Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis)

Abstract

Background Digitaria exilis, white fonio, is a minor but vital crop of West Africa that is valued for its resilience in hot, dry, and low-fertility environments and for the exceptional quality of its grain for human nutrition. Its success is hindered, however, by a low degree of plant breeding and improvement. Findings We sequenced the fonio genome with long-read SMRT-cell technology, yielding a ∼761 Mb assembly in 3,329 contigs (N50, 1.73 Mb; L50, 126). The assembly approaches a high level of completion, with a BUSCO score of >99%. The fonio genome was found to be a tetraploid, with most of the genome retained as homoeologous duplications that differ overall by ∼4.3%, neglecting indels. The 2 genomes within fonio were found to have begun their independent divergence ∼3.1 million years ago. The repeat content (>49%) is fairly standard for a grass genome of this size, but the ratio of Gypsy to Copia long terminal repeat retrotransposons (∼6.7) was found to be exceptionally high. Several genes related to future improvement of the crop were identified including shattering, plant height, and grain size. Analysis of fonio population genetics, primarily in Mali, indicated that the crop has extensive genetic diversity that is largely partitioned across a north-south gradient coinciding with the Sahel and Sudan grassland domains. Conclusions We provide a high-quality assembly, annotation, and diversity analysis for a vital African crop. The availability of this information should empower future research into further domestication and improvement of fonio.

Current Advancements and Limitations of Gene Editing in Orphan Crops

“…The African Orphan Crops Consortium (AOCC) has the ambitious aim to sequence 101 orphan crop genomes [ Hendre et al, 2019 ; African Orphan Crops Consortium (AOCC), 2021 ] and has published eight new orphan crop genome assemblies to date ( Hendre et al, 2019 ), with four more expected shortly [ African Orphan Crops Consortium (AOCC), 2021 ]. Additionally, many orphan crops have been sequenced by independent research efforts and are not yet available on traditional genome browsers or the AOCC, including Cajanus cajan (pigeonpea; Varshney et al, 2012 ) and Digitaria exilis (white fonio; Wang et al, 2021 ). As genome sequencing methods have improved and become less expensive, more sequenced and annotated orphan crop genomes have become publicly available.…”

A review of the orphan small grain cereals improvement with a comprehensive plan for genomics‐assisted breeding of fonio millet in West Africa

“…(2020) highlighted two candidate genes namely DeGS35‐3A and DeSh1‐9A that could be analysed further to delineate their roles in conferring, respectively, seeds size and shattering in fonio. In addition to the aforementioned findings, two candidate genes SSH1 (Suppression of Seed Shattering‐1) and GW2 (Grain Weight‐2) controlling, respectively, seed shattering in maize and seed weight in rice have been reported successfully in fonio through comparative genomic (Wang et al., 2021). The dw3 (Dwarfing‐3) gene responsible for lodging resistance in sorghum has been reported also in fonio by these authors.…”

“…Fonio genomic resources that have been developed recently provided DNA sequence information that is extremely valuable for identifying candidate genes controlling important agronomic traits and also for identifying genetic variability among the cultivars (Abrouk et al., 2020; Wang et al., 2021). Furthermore, the availability of the reference genome would help to understand the genetic basis conferring fonio's desirable nutritional properties, investigating target genes for biotic and abiotic stresses and undertaking evolution studies of the genome.…”

Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species

“…However, white fonio has a low yield and minimal research has been undertaken into breeding to improve traits of this crop [ 46 ]. A genome sequence of white fonio has recently been assembled and annotated [ 17 , 47 ] and has been used for sequence-based genotyping [ 48 ]. Combining these genetic resources with other panicoid grass resources such as Setaria italica (foxtail millet) [ 49 ], Cenchrus americanus (pearl millet) [ 50 ], and Panicum miliaceum (proso millet) [ 51 ] through pangenomic and comparative genomic strategies may support white fonio research to benefit breeders and consumers [ 52 ].…”

“…Reference genome sequences have recently been assembled for some under-utilised crop species such as yam bean ( Pachyrhizus erosus ) [ 15 ], kenaf ( Hibiscus cannabinus ) [ 16 ] and white fonio ( Digitaria exilis ) [ 17 ]. However, using a single reference leads to bias due to the significant structural variation (SV) observed within a species [ 18 , 19 , 20 ].…”