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.

Fig. 1. Phenotype of fonio (Digitaria exilis).

a Field of cultivated fonio in Guinea. b Grains of maize, wheat, rice, and fonio (from left to right). c Plants of the fonio accession CM05836.

Fig. 2. Fonio genome features.

a Representative example of oligo painting FISH on mitotic metaphase chromosomes. Shown are probes designed from pseudomolecules 9A (green) and 9B (red) of the CM05836 assembly (scale bar = 5 µm). Oligo painting FISH experiment was repeated independently three times. b Principal component analysis (PCA) of the transposable element cluster RLG_Loris (upper panel) that allowed discrimination of the two sub-genomes. Blue dots represent elements found on the A sub-genome; pink triangles represent elements from the B sub-genome; black squares represent elements present on chromosome unanchored. PCA of the transposable element cluster RLG_Elodie (lower panel) that was specific to the B sub-genome. c Synteny and distribution of genome features. (I) Number and length of the pseudomolecules. The gray and black colors represent the two sub-genomes. (II, III) Density of genes and repeats along each pseudomolecule, respectively. Lines in the inner circle represent the homoeologous relationships. d Maximum likehood tree of 11 Poaceae species based on 30 orthologous gene groups. Topologies are supported by 1000 bootstrap replicates. Colors indicate the different clades.

Fig. 3. Genetic diversity and structure of D. exilis and D. longiflora diversity panel.

a Principal component analysis (PCA) of 157 D. exilis and 14 D. longiflora accessions using whole-genome single nucleotide polymorphisms (SNPs). D. exilis samples (circles), D. longiflora (triangles). b PCA of D. exilis accessions alone. Colors indicate the country of origin. c Population structure (from K = 3 to K = 6) of D. exilis accessions estimated with sNMF. Each bar represents an accession and the bars are filled by colors representing the likelihood of membership to each ancestry. Accessions are ordered from west to east; Guinea (Gu), Mali (M), Burkina Faso (B.F), Ghana (Gh), Togo (T), Benin (B), and Niger (N). d Geographic distribution of ancestry proportions of D. exilis accessions obtained from the structure analysis at K = 6. The colors represent the maximal local contribution of an ancestry. Black dots represent the coordinates of D. exilis accessions. e Effective population size history of D. exilis groups based on K = 6 and D. longiflora (in black).

Fig. 4. Detection of selection in fonio.

Manhattan plots showing detection of selection along the genome based on nucleotide diversity (π) ratio, F_ST and SweeD (from top to bottom). The location of orthologous genes of major seed shattering and plant architecture genes are indicated in the Manhattan plots. The black dashed lines indicate the 1% threshold. Some extreme outliers in the π ratio plot are not shown.

Fig. 5. Selective sweep at the GS5 locus in fonio.

a Smoothed representation of nucleotide diversity (π) in D. exilis in a 100 kb window surrounding the ortholog of the rice GS5 gene. The green curve shows π around DeGS5-3A on chromosome 3A and the blue curve shows π around DeGS5-3B on chromosome 3B. The dashed vertical red lines represent the location of the GS5 genes. The nucleotide diversity was calculated in overlapping 100 bp windows every 25 bp. b Schematic representation of the annotated genes in the GS5 regions and the orthologous gene relationships between chromosomes 3A (green) and 3B (blue). UF protein of unknown function, E3 E3 ubiquitin ligase, SCP (GS5) serine carboxypeptidase (Dexi3A01G0012320), GAOX gibberellin 2-beta-dioxygenase, ECH golgi apparatus membrane protein. DeGS5-3A and DeGS5-3B are indicated in red. The numbers in blue above and below the GS5 orthologs show their respective expression in transcripts per million (TPM) in grain tissue. c Two grains of D. exilis (top) and D. longiflora (bottom).

Fig. 6. Selective sweep at the Sh1 locus in fonio.

a Schematic representation of genes in the orthologous regions of the sorghum Sh1 gene. The top most panel shows the region on fonio chromosome 9A with the 60 kb deletion as it is found in 37% of all D. exilis accessions. The lower panel shows the genes in accessions without the deletion. The Sh1 ortholog DeSh1-9A is shown in red. b The Sh1 ortholog DeSh1-9B on chromosome 9B is present in all D. exilis accessions. The dashed lines represent orthologous relationships between the two sub-genomes. UF protein of unknown function, CDK cyclin-dependent kinase, Sh1 ortholog of sorghum Shattering 1 (Sh1), ST sulfate transporter; NT5C3B 7-methylguanosine phosphate-specific 5’-nucleotidase; MBD methyl-CpG-binding domain. c The violin plots show the probability distribution of the seed shattering percentage in fonio accessions carrying the DeSh1-9A deletion (∆DeSh1-9A) in pink compared to accessions with an intact DeSh1-9A in blue. The shape of the distribution indicates that the seed shattering percentages for both groups are concentrated around the median. The center of each plot depicts a boxplot, the box represents the interquartile range (IQR), the middle horizontal line represents the median, the vertical lines going down and up from the box are defined as first quartile (−1.5 IQR) and third quartile (+1.5 IQR), respectively. Circles in the plot represent the seed shattering percentage calculated from individual fonio panicles, one circle per panicle, jitter option was added to show all individual observations that overlapped. Mean seed shattering was 45% in ∆DeSh1-9A (±0.18 s.d.) and 52% in DeSh1-9A (±0.22 s.d.). (n = Three individual panicles of 43 ∆DeSh1-9A accessions and 39 DeSh-9A accessions, respectively; two-way ANOVA p = 0.008; df = 1).