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Independent domestication and cultivation histories of two West African indigenous fonio millet crops
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Edité par CCSD ; Nature Publishing Group -
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].. International audience. 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.
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