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Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement.
Nat Biotechnol. 2022 03; 40(3):422-431.NBio

Abstract

Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

Authors+Show Affiliations

John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA. Programa Nacional de Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental La Estanzuela, Colonia, Uruguay.Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.The John Bingham Laboratory, NIAB, Cambridge, UK.Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada. Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada.Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA. Bayer R&D Services LLC, Kansas City, MO, USA.Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK. National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China.John Innes Centre, Norwich Research Park, Norwich, UK. Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.John Innes Centre, Norwich Research Park, Norwich, UK. School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia.John Innes Centre, Norwich Research Park, Norwich, UK. Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.John Innes Centre, Norwich Research Park, Norwich, UK.Department of Agroecology, Global Rust Reference Center, Aarhus University, Slagelse, Denmark.Department of Agroecology, Global Rust Reference Center, Aarhus University, Slagelse, Denmark.Texas A&M AgriLife Research, Amarillo, TX, USA.Texas A&M AgriLife Research, Amarillo, TX, USA.Institute for Cereal Crops Improvement, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.Institute for Cereal Crops Improvement, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna, Austria.Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna, Austria. Laboratory of Plant Breeding, Department of Agronomy, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia.Department of Agrobiotechnology (IFA-Tulln), Institute of Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna, Austria.Department of Agronomy and Plant Breeding, Ilam University, Ilam, Iran.Institute of Botany, Plant Physiology and Genetics, Tajik National Academy of Sciences, Dushanbe, Tajikistan.Germplasm Resources Unit, John Innes Centre, Norwich Research Park, Norwich, UK.Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA.Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA.School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia.Wheat Research Department, Field Crops Research Institute, Agricultural Research Center, Giza, Egypt.Earlham Institute, Norwich Research Park, Norwich, UK.Earlham Institute, Norwich Research Park, Norwich, UK.Earlham Institute, Norwich Research Park, Norwich, UK.QIAGEN Aarhus A/S, Aarhus, Denmark.QIAGEN Aarhus A/S, Aarhus, Denmark.Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, USA.USDA-ARS, Plant Science Research Unit, Raleigh, NC, USA.USDA-ARS Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, USA.Department of Plant Sciences, University of California, Davis, CA, USA.Department of Plant Sciences, University of California, Davis, CA, USA.Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany.Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany.Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany. Faculty of Life Sciences, Technical University Munich, Weihenstephan, Germany.John Innes Centre, Norwich Research Park, Norwich, UK.Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.The John Bingham Laboratory, NIAB, Cambridge, UK. a.bentley@cgiar.org. International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico. a.bentley@cgiar.org.Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland. bkeller@botinst.uzh.ch.Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA. jpoland@ksu.edu. Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. jpoland@ksu.edu.John Innes Centre, Norwich Research Park, Norwich, UK. brande.wulff@kaust.edu.sa. Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. brande.wulff@kaust.edu.sa.

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

34725503

Citation

Gaurav, Kumar, et al. "Population Genomic Analysis of Aegilops Tauschii Identifies Targets for Bread Wheat Improvement." Nature Biotechnology, vol. 40, no. 3, 2022, pp. 422-431.
Gaurav K, Arora S, Silva P, et al. Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement. Nat Biotechnol. 2022;40(3):422-431.
Gaurav, K., Arora, S., Silva, P., Sánchez-Martín, J., Horsnell, R., Gao, L., Brar, G. S., Widrig, V., John Raupp, W., Singh, N., Wu, S., Kale, S. M., Chinoy, C., Nicholson, P., Quiroz-Chávez, J., Simmonds, J., Hayta, S., Smedley, M. A., Harwood, W., ... Wulff, B. B. H. (2022). Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement. Nature Biotechnology, 40(3), 422-431. https://doi.org/10.1038/s41587-021-01058-4
Gaurav K, et al. Population Genomic Analysis of Aegilops Tauschii Identifies Targets for Bread Wheat Improvement. Nat Biotechnol. 2022;40(3):422-431. PubMed PMID: 34725503.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement. AU - Gaurav,Kumar, AU - Arora,Sanu, AU - Silva,Paula, AU - Sánchez-Martín,Javier, AU - Horsnell,Richard, AU - Gao,Liangliang, AU - Brar,Gurcharn S, AU - Widrig,Victoria, AU - John Raupp,W, AU - Singh,Narinder, AU - Wu,Shuangye, AU - Kale,Sandip M, AU - Chinoy,Catherine, AU - Nicholson,Paul, AU - Quiroz-Chávez,Jesús, AU - Simmonds,James, AU - Hayta,Sadiye, AU - Smedley,Mark A, AU - Harwood,Wendy, AU - Pearce,Suzannah, AU - Gilbert,David, AU - Kangara,Ngonidzashe, AU - Gardener,Catherine, AU - Forner-Martínez,Macarena, AU - Liu,Jiaqian, AU - Yu,Guotai, AU - Boden,Scott A, AU - Pascucci,Attilio, AU - Ghosh,Sreya, AU - Hafeez,Amber N, AU - O'Hara,Tom, AU - Waites,Joshua, AU - Cheema,Jitender, AU - Steuernagel,Burkhard, AU - Patpour,Mehran, AU - Justesen,Annemarie Fejer, AU - Liu,Shuyu, AU - Rudd,Jackie C, AU - Avni,Raz, AU - Sharon,Amir, AU - Steiner,Barbara, AU - Kirana,Rizky Pasthika, AU - Buerstmayr,Hermann, AU - Mehrabi,Ali A, AU - Nasyrova,Firuza Y, AU - Chayut,Noam, AU - Matny,Oadi, AU - Steffenson,Brian J, AU - Sandhu,Nitika, AU - Chhuneja,Parveen, AU - Lagudah,Evans, AU - Elkot,Ahmed F, AU - Tyrrell,Simon, AU - Bian,Xingdong, AU - Davey,Robert P, AU - Simonsen,Martin, AU - Schauser,Leif, AU - Tiwari,Vijay K, AU - Randy Kutcher,H, AU - Hucl,Pierre, AU - Li,Aili, AU - Liu,Deng-Cai, AU - Mao,Long, AU - Xu,Steven, AU - Brown-Guedira,Gina, AU - Faris,Justin, AU - Dvorak,Jan, AU - Luo,Ming-Cheng, AU - Krasileva,Ksenia, AU - Lux,Thomas, AU - Artmeier,Susanne, AU - Mayer,Klaus F X, AU - Uauy,Cristobal, AU - Mascher,Martin, AU - Bentley,Alison R, AU - Keller,Beat, AU - Poland,Jesse, AU - Wulff,Brande B H, Y1 - 2021/11/01/ PY - 2021/02/01/received PY - 2021/08/16/accepted PY - 2021/11/3/pubmed PY - 2022/4/6/medline PY - 2021/11/2/entrez SP - 422 EP - 431 JF - Nature biotechnology JO - Nat Biotechnol VL - 40 IS - 3 N2 - Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding. SN - 1546-1696 UR - https://www.unboundmedicine.com/medline/citation/34725503/Population_genomic_analysis_of_Aegilops_tauschii_identifies_targets_for_bread_wheat_improvement_ L2 - https://doi.org/10.1038/s41587-021-01058-4 DB - PRIME DP - Unbound Medicine ER -