Einkorn genomics sheds light on history of the oldest domesticated wheat

Hanin Ahmed; Matthias Heuberger; Adam Schoen; Dal-Hoe Koo; Jesús Quiroz-Chávez; Laxman Adhikari; John Raupp; Stéphane Cauet; Nathalie Rodde; Charlotte Cravero; Caroline Callot; Gerard R. Lazo; Nagarajan Kathiresan; Parva K. Sharma; Ian Moot; Inderjit Singh Yadav; Lovepreet Singh; Gautam Saripalli; Nidhi Rawat; Raju Datla; Naveenkumar Athiyannan; Ricardo H. Ramirez-Gonzalez; Cristobal Uauy; Thomas Wicker; Vijay Tiwari; Michael Abrouk; Jesse Poland; Simon G. Krattinger

doi:10.1038/s41586-023-06389-7

Einkorn genomics sheds light on history of the oldest domesticated wheat

Hanin Ahmed, Matthias Heuberger, Adam Schoen, Dal-Hoe Koo, Jesús Quiroz-Chávez, Laxman Adhikari, John Raupp, Stéphane Cauet, Nathalie Rodde, Charlotte Cravero, Caroline Callot, Gerard R. Lazo, Nagarajan Kathiresan, Parva K. Sharma, Ian Moot, Inderjit Singh Yadav, Lovepreet Singh, Gautam Saripalli, Nidhi Rawat, Raju DatlaNaveenkumar Athiyannan, Ricardo H. Ramirez-Gonzalez, Cristobal Uauy, Thomas Wicker, Vijay Tiwari, Michael Abrouk, Jesse Poland, Simon G. Krattinger

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

34 Scopus citations

Abstract

Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.

Original language	English (US)
Journal	Nature
DOIs	https://doi.org/10.1038/s41586-023-06389-7
State	Published - Aug 2 2023

Bibliographical note

KAUST Repository Item: Exported on 2023-08-07
Acknowledgements: We thank the members of the KAUST Bioscience Core Laboratory for sequencing support; E. Cavalet-Giorsa for providing information on einkorn domestication and migration; L. Aouini for assistance with RNA extraction; L. Zou for greenhouse support; B. Gill for providing seeds of the tin3 mutant; and T. Quilichini for SEM images. We acknowledge support by the plant growth facility and the GENTYANE platform of the Clermont-Ferrand INRAE Centre for assisting in NGS sequencing; the Genotoul bioinformatics platform Toulouse Midi-Pyrenees (Bioinfo Genotoul, http://bioinfo.genotoul.fr) and the KAUST supercomputing facilities (https://www.hpc.kaust.edu.sa) for providing computing resources; GrainGenes resources for hosting the online database; and the University of Maryland supercomputing resources (http://hpcc.umd.edu) for developing the einkorn database and tin3 analysis. This publication is based on work supported by the King Abdullah University of Science and Technology, the UK Biotechnology and Biological Sciences Research Council (BBSRC; BB/P016855/1), the Mexican Consejo Nacional de Ciencia y Tecnología (CONACYT; 2018-000009-01EXTF-00306), the Global Institute for Food Security (to R.D.), the European Research Council (ERC-2019-COG-866328) and the United States Department of Agriculture National Institute of Food and Agriculture (USDA-NIFA; award 2020-67013-31460). D.-H.K. was supported by WGRC/IUCRC and NSF (grant 1822162).

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https://repository.kaust.edu.sa/bitstream/10754/693480/1/s41586-023-06389-7.pdf

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Ahmed, H., Heuberger, M., Schoen, A., Koo, D.-H., Quiroz-Chávez, J., Adhikari, L., Raupp, J., Cauet, S., Rodde, N., Cravero, C., Callot, C., Lazo, G. R., Kathiresan, N., Sharma, P. K., Moot, I., Yadav, I. S., Singh, L., Saripalli, G., Rawat, N., ... Krattinger, S. G. (2023). Einkorn genomics sheds light on history of the oldest domesticated wheat. Nature. https://doi.org/10.1038/s41586-023-06389-7

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title = "Einkorn genomics sheds light on history of the oldest domesticated wheat",

abstract = "Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.",

author = "Hanin Ahmed and Matthias Heuberger and Adam Schoen and Dal-Hoe Koo and Jes{\'u}s Quiroz-Ch{\'a}vez and Laxman Adhikari and John Raupp and St{\'e}phane Cauet and Nathalie Rodde and Charlotte Cravero and Caroline Callot and Lazo, {Gerard R.} and Nagarajan Kathiresan and Sharma, {Parva K.} and Ian Moot and Yadav, {Inderjit Singh} and Lovepreet Singh and Gautam Saripalli and Nidhi Rawat and Raju Datla and Naveenkumar Athiyannan and Ramirez-Gonzalez, {Ricardo H.} and Cristobal Uauy and Thomas Wicker and Vijay Tiwari and Michael Abrouk and Jesse Poland and Krattinger, {Simon G.}",

note = "KAUST Repository Item: Exported on 2023-08-07 Acknowledgements: We thank the members of the KAUST Bioscience Core Laboratory for sequencing support; E. Cavalet-Giorsa for providing information on einkorn domestication and migration; L. Aouini for assistance with RNA extraction; L. Zou for greenhouse support; B. Gill for providing seeds of the tin3 mutant; and T. Quilichini for SEM images. We acknowledge support by the plant growth facility and the GENTYANE platform of the Clermont-Ferrand INRAE Centre for assisting in NGS sequencing; the Genotoul bioinformatics platform Toulouse Midi-Pyrenees (Bioinfo Genotoul, http://bioinfo.genotoul.fr) and the KAUST supercomputing facilities (https://www.hpc.kaust.edu.sa) for providing computing resources; GrainGenes resources for hosting the online database; and the University of Maryland supercomputing resources (http://hpcc.umd.edu) for developing the einkorn database and tin3 analysis. This publication is based on work supported by the King Abdullah University of Science and Technology, the UK Biotechnology and Biological Sciences Research Council (BBSRC; BB/P016855/1), the Mexican Consejo Nacional de Ciencia y Tecnolog{\'i}a (CONACYT; 2018-000009-01EXTF-00306), the Global Institute for Food Security (to R.D.), the European Research Council (ERC-2019-COG-866328) and the United States Department of Agriculture National Institute of Food and Agriculture (USDA-NIFA; award 2020-67013-31460). D.-H.K. was supported by WGRC/IUCRC and NSF (grant 1822162).",

year = "2023",

month = aug,

day = "2",

doi = "10.1038/s41586-023-06389-7",

language = "English (US)",

journal = "Nature",

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Ahmed, H, Heuberger, M, Schoen, A, Koo, D-H, Quiroz-Chávez, J, Adhikari, L, Raupp, J, Cauet, S, Rodde, N, Cravero, C, Callot, C, Lazo, GR, Kathiresan, N, Sharma, PK, Moot, I, Yadav, IS, Singh, L, Saripalli, G, Rawat, N, Datla, R, Athiyannan, N, Ramirez-Gonzalez, RH, Uauy, C, Wicker, T, Tiwari, V, Abrouk, M , Poland, J & Krattinger, SG 2023, 'Einkorn genomics sheds light on history of the oldest domesticated wheat', Nature. https://doi.org/10.1038/s41586-023-06389-7

TY - JOUR

T1 - Einkorn genomics sheds light on history of the oldest domesticated wheat

AU - Ahmed, Hanin

AU - Heuberger, Matthias

AU - Schoen, Adam

AU - Koo, Dal-Hoe

AU - Quiroz-Chávez, Jesús

AU - Adhikari, Laxman

AU - Raupp, John

AU - Cauet, Stéphane

AU - Rodde, Nathalie

AU - Cravero, Charlotte

AU - Callot, Caroline

AU - Lazo, Gerard R.

AU - Kathiresan, Nagarajan

AU - Sharma, Parva K.

AU - Moot, Ian

AU - Yadav, Inderjit Singh

AU - Singh, Lovepreet

AU - Saripalli, Gautam

AU - Rawat, Nidhi

AU - Datla, Raju

AU - Athiyannan, Naveenkumar

AU - Ramirez-Gonzalez, Ricardo H.

AU - Uauy, Cristobal

AU - Wicker, Thomas

AU - Tiwari, Vijay

AU - Abrouk, Michael

AU - Poland, Jesse

AU - Krattinger, Simon G.

N1 - KAUST Repository Item: Exported on 2023-08-07 Acknowledgements: We thank the members of the KAUST Bioscience Core Laboratory for sequencing support; E. Cavalet-Giorsa for providing information on einkorn domestication and migration; L. Aouini for assistance with RNA extraction; L. Zou for greenhouse support; B. Gill for providing seeds of the tin3 mutant; and T. Quilichini for SEM images. We acknowledge support by the plant growth facility and the GENTYANE platform of the Clermont-Ferrand INRAE Centre for assisting in NGS sequencing; the Genotoul bioinformatics platform Toulouse Midi-Pyrenees (Bioinfo Genotoul, http://bioinfo.genotoul.fr) and the KAUST supercomputing facilities (https://www.hpc.kaust.edu.sa) for providing computing resources; GrainGenes resources for hosting the online database; and the University of Maryland supercomputing resources (http://hpcc.umd.edu) for developing the einkorn database and tin3 analysis. This publication is based on work supported by the King Abdullah University of Science and Technology, the UK Biotechnology and Biological Sciences Research Council (BBSRC; BB/P016855/1), the Mexican Consejo Nacional de Ciencia y Tecnología (CONACYT; 2018-000009-01EXTF-00306), the Global Institute for Food Security (to R.D.), the European Research Council (ERC-2019-COG-866328) and the United States Department of Agriculture National Institute of Food and Agriculture (USDA-NIFA; award 2020-67013-31460). D.-H.K. was supported by WGRC/IUCRC and NSF (grant 1822162).

PY - 2023/8/2

Y1 - 2023/8/2

N2 - Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.

AB - Einkorn (Triticum monococcum) was the first domesticated wheat species, and was central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent around 10,000 years ago1,2. Here we generate and analyse 5.2-Gb genome assemblies for wild and domesticated einkorn, including completely assembled centromeres. Einkorn centromeres are highly dynamic, showing evidence of ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing analysis of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions after the dispersal of domesticated einkorn from the Fertile Crescent. We also show that around 1% of the modern bread wheat (Triticum aestivum) A subgenome originates from einkorn. These resources and findings highlight the history of einkorn evolution and provide a basis to accelerate the genomics-assisted improvement of einkorn and bread wheat.

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UR - https://www.nature.com/articles/s41586-023-06389-7

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C2 - 37532937

SN - 0028-0836

JO - Nature

JF - Nature

ER -

Einkorn genomics sheds light on history of the oldest domesticated wheat

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Einkorn genomics sheds light on history of the oldest domesticated wheat

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