High selfing rate inferred for white fonio [Digitaria exilis (Kippist.) Stapf] reproductive system opens up opportunities for breeding programs

Barnaud, Adéline; Vigouroux, Yves; Diallo, Mamadou Alpha Tely; Saidou, Sani Idi; Piquet, Marie; Barry, Mamadou; Bakasso, Yacoubou; Zekraoui, Leïla; Rivallan, Ronan; Kane, Ndjido Ardo; Billot, Claire

doi:10.1007/s10722-017-0515-3

Cited by 15 publications

(9 citation statements)

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“…Fonio is a tetraploid species (2 n = 4× = 36) 22 with a highly inbreeding reproductive system 17 . To build a D. exilis reference assembly, we chose an accession from one of the driest regions of fonio cultivation, CM05836 from the Mopti region in Mali.…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2020

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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.

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Section: Resultsmentioning

confidence: 99%

“…White fonio (Digitaria exilis (Kippist) Stapf) ( Fig. 1) is an indigenous West African millet species with a great potential for agriculture in marginal environments 17,18 . Fonio is a small annual herbaceous C4 plant, which produces very small (∼1 mm) grains that are tightly surrounded by a husk 19 (Fig.…”

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

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“…Fonio is a tetraploid species (2n = 4x = 36) 21 with a high degree of selfing 17 . To build a D. exilis reference assembly, we chose an accession from one of the driest regions of fonio cultivation, CM05836 from the Mopti region in Mali.…”

Section: Resultsmentioning

confidence: 99%

“…White fonio ( Digitaria exilis (Kippist) Stapf) (Fig. 1) is an indigenous African millet species with a great potential for agriculture in marginal environments 17,18 . Fonio is cultivated under a large range of environmental conditions, from a tropical monsoon climate in western Guinea to a hot, arid desert climate (BWh) in the Sahel zone.…”

Section: Introductionmentioning

confidence: 99%

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

Abrouk

Ahmed

Cubry

et al. 2020

Preprint

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33Sustainable food production in the context of climate change necessitates diversification of 34 agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria 35 exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we 36 established high-quality genomic resources to facilitate fonio improvement through molecular 37 breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 38 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population 39 structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic 40 factors. Two genes associated with seed size and shattering showed signatures of selection. Most 41 known domestication genes from other cereal models however have not experienced strong 42 selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and 43 dry environments. 44 45 agriculture 1-3 . The Food and Agriculture Organization of the United Nations (FAO) stated that arid 50 and semi-arid regions are the most vulnerable environments to increasing uncertainties in regional 51 and global food production 4 . In most countries of Africa and the Middle East, agricultural 52 productivity will decline in the near future 4 , because of climate change, land degradation, and 53 groundwater depletion 5 . Agricultural selection, from the early steps of domestication to modern-54 day crop breeding, has resulted in a marked decrease in agrobiodiversity 6,7 . Today, three cereal 55 4 crops alone, bread wheat (Triticum aestivum), maize (Zea mays), and rice (Oryza sativa) account 56 for more than half of the globally consumed calories 8 . 57Many of today's major cereal crops, including rice and maize, originated in relatively humid 58 tropical and sub-tropical regions 9,10 . Although plant breeding has adapted the major cereal crops 59 to a wide range of climates and cultivation practices, there is limited genetic diversity within these 60 few plant species for cultivation in the most extreme environments. On the other hand, crop wild 61 relatives and orphan crops are often adapted to extreme environments and their utility to unlock 62 marginal lands for agriculture has recently regained interest 2,6,[11][12][13][14] . Current technological advances 63 in genomics and genome editing provide an opportunity to rapidly domesticate wild relatives and 64 to improve orphan crops 15,16 . De novo domestication of wild species or rapid improvement of semi-65 domesticated crops can be achieved in less than a decade by targeting a few key genes 6 . 66White fonio (Digitaria exilis (Kippist) Stapf) (Fig. 1) is an indigenous African millet species with 67 a great potential for agriculture in marginal environments 17,18 . Fonio is cultivated under a large 68 range of environmental conditions, from a tropical monsoon climate in western Guinea to a hot, 69 arid desert climate (BWh) in the Sahel zone. Some extra-early matur...

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“…D. exilis exhibits wide distribution from Senegal to Lake Chad, while D. iburua is restricted to Nigeria and Togo (Blench, 2012). Genomic data resources have been developed for D. exilis : 21 polymorphic microsatellites (Barnaud et al ., 2012, 2017), chloroplast SNPs (Scarcelli et al , 2011), full chloroplast genome sequences (Mariac et al ., 2014) and recently transcriptomic sequences (Sarah et al ., 2016). The polymorphic SSRs currently available for white fonio are still insufficient for accurate genetic studies of the population.…”

Section: Introductionmentioning

confidence: 99%

EST-SSR development for Digitaria exilis and its relatives D. iburua and D. longiflora from transcriptome sequences

Olodo¹,

Guèye²,

Calatayud³

et al. 2018

Plant Genet. Resour.

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Digitaria exilis is an important indigenous cereal in West Africa. The first fonio reference transcriptome was released and became a key tool for developing new molecular markers contributing to a better understanding of its genetic diversity. A total of 126 new putative primer pairs were successfully designed in 37,327 unigenes from the D. exilis transcriptome. Thirty-seven primer pairs were randomly selected and tested for their ability to cross-amplify to related species. Clear amplification patterns were observed on 24 primer pairs. Of these, 71, 74 and 35% showed polymorphism in three species: D. exilis, D. longiflora and D. iburua. The transferability from D. exilis was 96% to D. longiflora and 71% to D. iburua. The new SSR markers confirmed the close genetic proximity of D. exilis with D. longiflora and its stronger genetic difference of D. exilis from D. iburua. These markers will be valuable for completing future knowledge on Digitaria evolutionary history, and for testing gene flows between related species.

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High selfing rate inferred for white fonio [Digitaria exilis (Kippist.) Stapf] reproductive system opens up opportunities for breeding programs

Cited by 15 publications

References 16 publications

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

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

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

EST-SSR development for Digitaria exilis and its relatives D. iburua and D. longiflora from transcriptome sequences

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