
Abstract: Textile use of the cotton fibres from the Old World species Gossypium arboreum (Tree Cotton) and G. herbaceum (Levant Cotton) started around eight thousand years ago and possibly earlier. During the third millennium before the present, cotton cultivation, textile use and trading developed strongly in many places of the Indian Subcontinent and the Near East, but the species involved are often undetermined. Gossypium arboreum and G. herbaceum are difficult to distinguish morphologically when dealing with archaeological remains. Many traditional varieties have been described for each of these two species; an evolution is apparent from perennial, rather primitive forms through to annual varieties and modern phenotypes, with adaptations to cultivation in diverse conditions, including cold climates and short summers. The present work examines which varieties could have been cultivated in the Antiquity and in which regions had cotton cultivation spread then. Some extant varieties are hypothesized as close to the cultivars of Antiquity. The geographic distribution of each species probably reflects the initial domestication region and the subsequent adaptations, particularly regarding climate. Recent progress on ancient DNA analysis should permit easier specific assignments of archaeological remains of cotton seeds, fibres, threads or fabrics.
Published: 2019

30. The bracteatus pineapple genome and domestication of clonally propagated crops

Author: Chen, Li-Yu, VanBuren, Robert, Paris, Margot, Zhou, Hongye, Zhang, Xingtan, Wai, Ching Man, Yan, Hansong, Chen, Shuai, Alonge, Michael, Ramakrishnan, Srividya, Liao, Zhenyang, Liu, Juan, Lin, Jishan, Yue, Jingjing, Fatima, Mahpara, Lin, Zhicong, Zhang, Jisen, Huang, Lixian, Wang, Hao, Hwa, Teh-Yang, Kao, Shu-Min, Choi, Jae Young, Sharma, Anupma, Song, Jian, Wang, Lulu, Yim, Won C., Cushman, John C., Paull, Robert E., Matsumoto, Tracie, Qin, Yuan, Wu, Qingsong, Wang, Jianping, Yu, Qingyi, Wu, Jun, Zhang, Shaoling, Boches, Peter, Tung, Chih-Wei, Wang, Ming-Li, Coppens D'Eeckenbrugge, Geo, Sanewski, Garth M., Purugganan, Michael D., Schatz, Michael C., Bennetzen, Jeffrey L., Lexer, Christian, Ming, Ray, Chen, Li-Yu, VanBuren, Robert, Paris, Margot, Zhou, Hongye, Zhang, Xingtan, Wai, Ching Man, Yan, Hansong, Chen, Shuai, Alonge, Michael, Ramakrishnan, Srividya, Liao, Zhenyang, Liu, Juan, Lin, Jishan, Yue, Jingjing, Fatima, Mahpara, Lin, Zhicong, Zhang, Jisen, Huang, Lixian, Wang, Hao, Hwa, Teh-Yang, Kao, Shu-Min, Choi, Jae Young, Sharma, Anupma, Song, Jian, Wang, Lulu, Yim, Won C., Cushman, John C., Paull, Robert E., Matsumoto, Tracie, Qin, Yuan, Wu, Qingsong, Wang, Jianping, Yu, Qingyi, Wu, Jun, Zhang, Shaoling, Boches, Peter, Tung, Chih-Wei, Wang, Ming-Li, Coppens D'Eeckenbrugge, Geo, Sanewski, Garth M., Purugganan, Michael D., Schatz, Michael C., Bennetzen, Jeffrey L., Lexer, Christian, and Ming, Ray
Abstract: Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.
Published: 2019

31. Yam genomics supports West Africa as a major cradle of crop domestication

Author: Scarcelli, Nora, Cubry, Philippe, Akakpo, Roland, Thuillet, Anne-Céline, Obidiegwu, Jude, Baco, Mohamed N., Otoo, Emmanuel, Sonké, Bonaventure, Dansi, Alexandre, Djedatin, Gustave, Mariac, Cédric, Couderc, Marie, Causse, Sandrine, Alix, Karine, Chaïr, Hâna, François, Olivier, Vigouroux, Yves, Scarcelli, Nora, Cubry, Philippe, Akakpo, Roland, Thuillet, Anne-Céline, Obidiegwu, Jude, Baco, Mohamed N., Otoo, Emmanuel, Sonké, Bonaventure, Dansi, Alexandre, Djedatin, Gustave, Mariac, Cédric, Couderc, Marie, Causse, Sandrine, Alix, Karine, Chaïr, Hâna, François, Olivier, and Vigouroux, Yves
Abstract: While there has been progress in our understanding of the origin and history of agriculture in sub-Saharan Africa, a unified perspective is still lacking on where and how major crops were domesticated in the region. Here, we investigated the domestication of African yam (Dioscorea rotundata), a key crop in early African agriculture. Using whole-genome resequencing and statistical models, we show that cultivated yam was domesticated from a forest species. We infer that the expansion of African yam agriculture started in the Niger River basin. This result, alongside with the origins of African rice and pearl millet, supports the hypothesis that the vicinity of the Niger River was a major cradle of African agriculture.
Published: 2019

32. Pervasive hybridizations in the history of wheat relatives

Author: Glemin, Sylvain, Scornavacca, Céline, Dainat, Jacques, Burgarella, Concetta, Viader, Véronique, Ardisson, Morgane, Sarah, Gautier, Santoni, Sylvain, David, Jacques, Ranwez, Vincent, Glemin, Sylvain, Scornavacca, Céline, Dainat, Jacques, Burgarella, Concetta, Viader, Véronique, Ardisson, Morgane, Sarah, Gautier, Santoni, Sylvain, David, Jacques, and Ranwez, Vincent
Abstract: Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking. Using transcriptome data from all diploid species and a new methodological approach, our comprehensive phylogenomic analysis revealed that more than half of the species descend from an ancient hybridization event but with a more complex scenario involving a different parent than previously thought—Aegilops mutica, an overlooked wild species—instead of the B genome. We also detected other extensive gene flow events that could explain long-standing controversies in the classification of wheat relatives.
Published: 2019

33. Persistent effects of pre-Columbian plant domestication on Amazonian forest composition

Author: C. Levis, F. R. C. Costa, F. Bongers, M. Peña-Claros, C. R. Clement, A. B. Junqueira, E. G. Neves, E. K. Tamanaha, F. O. G. Figueiredo, R. P. Salomão, C. V. Castilho, W. E. Magnusson, O. L. Phillips, J. E. Guevara, D. Sabatier, J.-F. Molino, D. Cárdenas López, A. M. Mendoza, N. C. A. Pitman, A. Duque, P. Núñez Vargas, C. E. Zartman, R. Vasquez, A. Andrade, J. L. Camargo, T. R. Feldpausch, S. G. W. Laurance, W. F. Laurance, T. J. Killeen, H. E. Mendonça Nascimento, J. C. Montero, B. Mostacedo, I. L. Amaral, I. C. Guimarães Vieira, R. Brienen, H. Castellanos, J. Terborgh, M. de Jesus Veiga Carim, J. R. da Silva Guimarães, L. de Souza Coelho, F. D. de Almeida Matos, F. Wittmann, H. F. Mogollón, G. Damasco, N. Dávila, R. García-Villacorta, E. N. H. Coronado, T. Emilio, D. de Andrade Lima Filho, J. Schietti, P. Souza, N. Targhetta, J. A. Comiskey, B. S. Marimon, B.-H. Marimon, D. Neill, A. Alonso, L. Arroyo, F. A. Carvalho, F. C. de Souza, F. Dallmeier, M. P. Pansonato, J. F. Duivenvoorden, P. V. A. Fine, P. R. Stevenson, A. Araujo-Murakami, G. A. Aymard C., C. Baraloto, D. D. do Amaral, J. Engel, T. W. Henkel, P. Maas, P. Petronelli, J. D. Cardenas Revilla, J. Stropp, D. Daly, R. Gribel, M. Ríos Paredes, M. Silveira, R. Thomas-Caesar, T. R. Baker, N. F. da Silva, L. V. Ferreira, C. A. Peres, M. R. Silman, C. Cerón, F. C. Valverde, A. Di Fiore, E. M. Jimenez, M. C. Peñuela Mora, M. Toledo, E. M. Barbosa, L. C. de Matos Bonates, N. C. Arboleda, E. de Sousa Farias, A. Fuentes, J.-L. Guillaumet, P. Møller Jørgensen, Y. Malhi, I. P. de Andrade Miranda, J. F. Phillips, A. Prieto, A. Rudas, A. R. Ruschel, N. Silva, P. von Hildebrand, V. A. Vos, E. L. Zent, S. Zent, B. B. L. Cintra, M. T. Nascimento, A. A. Oliveira, H. Ramirez-Angulo, J. F. Ramos, G. Rivas, J. Schöngart, R. Sierra, M. Tirado, G. van der Heijden, E. V. Torre, O. Wang, K. R. Young, C. Baider, A. Cano, W. Farfan-Rios, C. Ferreira, B. Hoffman, C. Mendoza, I. Mesones, A. Torres-Lezama, M. N. U. Medina, T. R. van Andel, D. Villarroel, R. Zagt, M. N. Alexiades, H. Balslev, K. Garcia-Cabrera, T. Gonzales, L. Hernandez, I. Huamantupa-Chuquimaco, A. G. Manzatto, W. Milliken, W. P. Cuenca, S. Pansini, D. Pauletto, F. R. Arevalo, N. F. Costa Reis, A. F. Sampaio, L. E. Urrego Giraldo, E. H. Valderrama Sandoval, L. Valenzuela Gamarra, C. I. A. Vela, H. ter Steege, Museu Paraense Emílio Goeldi, University of Iceland [Reykjavik], Instituto Nacional de Tecnología Agropecuaria, Pergamino, Argentina, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Chercheur indépendant, Observatorio Nacional [Rio de Janeiro], Instituto de Ciencia Molecular (ICMol), Universitat de València (UV), Herbario Nacional del Ecuador, Applied Tumor Virology, German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Museo Noel Kempff Mercado, Neuro-Dol - Clermont Auvergne (Neuro-Dol), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), Université du Québec à Montréal (UQAM), Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Departamento de Ciências da Natureza, Central Science Laboratory, Association Euratom/CFN/IST, IST, CERN [Genève], Unité Matériaux et Transformations - UMR 8207 (UMET), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure de Chimie de Lille (ENSCL)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Scienze degli Alimenti, University of Parma, Hopital Erasme, Université Libre de Bruxelles [Bruxelles] (ULB), Oxford University Centre for the Environment (OUCE), University of Oxford [Oxford], Department of Automatic Control and Systems Engineering [Sevilla] (ISA), Instituto de Ciencias Naturales, Institut de Physique Théorique - UMR CNRS 3681 (IPHT), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), inconnu, Inconnu, Max Planck Institute for Chemistry (MPIC), Max-Planck-Gesellschaft, University of Adelaide, ICMCB (ICMCB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Universidad de Los Andes [Venezuela] (ULA), Universidad de Salamanca, Salamanca, Spain, Universidad de Salamanca, Pontificia Universidad Católica de Chile (UC), Edmund Mach Foundation (FEM), Instituto Nacional de Pesquisas da Amazônia (INPA), Systems Ecology, Museu Paraense Emílio Goeldi [Belém, Brésil] (MPEG), Neuro-Dol (Neuro-Dol), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université du Québec à Montréal = University of Québec in Montréal (UQAM), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure de Chimie de Lille (ENSCL)-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Università degli studi di Parma = University of Parma (UNIPR), Hôpital Erasme [Bruxelles] (ULB), Faculté de Médecine [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), University of Oxford, Universidad de Los Andes [Mérida, Venezuela] (ULA), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut de Chimie du CNRS (INC)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Nationale Supérieure de Chimie de Lille (ENSCL), University of Parma = Università degli studi di Parma [Parme, Italie], Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Université de Lille-Ecole Nationale Supérieure de Chimie de Lille (ENSCL)-Institut National de la Recherche Agronomique (INRA), Ecosystem and Landscape Dynamics (IBED, FNWI), Tamanaha, Eduardo, Guevara, Juan, and Cárdenas López, D.
Subjects: 0106 biological sciences, SELECTION, 010504 meteorology & atmospheric sciences, Amazonian, Pre-columbian archaeology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, K01 - Foresterie - Considérations générales, HISTORY, Forêt tropicale humide, ARQUEOLOGIA, Multidisciplinary, Ecology, Agroforestry, Amazon rainforest, Domestication des plantes, Soil Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, PE&RC, Ecologia historica, Amazonian forests, Geography, Amazony, Etnobotânica, F40 - Écologie végétale, Plant domestication, Structural basin, 010603 evolutionary biology, REGION, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, domesticated species, Life Science, Bosecologie en Bosbeheer, Domestication, SDG 2 - Zero Hunger, Relative species abundance, Bodembiologie, CROPS, 0105 earth and related environmental sciences, BASIN, forests, Amazonian forest, domesticação da paisagem, 15. Life on land, Forest Ecology and Forest Management, EVOLUTION, biodiversité forestière, CULTIVATION, SOILS, CLIMATE, PATTERNS, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; The marks of prehistoric human societies on tropical forests can still be detected today. Levis et al. performed a basin-wide comparison of plant distributions, archaeological sites, and environmental data. Plants domesticated by pre-Columbian peoples are much more likely to be dominant in Amazonian forests than other species. Furthermore, forests close to archaeological sites often have a higher abundance and richness of domesticated species. Thus, modern-day Amazonian tree communities across the basin remain largely structured by historical human use.Science, this issue p. 925The extent to which pre-Columbian societies altered Amazonian landscapes is hotly debated. We performed a basin-wide analysis of pre-Columbian impacts on Amazonian forests by overlaying known archaeological sites in Amazonia with the distributions and abundances of 85 woody species domesticated by pre-Columbian peoples. Domesticated species are five times more likely than nondomesticated species to be hyperdominant. Across the basin, the relative abundance and richness of domesticated species increase in forests on and around archaeological sites. In southwestern and eastern Amazonia, distance to archaeological sites strongly influences the relative abundance and richness of domesticated species. Our analyses indicate that modern tree communities in Amazonia are structured to an important extent by a long history of plant domestication by Amazonian peoples.
Published: 2017

34. Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication

Author: Gautier Sarah, Bouchaib Khadari, Sylvain Santoni, Muriel Gros-Balthazard, Julie Leclercq, Yan Holtz, Daniel Wegmann, Sylvain Glémin, Guillaume Besnard, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Fribourg, Swiss Institute of Bioinformatics [Genève] (SIB), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Uppsala University, Conservatoire Botanique National Méditerranéen de Porquerolles, OliveMed N° 1403‐026, Labex AGRO (ANR-10LABX-01-01), Agropolis Fondation, Labex CEBA (ANR‐10LABX‐25‐01), Agence Nationale de la Recherche, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Fribourg = University of Fribourg (UNIFR), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, 0301 basic medicine, approche transcriptomique, Biodiversité et Ecologie, [SDV]Life Sciences [q-bio], Plant Science, RNA‐sequencing, 01 natural sciences, Mediterranean Basin, F30 - Génétique et amélioration des plantes, Evolutionsbiologi, Transcriptome, Domestication, transcriptomics, F01 - Culture des plantes, Gene Expression Regulation, Plant, Olea europaea, ComputingMilieux_MISCELLANEOUS, Artificial selection, Differential expression analysis, Olea europaea (olive tree), Perennial crop, Transcriptomics, 2. Zero hunger, biology, Mediterranean Region, Domestication des plantes, domestication des espèces, F70 - Taxonomie végétale et phytogéographie, Genomics, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, expression différentielle, Olea, differential expression analysis, [SDE]Environmental Sciences, Original Article, Genome, Plant, RNA-sequencing, artificial selection, Sélection artificielle, Séquence d'ARN, Life history theory, Biodiversity and Ecology, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Evolution, Molecular, domestication, 03 medical and health sciences, Variation génétique, Species Specificity, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Genetik, Selection, Genetic, Gene, perennial crop, Evolutionary Biology, Genetic diversity, Transcription génique, Sequence Analysis, RNA, Genetic Variation, Cell Biology, Original Articles, 15. Life on land, biology.organism_classification, Olive trees, 030104 developmental biology, Evolutionary biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract: Summary The olive (Olea europaea L. subsp. europaea) is one of the oldest and most socio‐economically important cultivated perennial crop in the Mediterranean region. Yet, its origins are still under debate and the genetic bases of the phenotypic changes associated with its domestication are unknown. We generated RNA‐sequencing data for 68 wild and cultivated olive trees to study the genetic diversity and structure both at the transcription and sequence levels. To localize putative genes or expression pathways targeted by artificial selection during domestication, we employed a two‐step approach in which we identified differentially expressed genes and screened the transcriptome for signatures of selection. Our analyses support a major domestication event in the eastern part of the Mediterranean basin followed by dispersion towards the West and subsequent admixture with western wild olives. While we found large changes in gene expression when comparing cultivated and wild olives, we found no major signature of selection on coding variants and weak signals primarily affected transcription factors. Our results indicated that the domestication of olives resulted in only moderate genomic consequences and that the domestication syndrome is mainly related to changes in gene expression, consistent with its evolutionary history and life history traits., Significance Statement We revisited the evolutionary history of the iconic olive tree by reconstructing a model of domestication and inferring the genomic changes associated with its cultivation. Although more challenging than studying annual crops, further studies of the genomic of the domestication process in perennial should broaden our understanding of the genomic bases and dynamics of adaptation.
Published: 2019

35. The bracteatus pineapple genome and domestication of clonally propagated crops

Author: Michael C. Schatz, Michael Alonge, Juan Liu, Anupma Sharma, Geo Coppens D'Eeckenbrugge, Jeffrey L. Bennetzen, Xingtan Zhang, Lixian Huang, Ray Ming, Jingjing Yue, Jisen Zhang, Ming Li Wang, John C. Cushman, Srividya Ramakrishnan, Jae Young Choi, Teh Yang Hwa, Ching Man Wai, Shu-Min Kao, Hao Wang, Peter Boches, Qingsong Wu, Zhenyang Liao, Robert E. Paull, Christian Lexer, Chih-Wei Tung, Shuai Chen, Jianping Wang, Tracie K. Matsumoto, Hongye Zhou, Li Yu Chen, Margot Paris, Jian Song, Won Cheol Yim, Robert VanBuren, Garth M. Sanewski, Michael D. Purugganan, Mahpara Fatima, Yuan Qin, Hansong Yan, Shaoling Zhang, Lulu Wang, Jun Wu, Zhicong Lin, Qingyi Yu, Jishan Lin, Fujian Agriculture and Forestry University (FAFU), University of Illinois at Urbana-Champaign [Urbana], University of Illinois System, Department of Horticulture, University of Wisconsin-Madison, Department of Biology, Northern Arizona University [Flagstaff], Department of Genetics, University of Georgia [USA], Johns Hopkins University (JHU), National Taiwan University, New York University [New York] (NYU), NYU System (NYU), Texas A&M University System, Department of agronomy, University of Florida [Gainesville] (UF), Department of Biochemistry and Molecular Biology, University of Nevada [Reno], University of Hawaii at Manoa, Partenaires INRAE, USDA-ARS : Agricultural Research Service, South Subtropical Crops Research Institute, CATAS, Nanjing Agricultural University, Hawaii Agriculture Research Center, Queensland Department of Agriculture and Fisheries, Department of Botany and Biodiversity Research, University of Vienna [Vienna], Department of Science and Technology of Fujian Province : 2016NZ0001-1, National Natural Science Foundation of China : U1605212, 31628013, 31701874, Fuzhou Science and Technology project : 2017-N-33, Distinguished Young Scholars Fund in Fujian Agriculture and Forestry University : xjq201609, National Science Foundation (NSF) : DBI-1401572, DBI1350041, United States Department of Health & Human Services, National Institutes of Health (NIH) - USA : R01-HG006677, NSF Plant Genome grants : 0607123, 043707-01, IOS-1546218, Zegar Family Foundatio : A16-0051-001, and Swiss National Science Foundation (SNSF) : CRSII3_147630
Subjects: 0106 biological sciences, Crops, Agricultural, Population Dynamics, Sequence assembly, Genomics, Quantitative trait locus, Ananas, 01 natural sciences, Genetic recombination, Genome, F30 - Génétique et amélioration des plantes, Domestication, 03 medical and health sciences, Ressource génétique végétale, Quantitative Trait, Heritable, Gene Expression Regulation, Plant, Multiplication végétative, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, 030304 developmental biology, Plant Proteins, 2. Zero hunger, 0303 health sciences, Vegetal Biology, Génome, biology, Domestication des plantes, biology.organism_classification, Plants, Genetically Modified, Bromelains, Phenotype, F02 - Multiplication végétative des plantes, Evolutionary biology, Ananas comosus, Sugars, Biologie végétale, Genome, Plant, 010606 plant biology & botany
Abstract: Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a ‘one-step operation’. We sequenced the genome ofAnanas comosusvar.bracteatusCB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89Ananasgenomes. Cultivars ‘Smooth Cayenne’ and ‘Queen’ exhibited ancient and recent admixture, while ‘Singapore Spanish’ supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.
Published: 2019

36. Genome ancestry mosaics reveal multiple and cryptic contributors to cultivated banana

Author: Martin, guillaume, Cardi, Céline, Sarah, Gautier, Ricci, Sébastien, Jenny, Christophe, Fondi, Emmanuel, PERRIER, Xavier, Glaszmann, Jean-Christophe, D'Hont, Angélique, Yahiaoui, Nabila, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), African Center for Research on Bananas and Plantains = Centre Africain de Recherches sur Bananiers et Plantains (CARBAP), French National Research Agency (ANR) : 0900-001, ANR-10-LABX-0001-01, French National Research Agency (ANR) : ANR-10-LABX-0001-01, 1504-006, CGIAR Research Programme on Roots, Tubers, and Bananas (RTB), CIRAD - UMR AGAP HPC Data Center of the South Green Bioinfor-matics platform, and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: Crops, Agricultural, Hybridation intergénérique, Musa acuminata, Chromosomes, Plant, diversity, F30 - Génétique et amélioration des plantes, Variation génétique, admixture, genome ancestry, hybridization, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Variété, Génome, Vegetal Biology, Domestication des plantes, fungi, food and beverages, Musa, Original Articles, F70 - Taxonomie végétale et phytogéographie, Hybridization, Genetic, Original Article, Genome, Plant, Biologie végétale
Abstract: Summary Hybridizations between closely related species commonly occur in the domestication process of many crops. Banana cultivars are derived from such hybridizations between species and subspecies of the Musa genus that have diverged in various tropical Southeast Asian regions and archipelagos. Among the diploid and triploid hybrids generated, those with seedless parthenocarpic fruits were selected by humans and thereafter dispersed through vegetative propagation. Musa acuminata subspecies contribute to most of these cultivars. We analyzed sequence data from 14 M. acuminata wild accessions and 10 M. acuminata‐based cultivars, including diploids and one triploid, to characterize the ancestral origins along their chromosomes. We used multivariate analysis and single nucleotide polymorphism clustering and identified five ancestral groups as contributors to these cultivars. Four of these corresponded to known M. acuminata subspecies. A fifth group, found only in cultivars, was defined based on the ‘Pisang Madu’ cultivar and represented two uncharacterized genetic pools. Diverse ancestral contributions along cultivar chromosomes were found, resulting in mosaics with at least three and up to five ancestries. The commercially important triploid Cavendish banana cultivar had contributions from at least one of the uncharacterized genetic pools and three known M. acuminata subspecies. Our results highlighted that cultivated banana origins are more complex than expected – involving multiple hybridization steps – and also that major wild banana ancestors have yet to be identified. This study revealed the extent to which admixture has framed the evolution and domestication of a crop plant., Significance Statement Hybridizations between subspecies of Musa acuminata are at the origin of a diversity of banana cultivars whose genomes remain to be fully characterized for their ancestry. We developed a bioinformatics approach to decipher the genome ancestry mosaic in a set of banana cultivars including the commercially important Cavendish banana. We revealed that the cultivars resulted from multiple hybridization events involving known M. acuminata subspecies but also unknown contributors still to be discovered. These results bring essential information for breeding strategies in this crop that is particularly threatened by disease.
Published: 2019

37. Domestication and varietal diversification of Old World cultivated cottons ( Gossypium sp.) in the Antiquity

Author: Christopher Viot
Subjects: Old World, Perennial plant, Tree cotton, lcsh:Anthropology, Gossypium, Coton, Gossypium herbaceum, Histoire, domestication, diversification variétale, varietal diversification, F01 - Culture des plantes, Botany, Cultivar, Variété, Domestication, B50 - Histoire, Gossypium arboreum, biology, lcsh:GN1-890, Domestication des plantes, General Medicine, biology.organism_classification, Ancient DNA
Abstract: Textile use of the cotton fibres from the Old World species Gossypium arboreum (Tree Cotton) and G. herbaceum (Levant Cotton) started around eight thousand years ago and possibly earlier. During the third millennium before the present, cotton cultivation, textile use and trading developed strongly in many places of the Indian Subcontinent and the Near East, but the species involved are often undetermined. Gossypium arboreum and G. herbaceum are difficult to distinguish morphologically when dealing with archaeological remains. Many traditional varieties have been described for each of these two species; an evolution is apparent from perennial, rather primitive forms through to annual varieties and modern phenotypes, with adaptations to cultivation in diverse conditions, including cold climates and short summers. The present work examines which varieties could have been cultivated in the Antiquity and in which regions had cotton cultivation spread then. Some extant varieties are hypothesized as close to the cultivars of Antiquity. The geographic distribution of each species probably reflects the initial domestication region and the subsequent adaptations, particularly regarding climate. Recent progress on ancient DNA analysis should permit easier specific assignments of archaeological remains of cotton seeds, fibres, threads or fabrics. L’usage textile des fibres de coton des espèces de l’Ancien Monde, Gossypium arboreum et G. herbaceum, a commencé il y a huit millénaires, et possiblement plus tôt. Au cours du troisième millénaire avant le présent, la culture, l’utilisation textile et le commerce du coton se sont fortement développés dans de nombreux sites du sous-continent Indien et du Moyen-Orient, mais sans détermination, souvent, de l’espèce impliquée dans chaque cas. G. arboreum et G. herbaceum sont très difficilement distinguables morphologiquement dans les vestiges archéologiques. Plusieurs variétés traditionnelles ont été décrites pour chacune des deux espèces ; une évolution apparaît depuis des formes pérennes relativement primitives jusqu’à des types annuels de morphologie moderne, avec l’adaptation à la culture en conditions très diverses incluant climats froids et étés courts. Le présent travail examine lesquelles de ces variétés ont pu être cultivées dans l’Antiquité et dans quelles régions de l’Ancien Monde avait alors diffusé la culture du coton. Certaines des variétés actuelles peuvent être supposées représentatives des cultivars de l’Antiquité. La répartition géographique des deux espèces résulte à la fois du lieu initial de domestication et de leurs adaptations agronomiques, particulièrement concernant le climat. Les progrès récents en analyse des ADN anciens devraient permettre de déterminer plus facilement l’espèce des graines, fibres et textiles archéologiques de coton.
Published: 2019

38. Stratégies paysannes de participation à la domestication du poivre sauvage de Madagascar, leTsiperifery

Author: Romaine Ramananarivo, Jules Razafiarijaona, Frédérique Jankowski, Tahiry Rabefarihy, Jérôme Queste, Sedera Norotiana Rasambo, and Sarah Audouin
Subjects: 0106 biological sciences, F08 - Systèmes et modes de culture, Management, Monitoring, Policy and Law, 01 natural sciences, 030308 mycology & parasitology, recherche participative, 03 medical and health sciences, F01 - Culture des plantes, E50 - Sociologie rurale, 0303 health sciences, Technique de culture, Comportement collectif, Domestication des plantes, Sociologie rurale, approches participatives, Animal Science and Zoology, Piper, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: À Madagascar, leTsiperifery, une espèce de poivrier sauvage endémique de l’île, est actuellement soumis à une surexploitation. Un programme participatif de domestication de cette plante a été lancé pour assurer la durabilité de son exploitation. Des techniques de culture sont co-construites par des chercheurs et des paysans sur trois sites pilotes. Cette étude s’intéresse aux facteurs influençant la propension des paysans à co-construire et expérimenter ces techniques. Les données collectéesvia90 entretiens semi-dirigés ont été traitées en suivant les principes de l’approche « grounded theory ». Les principaux déterminants influençant le comportement des paysans sont (i) la logique économique, (ii) le contexte informationnel, (iii) l’accès au marché, (iv) les capacités productives de l’exploitation et (v) l’esprit de conservation de la nature. À partir de ces déterminants, nous avons pu définir cinq types de stratégies paysannes : les « homo-economicus » ; les « conservationnistes » ; les « opportunistes », les « exclus » et les « suiveurs ». Cette meilleure compréhension des stratégies paysannes permet d’améliorer la conception et la conduite des programmes de recherche participative.
Published: 2021

39. Coconut domestication. Chapter 2. Where we are today

Author: Coppens D'Eeckenbrugge, Geo, Gunn, Bee, Baudoin, L., Coppens D'Eeckenbrugge, Geo, Gunn, Bee, and Baudoin, L.
Published: 2018

40. Genomics of the origin and evolution of Citrus

Author: Wu, Guohong Albert, Terol, Javier F., Ibáñez, Victoria, López-García, Antonio, Pérez-Román, Estela, Borredá, Carles, Domingo, Concha, Tadeo, Francisco, Carbonell-Caballero, Jose, Alonso, Roberto, Curk, Franck, Du, Dongliang, Ollitrault, Patrick, Roose, Mikeal L., Dopazo, Joaquin, Gmitter, Frederick G., Rokhsar, Daniel S., Talon, Manuel, Wu, Guohong Albert, Terol, Javier F., Ibáñez, Victoria, López-García, Antonio, Pérez-Román, Estela, Borredá, Carles, Domingo, Concha, Tadeo, Francisco, Carbonell-Caballero, Jose, Alonso, Roberto, Curk, Franck, Du, Dongliang, Ollitrault, Patrick, Roose, Mikeal L., Dopazo, Joaquin, Gmitter, Frederick G., Rokhsar, Daniel S., and Talon, Manuel
Abstract: The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus.
Published: 2018

41. CRISPR/Cas9-mediated efficient targeted mutagenesis has the potential to accelerate the domestication of Coffea canephora

Author: Jean-Christophe Breitler, Eveline Dechamp, Claudine Campa, Hervé Etienne, Romain Guyot, Leonardo Augusto Zebral Rodrigues, Pierre Marraccini, UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Federal University of Lavras, and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: 0106 biological sciences, 0301 basic medicine, Phytoene desaturase, Targeted mutagenesis, Agrobacterium, Mutagénèse, F62 - Physiologie végétale - Croissance et développement, Computational biology, Horticulture, Biology, Coffea canephora, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, Genome editing, Embryogénèse somatique, CRISPR, Gene, 2. Zero hunger, Physiologie du développement, Génome, Cas9, Domestication des plantes, Biologie moléculaire, CRISPR/CA9, CRISPRCas9, Somatic embryogenesis, biology.organism_classification, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 030104 developmental biology, Phytoene Desaturase, 010606 plant biology & botany
Abstract: International audience; Genome editing, which is an unprecedented technological breakthrough, has provided a valuable means of creating targeted mutations in plant genomes. In this study, we developed a genomic web tool to identify all gRNA target sequences in the coffee genome, along with potential off-targets. In all, 8,145,748 CRISPR guides were identified in the draft genome of Coffea canephora corresponding to 5,338,568 different sequences and, of these, 4,655,458 were single, and 514,591 were covering exons. The proof of concept was established by targeting the phytoene desaturase gene (CcPDS) using the Agrobacterium tumefaciens transformation technique and somatic embryogenesis as the plant regeneration method. An analysis of the RNA-guided genome-editing events showed that 22.8% of the regenerated plants were heterozygous mutants and 7.6% were homozygous mutants. Mutation efficiency at the target site was estimated to be 30.4%. We demonstrated that genome editing by the CRISPR/Cas9 method is an efficient and reliable way of knocking out genes of agronomic interest in the coffee tree, opening up the way for coffee molecular breeding. Our results also showed that the use of somatic embryogenesis, as the method for regenerating genome-edited plants, could restrict the choice of targeted genes to those that are not essential to the embryo development and germination steps
Published: 2018

42. Capsicum annuum (piment/poivron) : une plante venue du Mexique : quand une espèce se décline en dizaines de variétés

Author: Katz, Esther and Aguilar-Melendez, A.
Subjects: ETHNOBOTANIQUE, DOMESTICATION DES PLANTES, COUTUME ALIMENTAIRE, PLANTE UTILE
Published: 2018

43. The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon

Author: Michael Blake, Julio Hurtado, Isabelle Lesur, Rey Gaston Loor Solorzano, Olivier Fouet, Hélène Vignes, Xavier Argout, Claire Lanaud, Sonia Zarrillo, Nilesh W. Gaikwad, Terry G. Powis, Alexandra Yepez, Patrick Severts, Franck Salin, Louis E. Grivetti, Francisco Valdez, Erwan Guichoux, Christopher Viot, Olivier Bouchez, University of Calgary, University of British Columbia (UBC), University of California [Davis] (UC Davis), University of California, Gaikwad Steroidomics Laboratory, Partenaires INRAE, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Kennesaw State University (KSU), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Instituto Nacional de Investigaciones Agropecuarias (INIAP), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), New South Associates Inc., Ministerio de Cultura y Patrimonio, Department of Nutrition, Patrimoines locaux, Environnement et Globalisation (PALOC), Sorbonne Université (SU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD), Social Sciences and Humanities Research Council of Canada Doctoral Fellowship, Honorary Isaak Walton Killam Memorial Scholarship, Faculty of Graduate Studies Travel Award, Hampton Research Grant from the University of British Columbia : F11-00878, Agropolis Fondation : 1202-029, ANR-10-LABX-0001-01, Commissariat aux Grands Investissements : ANR-10-INBS-0009, Martha Biggar Anders Memorial Award, IRD, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), and Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)
Subjects: 0301 basic medicine, Mesoamerica, F40 - Écologie végétale, Theobroma, Genomic research, [SDV]Life Sciences [q-bio], Crop, Domestication, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Theobroma cacao, DNA, Ancient, Ecology, Evolution, Behavior and Systematics, Holocene, Cacao, Histoire naturelle, [SDV.GEN]Life Sciences [q-bio]/Genetics, Ecology, biology, Amazon rainforest, Domestication des plantes, F70 - Taxonomie végétale et phytogéographie, 15. Life on land, biology.organism_classification, Archaeology, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Geography, Ecuador, P01 - Conservation de la nature et ressources foncières
Abstract: International audience; Cacao (Theobroma cacao L.) is an important economic crop, yet studies of its domestication history and early uses are limited. Traditionally, cacao is thought to have been first domesticated in Mesoamerica. However, genomic research shows that T. cacao’s greatest diversity is in the upper Amazon region of northwest South America, pointing to this region as its centre of origin. Here, we report cacao use identified by three independent lines of archaeological evidence—cacao starch grains, absorbed theobromine residues and ancient DNA—dating from approximately 5,300 years ago recovered from the Santa Ana-La Florida (SALF) site in southeast Ecuador. To our knowledge, these findings constitute the earliest evidence of T. cacao use in the Americas and the first unequivocal archaeological example of its pre-Columbian use in South America. They also reveal the upper Amazon region as the oldest centre of cacao domestication yet identified.
Published: 2018

44. Origin and evolution

Author: Coppens D'Eeckenbrugge, Geo, Duval, Marie-France, and Leal, Freddy
Subjects: Histoire naturelle, Ressource génétique, F40 - Écologie végétale, Domestication des plantes, Évolution, F70 - Taxonomie végétale et phytogéographie, F30 - Génétique et amélioration des plantes, Variation génétique, F01 - Culture des plantes, Ananas (genre)
Published: 2018

45. The pineapple success story: from domestication to pantropical diffusion

Author: Marie-France Duval, Géo Coppens D'Eeckenbrugge, and Freddy Leal
Subjects: food.ingredient, E70 - Commerce, commercialisation et distribution, Introgression, Pantropical, F30 - Génétique et amélioration des plantes, food, F01 - Culture des plantes, Botany, Cultivar, Domestication, Ananas, B50 - Histoire, biology, Amazon rainforest, Microstachys, Domestication des plantes, biology.organism_classification, Ananas comosus, Biodiversité, Ananas (fruits), Tropical Asia
Abstract: Although the pineapple was common throughout tropical America well before 1492, its wild and cultivated forms were poorly known until the late twentieth century. The genus Ananas includes A. comosus, a self-incompatible diploid, vegetatively propagated from axillary suckers and the fruit crown, and A. macrodontes, a self-fertile, crownless tetraploid reproducing through seeds and stolons. The former presents five botanical varieties: the wild var. microstachys and var. parguazensis; the edible pineapple, var. comosus; the smooth-leaved var. erectifolius; and the spiny var. bracteatus, two fiber cultigens now exploited as ornamentals. Diversity studies indicate that var. comosus and var. erectifolius are related to populations of var. microstachys from the northern Amazon, whereas var. bracteatus evolved in the southeast, through the introgression of A. macrodontes genes. While the Guianas constitute the likely center of pineapple domestication from wild and intermediate forms, the wide western Amazon cultivar diversity suggests a secondary center where sexual recombination mostly involved domesticated forms. According to archaeological and linguistic data, the edible pineapple has been cultivated for more than 3000 years in Amazonia and coastal Peru, and 2500 years in Mesoamerica, implying a very early domestication and neotropical diffusion. In the sixteenth century, Portuguese traders diffused Cultivars Singapore Canning, Selangor Green, and Perola from coastal Brazil to tropical Asia and coastal Africa. A wider diversity was cultivated in the nineteenth-century European glasshouses, of which only 'Queen' and 'Smooth Cayenne' have survived and diffused to tropical production regions. The much wider Amazonian cultivar diversity has not been exploited yet.
Published: 2018

46. Genomics of the origin and evolution of Citrus

Author: Manuel Talon, Joaquín Dopazo, Francisco R. Tadeo, Concha Domingo, Dongliang Du, Estela Pérez-Román, Victoria Ibanez, Guohong Albert Wu, José Carbonell-Caballero, Carles Borredá, Patrick Ollitrault, Daniel S. Rokhsar, Javier Terol, Antonio López-García, Roberto Alonso, Mikeal L. Roose, Frederick G. Gmitter, Franck Curk, Wu, Guohong Albert, Rokhsar, Daniel S., Talon, Manuel, United States Department of Energy, Centro de Genómica - Centre de Genòmica [IVIA], Instituto Valenciano de Investigaciones Agrarias - Institut Valencià d'Investigacions Agraries - Valencian Institute for agricultural Research (IVIA), Centro de Investigación Príncipe Felipe (CIPF), Amélioration Génétique et Adaptation des Plantes méditerranéennes et Tropicales Corse - Antenne Corse (AGAP-Corse), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), University of South Florida [Tampa] (USF), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Botany and Plant Sciences, University of California, Spanish National Bioinformatics Institute (INB), University of Florida [Gainesville] (UF), IFAS, Unite de recherche migrations et sociétés (URMIS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), University of California [Berkeley], Technology Graduate University, and Okinawa Institute of Science and Technology Graduate University (OIST)
Subjects: 0301 basic medicine, Citrus, Phylogénie, [SDV]Life Sciences [q-bio], Plant genetics, Biodiversity, Évolution, F30 - Génétique et amélioration des plantes, Génétique des populations, Asia, Southeastern, History, Ancient, Phylogeny, Multidisciplinary, Domestication des plantes, food and beverages, Genomics, F70 - Taxonomie végétale et phytogéographie, Crop Production, Provenance, Genome, Plant, Citrus hybrids, Heterozygote, Genetic Speciation, Human Migration, Introgression, Biology, Southeast asian, génomique, Evolution, Molecular, 03 medical and health sciences, Variation génétique, Phylogenetics, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Domestication, Hybrid, Génome, 15. Life on land, biology.organism_classification, 030104 developmental biology, Haplotypes, Hybridization, Genetic
Abstract: The genus Citrus, comprising some of the most widely cultivated fruit crops worldwide, includes an uncertain number of species. Here we describe ten natural citrus species, using genomic, phylogenetic and biogeographic analyses of 60 accessions representing diverse citrus germ plasms, and propose that citrus diversified during the late Miocene epoch through a rapid southeast Asian radiation that correlates with a marked weakening of the monsoons. A second radiation enabled by migration across the Wallace line gave rise to the Australian limes in the early Pliocene epoch. Further identification and analyses of hybrids and admixed genomes provides insights into the genealogy of major commercial cultivars of citrus. Among mandarins and sweet orange, we find an extensive network of relatedness that illuminates the domestication of these groups. Widespread pummelo admixture among these mandarins and its correlation with fruit size and acidity suggests a plausible role of pummelo introgression in the selection of palatable mandarins. This work provides a new evolutionary framework for the genus Citrus. The origin, evolution and domestication of Citrus and the genealogy of the most important wild and cultivated citrus varieties. Citrus fruits are one of the most cultivated crops worldwide, yet the evolutionary relationships among citrus species remain uncertain. Daniel Rokhsar, Manuel Talon and colleagues analyse the genomes of 60 accessions that represent a diverse range of citrus species, including 30 newly sequenced citrus genomes. They characterize the diversity and evolution of citrus at the species level and identify interspecific citrus hybrids and admixtures—genetic mixing between previously isolated populations—that could be the result of human activities such as migration and agriculture. The authors identify 10 progenitor species and suggest that citrus originated in southeast Asia, diversifying during the late Miocene epoch through a rapid southeast Asian radiation that correlated with a changing climate, including the weakening of the monsoons. They also find extensive relatedness among mandarins and sweet oranges, showing a complex history of admixture during the domestication of these groups.
Published: 2018

47. « Révolution agricole » au Néolithique proche-oriental : quelle réalité ?

Author: Douché, Carolyne
Subjects: Syria, transformation, History & Archaeology, HB, Syrie, permanency, permanences, beginning of agriculture, agricultural revolution, innovation, domestication des plantes, revolution, time discontinuity, Neolithic Period, evolution, change, révolution agricole, rupture, HIS000000, début agriculture, plants domestication, évolution, Sociology & Anthropology, néolithique, révolution
Abstract: À partir des années 1950, le terme de « Révolution néolithique » a été utilisé pour désigner l’ensemble des changements techniques et sociétaux qui ont eu lieu au Proche Orient ancien. Parmi ceux-ci, la mise en place de l’agriculture a fait l’objet d’un intérêt tout particulier. Néanmoins, depuis une dizaine d’année, le terme de « révolution » est relativisé par le fait que les changements n’ont pas été soudains, mais se sont au contraire déroulés sur un temps relativement long.Les premiers indices de développement de l’agriculture apparaissent au Proche-Orient, au Néolithique acéramique (Xe-VIIe millénaire av. n. è.). A cette période, les sites attestant de la mise en place de pratiques agricoles se multiplient. Parmi les témoins de ces changements, les plantes cultivées - et plus particulièrement les céréales - offrent un aperçu du processus qui se met en place.Ainsi, l’étude archéobotanique de deux sites syriens, Dja’de el-mughara et Tell Aswad, apportent de nouvelles données concernant le « quand ? » et le « comment ? » l’agriculture s’est développée dans la région levantine, et quelles en ont été les conséquences. Ces deux villages agricoles se caractérisent par une occupation continue, au cours de laquelle de nombreux changements techniques et sociétaux sont apparus, parallèlement à la mise en place et à l’évolution de nouvelles stratégies de subsistance. Nous verrons donc quelles ont été les premières plantes utilisées par les populations néolithiques et si les changements de cortèges floristiques reflètent une « r-évolution » des pratiques. Since the 1950’s, the term « Neolithic Revolution » refers to the technical and social changes that happened in the Ancient Near East. Among those changes, there was a particular emphasis placed on the beginning of agriculture. Nonetheless, since a decade, the concept of « revolution » is questionned as changes happened on the long run.Agriculture started during the Pre-Pottery Neolithic period (PPN) (Xe-VIIe millenium cal. B.C.). At that time, we observe an increase of the amount of villages showing agricultural signs, and cultivated plants - mainly cereals - offer a good opportunity to analyse the process.Thus, the archaeobotanical study of two syrian sites, Dja’de el-mughara and Tell Aswad, brings new data about the « when » and the « how » agriculture emerged in the Levantine area, and what the consequences were. Those two early villages present a long and continuous occupation, with technical and social changes as the set up and the complexification of a new subsistance economy. In this paper, we will see what the first plants exploited by the Neolithic communities were and if we can observe a « r-evolution » through archaeobotanical data.
Published: 2017

48. Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes

Author: Anne-Céline Thuillet, Karine Alix, Alexandre Dansi, Nora Scarcelli, Olivier François, Bénédicte Rhoné, Roland Akakpo, Yves Vigouroux, Gustave Djedatin, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Abomey Calavi (UAC), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), BID, Agence Nationale de la Recherche [ANR-13-BSV7-0017], ANR-13-BSV7-0017,AfriCrop,Etude de l'histoire évolutive des plantes domestiquées africaines(2013), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Université Grenoble Alpes (UGA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-IMAG-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Université d’Abomey-Calavi = University of Abomey Calavi (UAC), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) ( GQE-Le Moulon ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), Diversité, adaptation, développement des plantes ( DIADE ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ), Université d'Abomey Calavi, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales ( UMR AGAP ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Grenoble-Alpes, Akapo, Roland, Scarcelli, Nora, and Vigouroux, Yves
Subjects: 0301 basic medicine, Starch, Population genomics selection, Métabolisme des glucides, [SDV]Life Sciences [q-bio], Biosynthèse, Dioscorea rotundata, Plant Roots, F50 - Anatomie et morphologie des plantes, F30 - Génétique et amélioration des plantes, Système racinaire, Domestication, chemistry.chemical_compound, Génétique des populations, Photosynthesis, 2. Zero hunger, biology, Dioscorea, Domestication des plantes, Genomics of domestication, food and beverages, F70 - Taxonomie végétale et phytogéographie, Starch biosynthesis, Sucrose synthase, Amidon, Population genomics, selection, Research Article, Développement biologique, Biotechnology, Dioscorea spp, lcsh:QH426-470, F60 - Physiologie et biochimie végétale, lcsh:Biotechnology, selection, Genes, Plant, Evolution, Molecular, 03 medical and health sciences, lcsh:TP248.13-248.65, Botany, Plant development, Genetics, Selection, Genetic, Adaptation, Phototropism, [ SDV ] Life Sciences [q-bio], fungi, Genetic Variation, Population genomics, Root development, 15. Life on land, biology.organism_classification, lcsh:Genetics, 030104 developmental biology, chemistry, biology.protein
Abstract: Background After cereals, root and tuber crops are the main source of starch in the human diet. Starch biosynthesis was certainly a significant target for selection during the domestication of these crops. But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat. Results We studied here, the molecular basis of domestication in African yam, Dioscorea rotundata. The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. Two percent of all the genes studied showed evidences of selection. Two genes associated with the earliest stages of starch biosynthesis and storage, the sucrose synthase 4 and the sucrose-phosphate synthase 1 showed evidence of selection. An adventitious root development gene, a SCARECROW-LIKE gene was also selected during yam domestication. Significant selection for genes associated with photosynthesis and phototropism were associated with wild to cultivated change of habitat. If the wild species grow as vines in the shade of their tree tutors, cultivated yam grows in full light in open fields. Conclusions Major rewiring of aerial development and adaptation for efficient photosynthesis in full light characterized yam domestication. Electronic supplementary material The online version of this article (10.1186/s12864-017-4143-2) contains supplementary material, which is available to authorized users.
Published: 2017

49. Combining conservative and variable markers to infer the evolutionary history of Prunus subgen. Amygdalus s.l. under domestication

Author: Nadir Alvarez, Hélène Joly, Malou Delplancke, Mariana Yazbek, Anahí Espíndola, and Nils Arrigo
Subjects: 0301 basic medicine, Phylogénie, Locus des caractères quantitatifs, Séquence nucléotidique, Prunus americana, Biogéographie, Évolution, Plasmide, Plant Science, Biology, F30 - Génétique et amélioration des plantes, Coalescent theory, 03 medical and health sciences, Prunus, Phylogenetics, Botany, Genetics, Marqueur génétique, Domestication, Ecology, Evolution, Behavior and Systematics, Prunus persica, Phylogenetic tree, Domestication des plantes, food and beverages, F70 - Taxonomie végétale et phytogéographie, Taxonomie, Prunus dulcis, 030104 developmental biology, Evolutionary biology, Gene pool, Subgenus, Agronomy and Crop Science
Abstract: The genus Prunus L. is large and economically important. However, phylogenetic relationships within Prunus at low taxonomic level, particularly in the subgenus Amygdalus L. s.l., remain poorly investigated. This paper attempts to document the evolutionary history of Amygdalus s.l. and establishes a temporal framework, by assembling molecular data from conservative and variable molecular markers. The nuclear s6pdh gene in combination with the plastid trnSG spacer are analyzed with bayesian and maximum likelihood methods. Since previous phylogenetic analysis with these markers lacked resolution, we additionally analyzed 13 nuclear SSR loci with the δµ2 distance, followed by an unweighted pair group method using arithmetic averages algorithm. Our phylogenetic analysis with both sequence and SSR loci confirms the split between sections Amygdalus and Persica, comprising almonds and peaches, respectively. This result is in agreement with biogeographic data showing that each of the two sections is naturally distributed on each side of the Central Asian Massif chain. Using coalescent based estimations, divergence times between the two sections strongly varied when considering sequence data only or combined with SSR. The sequence-only based estimate (5 million years ago) was congruent with the Central Asian Massif orogeny and subsequent climate change. Given the low level of differentiation within the two sections using both marker types, the utility of combining microsatellites and data sequences to address phylogenetic relationships at low taxonomic level within Amygdalus is discussed. The recent evolutionary histories of almond and peach are discussed in view of the domestication processes that arose in these two phenotypically-diverging gene pools: almonds and peaches were domesticated from the Amygdalus s.s. and Persica sections, respectively. Such economically important crops may serve as good model to study divergent domestication process in close genetic pool.
Published: 2015

50. Domestication reduces alternative splicing expression variations in sorghum

Author: Ranwez, Vincent, Serra, Audrey, Pot, David, Chantret, Nathalie, Ranwez, Vincent, Serra, Audrey, Pot, David, and Chantret, Nathalie
Abstract: Domestication is known to strongly reduce genomic diversity through population bottlenecks. The resulting loss of polymorphism has been thoroughly documented in numerous cultivated species. Here we investigate the impact of domestication on the diversity of alternative transcript expressions using RNAseq data obtained on cultivated and wild sorghum accessions (ten accessions for each pool). In that aim, we focus on genes expressing two isoforms in sorghum and estimate the ratio between expression levels of those isoforms in each accession. Noticeably, for a given gene, one isoform can either be overexpressed or underexpressed in some wild accessions, whereas in the cultivated accessions, the balance between the two isoforms of the same gene appears to be much more homogenous. Indeed, we observe in sorghum significantly more variation in isoform expression balance among wild accessions than among domesticated accessions. The possibility exists that the loss of nucleotide diversity due to domestication could affect regulatory elements, controlling transcription or degradation of these isoforms. Impact on the isoform expression balance is discussed. As far as we know, this is the first time that the impact of domestication on transcript isoform balance has been studied at the genomic scale. This could pave the way towards the identification of key domestication genes with finely tuned isoform expressions in domesticated accessions while being highly variable in their wild relatives.
Published: 2017

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