Independent domestication and cultivation histories of two West African indigenous fonio millet crops
2025
Kaczmarek, Thomas | Cubry, Philippe | Champion, Louis | Causse, Sandrine | Couderc, Marie | Orjuela, Julie | Uyoh, Edak | Oselebe, Happiness, O | Dachi, Stephen, N. | Adje, Charlotte, O. A. | Sekloka, Emmanuel | Achigan-Dako, Enoch, G. | Ibrahim Bio Yerima, Abdou, R. | Saidou, Sani Idi | Bakasso, Yacoubou | Diop, Baye, M. | Guèye, Mame, C. | Agyare, Richard, Y. | Adjebeng-Danquah, Joseph | Gueye, Mathieu | Wieringa, Jan, J. | Vigouroux, Yves | Billot, Claire | Barnaud, Adeline | Leclerc, Christian | 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) | Diversité, adaptation, développement des plantes (UMR DIADE) ; 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 [Occitanie])-Université de Montpellier (UM) | University of Calabar (UNICAL) | Ebonyi State University (EBSU) | University of Jos [Nigeria] | Université d’Abomey-Calavi = University of Abomey Calavi (UAC) | Université de Parakou = University of Parakou (UP) | Institut National de Recherches Agronomiques du Niger [Niamey] (INRAN Niamey) | Université de Diffa | Abdou Moumouni University of Niamey = Université Abdou Moumouni de Niamey (UAM) | Institut sénégalais de recherches agricoles [Dakar] (ISRA) | Centre d'Etude Regional Pour l'Amelioration de l'Adaptation A la Secheresse (CERAAS) | Council for Scientific and Industrial Research [Ghana] (CSIR) | Savannah Agricultural Research Institute (CSIR SARI) | Université Cheikh Anta Diop de Dakar [Sénégal] (UCAD) | Naturalis Biodiversity Center [Leiden] | Collection and genetic analysis of fonio landrace diversity over the last decade have been supported through several research projects funded by WAAPP/PPAAO 2A (CERA58ID06 SE), Agropolis Fondation (Agropolis Resource Center for Crop Adaptation and Diversity [ARCAD] project and the Cultivar project—ID 1504-007) through the Investissements d’Avenir programme (Labex Agro: ANR-10-LABX-0001) within the framework of I-SITE MUSE (ANR-16-IDEX-0006), by the French national ANR project (AfriCrop project, ANR-13-BSV7-0017) and by the European Union Horizon 2020 research and innovation programme (EWA-BELT, 862848, ‘Linking East and West African farming systems experience into a BELT of sustainable intensification’). We are grateful to the ALF CIRAD herbarium and the herbarium of the Muséum National d’Histoire Naturelle (MNHN) in Paris for providing the D. ternata specimens. The bioinformatics analyses were performed on the Core Cluster of the Institut Français de Bioinformatique (IFB) (ANR-11-INBS-0013). | ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010) | ANR-16-IDEX-0006,MUSE,MUSE(2016) | ANR-13-BSV7-0017,AfriCrop,Etude de l'histoire évolutive des plantes domestiquées africaines(2013) | ANR-11-INBS-0013,IFB (ex Renabi-IFB),Institut français de bioinformatique(2011) | European Project: 862848 ,H2020-EU.3.2. - SOCIETAL CHALLENGES - Food security, sustainable agriculture and forestry, marine, maritime and inland water research, and the bioeconomy ,EWA - BELT(2020)
Data availability: White and black fonio accessions are conserved in national collections, and duplicates covered by the Material Transfer Agreement (MTA) are stored in the ARCAD gene bank (Montpellier, France). The raw sequences retrieved from Abrouk et al. are available on EBI-ENA under accession PRJEB36539. The annotation of the CM05836 genome is available at the DRYAD database [https://doi.org/10.5061/dryad.2v6wwpzj0]. The new raw sequencing data re-sequenced in this study are available at EBI-ENA under accession PRJEB80862. Passport data of the accessions and VCF files used to perform the analyses are openly available in DataSuds repository [https://doi.org/10.18167/DVN1/OYTQO6]. Data reuse is granted under CC-BY licence. Source data are provided with this paper.Code availability: Scripts for the bioinformatics pipeline and for the different analyses carried out throughout the paper are available in the Zenodo repository [https://zenodo.org/records/15267221]. Previously reported pipeline and codes to run the k-mer analyses are available on the IRD Forge [https://forge.ird.fr/diade/iKISS].
اظهر المزيد [+] اقل [-]International audience
اظهر المزيد [+] اقل [-]إنجليزي. Crop evolutionary history and domestication processes are key issues for better conservation and effective use of crop genetic diversity. Black and white fonio ( Digitaria iburua and D. exilis , respectively) are two small indigenous grain cereals grown in West Africa. The relationship between these two cultivated crops and wild Digitaria species is still unclear. Here, we analyse whole genome sequences of 265 accessions comprising these two cultivated species and their close wild relatives. We show that white and black fonio were the result of two independent domestications without gene flow. We infer a cultivation expansion that began at the outset of the CE era, coinciding with the earliest discovered archaeological fonio remains in Nigeria. Fonio population sizes declined a few centuries ago, probably due to a combination of several factors, including major social and agricultural changes, intensification of the slave trade and the introduction of new, less labour-intensive crops. The key knowledge and genomic resources outlined here will help to promote and conserve these neglected climate-resilient crops and thereby provide an opportunity to tailor agriculture to the changing world.
اظهر المزيد [+] اقل [-]المعلومات البيبليوغرافية
تم تزويد هذا السجل من قبل Institut national de la recherche agronomique