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

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.

Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae)

“…The complete loss of one parental genome from a wide cross is well-documented for maize X oat crosses ( Riera-Lizarazu et al, 1996 ), and is the basis of wheat haploid generation in maize X wheat crosses ( Laurie and O’Donoughue, 1994 ) or wheat X wild barley ( Inagaki and Tahir, 1990 ). Moreover, the transposition of TE families distinctive to one genome parent in an allopolyploid origin into the other parental genome has been documented in teff and several other genomes and, in fact, has been used to date the origin of the allopolyploidy event ( Abrouk et al, 2020 ; VanBuren et al, 2020 ).…”

DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web

“…In particular, DeepGOWeb can be used to provide whole genome functional annotations of newly sequenced organisms for which no additional information is available. DeepGOPlus has previously been used to annotate newly sequenced crop plants, in particular fonio millet ( Digitaria exilis ) ( 32 ), and early SARS-CoV-2 sequences ( 33 ); however, DeepGOPlus places no restrictions on the protein sequences and can be used to prediction functions for proteins from any organism. DeepGOPlus and DeepGOWeb are available as Free Software ( 34 ) at https://deepgo.cbrc.kaust.edu.sa/ .…”

Plant genomics in Africa: present and prospects

“…The second 'African' Poaceae family member whose genome has been sequenced is fonio millet (Digitaria exilis), an African orphan cereal crop that has great potential for dryland agriculture. Abrouk et al (2020) established high-quality genomic resources to improve fonio by molecular breeding. This study has provided new insights into the genetic diversity, population structure, and domestication of fonio millet (Abrouk et al, 2020).…”

“…Abrouk et al (2020) established high-quality genomic resources to improve fonio by molecular breeding. This study has provided new insights into the genetic diversity, population structure, and domestication of fonio millet (Abrouk et al, 2020).…”