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

Author

Michael Abrouk, Hanin Ibrahim Ahmed, Philippe Cubry, Denisa Šimoníková, Stéphane Cauet, Yveline Pailles, Jan Bettgenhaeuser, Liubov Gapa, Nora Scarcelli, Marie Couderc, Leila Zekraoui, Nagarajan Kathiresan, Jana Čížková, Eva Hřibová, Jaroslav Doležel, Sandrine Arribat, Hélène Bergès, Jan J. Wieringa, Mathieu Gueye, Ndjido A. Kane, Christian Leclerc, Sandrine Causse, Sylvie Vancoppenolle, Claire Billot, Thomas Wicker, Yves Vigouroux, Adeline Barnaud, and Simon G. Krattinger

Subjects
Science
Abstract

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
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2. 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

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