1
|
Sharma PK, Ahmed HI, Heuberger M, Koo DH, Quiroz-Chavez J, Adhikari L, Raupp J, Cauet S, Rodde N, Cravero C, Callot C, Yadav IS, Kathiresan N, Athiyannan N, Ramirez-Gonzalez RH, Uauy C, Wicker T, Abrouk M, Gu YQ, Poland J, Krattinger SG, Lazo GR, Tiwari VK. An online database for einkorn wheat to aid in gene discovery and functional genomics studies. Database (Oxford) 2023; 2023:baad079. [PMID: 37971714 PMCID: PMC10653128 DOI: 10.1093/database/baad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/02/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help wheat research and breeding. Database URL https://wheat.pw.usda.gov/GG3/pangenome.
Collapse
Affiliation(s)
- Parva Kumar Sharma
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
| | - Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, 107, Zurich, Zollikerstrasse CH-8008, Switzerland
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, 4024 Throckmorton, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jesus Quiroz-Chavez
- John Innes Centre John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Laxman Adhikari
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - John Raupp
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, 4024 Throckmorton, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Stéphane Cauet
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Nathalie Rodde
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Charlotte Cravero
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Caroline Callot
- INRAE, CNRGV French Plant Genomic Resource Center, 24 Chemin de Borde Rouge, Castanet Tolosan F-31320, France
| | - Inderjit Singh Yadav
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
| | - Nagarajan Kathiresan
- Supercomputing Core Lab, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | | | - Cristobal Uauy
- John Innes Centre John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 107, Zurich, Zollikerstrasse CH-8008, Switzerland
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Yong Q Gu
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
- Center for Desert Agriculture, KAUST, 4700 KAUST, Thuwal, Kingdom of Saudi Arabia 23955-6900, Saudi Arabia
| | - Gerard R Lazo
- United States Department of Agriculture—Agricultural Research Service, Western Regional Research Center, Crop Improvement and Genetics Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, Fieldhouse Dr. College Park, MD 20742, USA
| |
Collapse
|
2
|
Ahmed HI, Heuberger M, Schoen A, Koo DH, Quiroz-Chavez 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 VK, Abrouk M, Poland J, Krattinger SG. Einkorn genomics sheds light on history of the oldest domesticated wheat. Nature 2023; 620:830-838. [PMID: 37532937 PMCID: PMC10447253 DOI: 10.1038/s41586-023-06389-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 06/29/2023] [Indexed: 08/04/2023]
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.
Collapse
Affiliation(s)
- Hanin Ibrahim Ahmed
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Adam Schoen
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | | | - Laxman Adhikari
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - John Raupp
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Stéphane Cauet
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Nathalie Rodde
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Charlotte Cravero
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Caroline Callot
- INRAE, CNRGV French Plant Genomic Resource Center, Castanet-Tolosan, France
| | - Gerard R Lazo
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Albany, CA, USA
| | - Nagarajan Kathiresan
- KAUST Supercomputing Core Lab (KSL), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Parva K Sharma
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Ian Moot
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Inderjit Singh Yadav
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Lovepreet Singh
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Gautam Saripalli
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Naveenkumar Athiyannan
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Vijay K Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
| | - Michael Abrouk
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Jesse Poland
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Simon G Krattinger
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| |
Collapse
|