Einkorn genomics sheds light on evolutionary history of the oldest domesticated wheat

Authors: AHMED, HANIN IBRAHIM - University Of Zurich; HEUBERGER, MATTIAS - King Abdullah University Of Science And Technology; KOO, DAL-HOE - Kansas State University; QUIROZ-CHAVEZ, JESUS - John Innes Center; ADHIKARI, LAXMAN - King Abdullah University Of Science And Technology; SHARMA, PARVA - University Of Maryland; RAUPP, JOHN - Kansas State University; CAUET, STEPHANE - Inrae; RODDES, NATHALIE - Inrae; CRAVERO, CHARLOTTE - Inrae; CALLOT, CAROLINE - Inrae; Lazo, Gerard; KATHIRESAN, NAGARAJAN - King Abdullah University Of Science And Technology; ATHIYANNAN, NAVEENKUMAR - King Abdullah University Of Science And Technology; SARIPALLI, GAUTAM - University Of Maryland; RAMIREZ GONZALEZ, RICARDO - John Innes Center; TIWARI, VIJAY - University Of Maryland; UAUY, CRISTOBAL - John Innes Center; ...KRATTINGER - King Abdullah University Of Science And Technology

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/29/2023
Publication Date: 8/2/2023
Citation: Ahmed, H., Heuberger, M., Koo, D., Quiroz-Chavez, J., Adhikari, L., Sharma, P.K., Raupp, J., Cauet, S., Roddes, N., Cravero, C., Callot, C., Lazo, G.R., Kathiresan, N., Athiyannan, N., Saripalli, G., Ramirez Gonzalez, R.H., Tiwari, V., Uauy, C., ...Krattinger 2023. Einkorn genomics sheds light on evolutionary history of the oldest domesticated wheat. Nature. 620, p.830–838. https://doi.org/10.1038/s41586-023-06389-7.
DOI: https://doi.org/10.1038/s41586-023-06389-7

Interpretive Summary: Einkorn (Triticum monococcum) is the first domesticated wheat species, being central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent ~10,000 years ago. Here, we generate and analyze 5.2 Gb genome assemblies for a wild and a domesticated einkorn, which represent the most contiguous Triticeae assemblies to date, including completely assembled centromeres. Einkorn centromeres are highly dynamic, including ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions following the dispersal of domesticated einkorn from the Fertile Crescent. We also discovered 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 genomics-assisted improvement of einkorn and bread wheat.

Technical Abstract: Einkorn (Triticum monococcum) is the first domesticated wheat species, being central to the birth of agriculture and the Neolithic Revolution in the Fertile Crescent ~10,000 years ago. Here, we generate and analyze 5.2 Gb genome assemblies for a wild and a domesticated einkorn, which represent the most contiguous Triticeae assemblies to date, including completely assembled centromeres. Einkorn centromeres are highly dynamic, including ancient and recent centromere shifts caused by structural rearrangements. Whole-genome sequencing of a diversity panel uncovered the population structure and evolutionary history of einkorn, revealing complex patterns of hybridizations and introgressions following the dispersal of domesticated einkorn from the Fertile Crescent. We also discovered 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 genomics-assisted improvement of einkorn and bread wheat.