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

Michael Abrouk; Hanin Ibrahim Ahmed; Philippe Cubry; Denisa Šimoníková; Stéphane Cauet; Yveline Pailles; Jan Bettgenhaeuser; Liubov Gapa; Nora Scarcelli; Marie Couderc; Leila Zekraoui; Nagarajan Kathiresan; Jana Čížková; Eva Hřibová; Jaroslav Doležel; Sandrine Arribat; Hélène Bergès; Jan J. Wieringa; Mathieu Gueye; Ndjido A. Kane; Christian Leclerc; Sandrine Causse; Sylvie Vancoppenolle; Claire Billot; Thomas Wicker; Yves Vigouroux; Adeline Barnaud; Simon G. Krattinger

doi:10.1038/s41467-020-18329-4

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

Michael Abrouk, Hanin Ibrahim Ahmed, Philippe Cubry, Denisa Šimoníková, Stéphane Cauet, Yveline Pailles, Jan Bettgenhaeuser, Liubov Gapa, Nora Scarcelli, Marie Couderc, Leila Zekraoui, Nagarajan Kathiresan, Jana Čížková, Eva Hřibová, Jaroslav Doležel, Sandrine Arribat, Hélène Bergès, Jan J. Wieringa, Mathieu Gueye, Ndjido A. KaneChristian Leclerc, Sandrine Causse, Sylvie Vancoppenolle, Claire Billot, Thomas Wicker, Yves Vigouroux, Adeline Barnaud, Simon G. Krattinger

Research output: Contribution to journal › Article › peer-review

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Abstract

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.

Original language	English (US)
Journal	Nature Communications
Volume	11
Issue number	1
DOIs	https://doi.org/10.1038/s41467-020-18329-4 https://doi.org/10.1101/2020.04.11.037671
State	Published - Sep 10 2020

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Abrouk, M., Ahmed, H. I., Cubry, P., Šimoníková, D., Cauet, S., Pailles, Y., Bettgenhaeuser, J., Gapa, L., Scarcelli, N., Couderc, M., Zekraoui, L., Kathiresan, N., Čížková, J., Hřibová, E., Doležel, J., Arribat, S., Bergès, H., Wieringa, J. J., Gueye, M., ... Krattinger, S. G. (2020). Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-18329-4, https://doi.org/10.1101/2020.04.11.037671

Abrouk, Michael ; Ahmed, Hanin Ibrahim ; Cubry, Philippe ; Šimoníková, Denisa ; Cauet, Stéphane ; Pailles, Yveline ; Bettgenhaeuser, Jan ; Gapa, Liubov ; Scarcelli, Nora ; Couderc, Marie ; Zekraoui, Leila ; Kathiresan, Nagarajan ; Čížková, Jana ; Hřibová, Eva ; Doležel, Jaroslav ; Arribat, Sandrine ; Bergès, Hélène ; Wieringa, Jan J. ; Gueye, Mathieu ; Kane, Ndjido A. ; Leclerc, Christian ; Causse, Sandrine ; Vancoppenolle, Sylvie ; Billot, Claire ; Wicker, Thomas ; Vigouroux, Yves ; Barnaud, Adeline ; Krattinger, Simon G. / Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. In: Nature Communications. 2020 ; Vol. 11, No. 1.

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title = "Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate",

abstract = "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.",

author = "Michael Abrouk and Ahmed, {Hanin Ibrahim} and Philippe Cubry and Denisa {\v S}imon{\'i}kov{\'a} and St{\'e}phane Cauet and Yveline Pailles and Jan Bettgenhaeuser and Liubov Gapa and Nora Scarcelli and Marie Couderc and Leila Zekraoui and Nagarajan Kathiresan and Jana {\v C}{\'i}{\v z}kov{\'a} and Eva H{\v r}ibov{\'a} and Jaroslav Dole{\v z}el and Sandrine Arribat and H{\'e}l{\`e}ne Berg{\`e}s and Wieringa, {Jan J.} and Mathieu Gueye and Kane, {Ndjido A.} and Christian Leclerc and Sandrine Causse and Sylvie Vancoppenolle and Claire Billot and Thomas Wicker and Yves Vigouroux and Adeline Barnaud and Krattinger, {Simon G.}",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We are grateful to Vinicius M. Lube, Samantha Bazan, Ablaye Ngom, Marie Piquet, H{\'e}l{\`e}ne Adam, and Carole Gauron for their technical assistance in Herbarium sampling and photography. Cirad herbarium samples of Digitaria longiflora were provided by Samantha Bazan (ALF [http://publish.plantnet-project.org/]). We thank Soukeye Conde for valuable insight, funded by the project Cultivar, reference ANR-16-IDEX-0006, through the Investissements d{\textquoteright}avenir program (Labex Agro: ANR-10-LABX-0001-01). This work was supported by the CIRAD-UMR AGAP and IRD UMR DIADE HPC Data Center of the South Green Bioinformatics platform [http://www.southgreen.fr/] and the Center for Desert Agriculture of the King Abdullah University of Science and Technology (KAUST). D.S., J.C., E.H. and J.D. were in part supported by the European Regional Development Fund OPVVV project {\textquoteleft}Plants as a tool for sustainable development{\textquoteright} number CZ.02.1.01/0.0/0.0/16_019/0000827.",

year = "2020",

month = sep,

day = "10",

doi = "10.1038/s41467-020-18329-4",

language = "English (US)",

volume = "11",

journal = "Nature Communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

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Abrouk, M, Ahmed, HI, Cubry, P, Šimoníková, D, Cauet, S, Pailles, Y, Bettgenhaeuser, J, Gapa, L, Scarcelli, N, Couderc, M, Zekraoui, L, Kathiresan, N, Čížková, J, Hřibová, E, Doležel, J, Arribat, S, Bergès, H, Wieringa, JJ, Gueye, M, Kane, NA, Leclerc, C, Causse, S, Vancoppenolle, S, Billot, C, Wicker, T, Vigouroux, Y, Barnaud, A & Krattinger, SG 2020, 'Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate', Nature Communications, vol. 11, no. 1. https://doi.org/10.1038/s41467-020-18329-4, https://doi.org/10.1101/2020.04.11.037671

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. / Abrouk, Michael; Ahmed, Hanin Ibrahim; Cubry, Philippe; Šimoníková, Denisa; Cauet, Stéphane; Pailles, Yveline; Bettgenhaeuser, Jan; Gapa, Liubov; Scarcelli, Nora; Couderc, Marie; Zekraoui, Leila; Kathiresan, Nagarajan; Čížková, Jana; Hřibová, Eva; Doležel, Jaroslav; Arribat, Sandrine; Bergès, Hélène; Wieringa, Jan J.; Gueye, Mathieu; Kane, Ndjido A.; Leclerc, Christian; Causse, Sandrine; Vancoppenolle, Sylvie; Billot, Claire; Wicker, Thomas; Vigouroux, Yves; Barnaud, Adeline; Krattinger, Simon G.

In: Nature Communications, Vol. 11, No. 1, 10.09.2020.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

AU - Abrouk, Michael

AU - Ahmed, Hanin Ibrahim

AU - Cubry, Philippe

AU - Šimoníková, Denisa

AU - Cauet, Stéphane

AU - Pailles, Yveline

AU - Bettgenhaeuser, Jan

AU - Gapa, Liubov

AU - Scarcelli, Nora

AU - Couderc, Marie

AU - Zekraoui, Leila

AU - Kathiresan, Nagarajan

AU - Čížková, Jana

AU - Hřibová, Eva

AU - Doležel, Jaroslav

AU - Arribat, Sandrine

AU - Bergès, Hélène

AU - Wieringa, Jan J.

AU - Gueye, Mathieu

AU - Kane, Ndjido A.

AU - Leclerc, Christian

AU - Causse, Sandrine

AU - Vancoppenolle, Sylvie

AU - Billot, Claire

AU - Wicker, Thomas

AU - Vigouroux, Yves

AU - Barnaud, Adeline

AU - Krattinger, Simon G.

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We are grateful to Vinicius M. Lube, Samantha Bazan, Ablaye Ngom, Marie Piquet, Hélène Adam, and Carole Gauron for their technical assistance in Herbarium sampling and photography. Cirad herbarium samples of Digitaria longiflora were provided by Samantha Bazan (ALF [http://publish.plantnet-project.org/]). We thank Soukeye Conde for valuable insight, funded by the project Cultivar, reference ANR-16-IDEX-0006, through the Investissements d’avenir program (Labex Agro: ANR-10-LABX-0001-01). This work was supported by the CIRAD-UMR AGAP and IRD UMR DIADE HPC Data Center of the South Green Bioinformatics platform [http://www.southgreen.fr/] and the Center for Desert Agriculture of the King Abdullah University of Science and Technology (KAUST). D.S., J.C., E.H. and J.D. were in part supported by the European Regional Development Fund OPVVV project ‘Plants as a tool for sustainable development’ number CZ.02.1.01/0.0/0.0/16_019/0000827.

PY - 2020/9/10

Y1 - 2020/9/10

N2 - 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.

AB - 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.

UR - http://hdl.handle.net/10754/662572

UR - http://www.nature.com/articles/s41467-020-18329-4

U2 - 10.1038/s41467-020-18329-4

DO - 10.1038/s41467-020-18329-4

M3 - Article

C2 - 32901040

VL - 11

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

ER -

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

Abstract

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