Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate
Ahmed, Hanin Ibrahim
Wieringa, Jan J.
Kane, Ndjido A.
Krattinger, Simon G.
KAUST DepartmentBiological and Environmental Sciences and Engineering (BESE) Division
Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Desert Agriculture Initiative
Online Publication Date2020-09-08
Print Publication Date2020-12
Permanent link to this recordhttp://hdl.handle.net/10754/662572
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AbstractAbstract 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.
CitationAbrouk, M., Ahmed, H. I., Cubry, P., Šimoníková, D., Cauet, S., Pailles, Y., … Krattinger, S. G. (2020). Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nature Communications, 11(1). doi:10.1038/s41467-020-18329-4
SponsorsWe are grateful to Vinicius M. Lube, Samantha Bazan, Ablaye Ngom, Marie Piquet, Hélène Adam, and Carole Gauron for their technical assistance in Herbarium sampling and photography. Cirad herbarium samples of Digitaria longiflora were provided by Samantha Bazan (ALF [http://publish.plantnet-project.org/]). We thank Soukeye Conde for valuable insight, funded by the project Cultivar, reference ANR-16-IDEX-0006, through the Investissements d’avenir program (Labex Agro: ANR-10-LABX-0001-01). This work was supported by the CIRAD-UMR AGAP and IRD UMR DIADE HPC Data Center of the South Green Bioinformatics platform [http://www.southgreen.fr/] and the Center for Desert Agriculture of the King Abdullah University of Science and Technology (KAUST). D.S., J.C., E.H. and J.D. were in part supported by the European Regional Development Fund OPVVV project ‘Plants as a tool for sustainable development’ number CZ.02.1.01/0.0/0.0/16_019/0000827.
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Title: Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Publication Date: 2020-04-18. bioproject: PRJEB36539 Handle: 10754/666537
Abrouk, M., Ahmed, H. I., Cubry, P., Šimoníková, D., Cauet, S., Pailles, Y., Bettgenhaeuser, J., Gapa, L., Scarcelli, N., Couderc, M., Zekraoui, L., Kathiresan, N., Čížková, J., Hřibová, E., Doležel, J., Arribat, S., Bergès, H., Wieringa, J., Gueye, M., … Krattinger, S. (2020). Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate (Version 11) [Data set]. Dryad. https://doi.org/10.5061/DRYAD.2V6WWPZJ0. DOI: 10.5061/dryad.2v6wwpzj0 Handle: 10754/667866
Title: Africrop/fonio_smcpp: fonio_smcpp. Publication Date: 2020-03-30. github: Africrop/fonio_smcpp Handle: 10754/667875
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