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Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement

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DOI

  • Kumar Gaurav, Norwich Research Park
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  • Sanu Arora, Norwich Research Park
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  • Paula Silva, Kansas State University, National Institute for Agricultural Research
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  • Javier Sánchez-Martín, University of Zurich
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  • Richard Horsnell, National Institute of Agricultural Botany
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  • Liangliang Gao, Kansas State University
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  • Gurcharn S. Brar, University of Saskatchewan, University of British Columbia
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  • Victoria Widrig, University of Zurich
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  • W. John Raupp, Kansas State University
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  • Narinder Singh, Kansas State University, Bayer R&D Services LLC
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  • Shuangye Wu, Kansas State University
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  • Sandip M. Kale, Leibniz Institute of Plant Genetics and Crop Plant Research
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  • Catherine Chinoy, Norwich Research Park
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  • Paul Nicholson, Norwich Research Park
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  • Jesús Quiroz-Chávez, Norwich Research Park
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  • James Simmonds, Norwich Research Park
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  • Sadiye Hayta, Norwich Research Park
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  • Mark A. Smedley, Norwich Research Park
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  • Wendy Harwood, Norwich Research Park
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  • Suzannah Pearce, Norwich Research Park
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  • David Gilbert, Norwich Research Park
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  • Ngonidzashe Kangara, Norwich Research Park
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  • Catherine Gardener, Norwich Research Park
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  • Macarena Forner-Martínez, Norwich Research Park
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  • Jiaqian Liu, Norwich Research Park, Nanjing Agricultural University
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  • Guotai Yu, Norwich Research Park
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  • Scott A. Boden, Norwich Research Park, University of Adelaide
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  • Attilio Pascucci, Norwich Research Park, University of Bologna
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  • Sreya Ghosh, Norwich Research Park
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  • Amber N. Hafeez, Norwich Research Park
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  • Tom O’Hara, Norwich Research Park
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  • Joshua Waites, Norwich Research Park
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  • Jitender Cheema, Norwich Research Park
  • ,
  • Burkhard Steuernagel, Norwich Research Park
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  • Mehran Patpour
  • Annemarie Fejer Justesen
  • Shuyu Liu, Texas A and M University
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  • Jackie C. Rudd, Texas A and M University
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  • Raz Avni, Tel Aviv University
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  • Amir Sharon, Tel Aviv University
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  • Barbara Steiner, University of Natural Resources and Life Sciences, Vienna
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  • Rizky Pasthika Kirana, University of Natural Resources and Life Sciences, Vienna, Gadjah Mada University
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  • Hermann Buerstmayr, University of Natural Resources and Life Sciences, Vienna
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  • Ali A. Mehrabi, Ilam University
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  • Firuza Y. Nasyrova, Academy of Sciences of the Republic of Tadzhikistan
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  • Noam Chayut, Norwich Research Park
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  • Oadi Matny, University of Minnesota
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  • Brian J. Steffenson, University of Minnesota
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  • Nitika Sandhu, Punjab Agricultural University
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  • Parveen Chhuneja, Punjab Agricultural University
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  • Evans Lagudah, CSIRO
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  • Ahmed F. Elkot, Agricultural Research Center
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  • Simon Tyrrell, Norwich Research Park
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  • Xingdong Bian, Norwich Research Park
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  • Robert P. Davey, Norwich Research Park
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  • Martin Simonsen, QIAGEN Aarhus A/S
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  • Leif Schauser, QIAGEN Aarhus A/S
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  • Vijay K. Tiwari, University of Maryland, College Park
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  • H. Randy Kutcher, University of Saskatchewan
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  • Pierre Hucl, University of Saskatchewan
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  • Aili Li, Chinese Academy of Agricultural Sciences
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  • Deng Cai Liu, Sichuan Agricultural University
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  • Long Mao, Chinese Academy of Agricultural Sciences
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  • Steven Xu, United States Department of Agriculture
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  • Gina Brown-Guedira, North Carolina State University
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  • Justin Faris, United States Department of Agriculture
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  • Jan Dvorak, University of California at Davis
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  • Ming Cheng Luo, University of California at Davis
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  • Ksenia Krasileva, University of California
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  • Thomas Lux, Helmholtz Zentrum München - German Research Center for Environmental Health
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  • Susanne Artmeier, Helmholtz Zentrum München - German Research Center for Environmental Health
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  • Klaus F.X. Mayer, Helmholtz Zentrum München - German Research Center for Environmental Health, Technical University Munich
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  • Cristobal Uauy, Norwich Research Park
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  • Martin Mascher, Leibniz Institute of Plant Genetics and Crop Plant Research, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig
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  • Alison R. Bentley, National Institute of Agricultural Botany
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  • Beat Keller, University of Zurich
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  • Jesse Poland, Kansas State University
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  • Brande B.H. Wulff, Norwich Research Park

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.

OriginalsprogEngelsk
TidsskriftNature Biotechnology
Vol/bind40
Nummer3
Sider (fra-til)422-431
Antal sider10
ISSN1087-0156
DOI
StatusUdgivet - mar. 2022

Bibliografisk note

Funding Information:
We are grateful to the germplasm banks at Kansas State University Wheat Genetics Resource Center, International Center for Agricultural Research in the Dry Areas, USDA-ARS National Small Grains Collection, Leibniz Institute of Plant Genetics and Crop Plant Research, Ilam University, Tajikistan Academy of Sciences and the N. I. Vavilov Research Institute of Plant Industry for providing seed and/or collection data of Ae. tauschii. We thank our colleagues Y. Yue, P. Crane and S. Burrows and John Innes Centre (JIC) Horticultural Services for plant husbandry, M. Ambrose for help with public distribution of germplasm, M. Craze and S. Bowden for help with creation of synthetic wheats, H. Jones for help with elucidating provenance of Ae. tauschii donors used for synthetic wheats, C. Kling for developing and making available the durum wheat line Hoh-501 used for generating synthetic wheats, R. Graf for supplying wheat cv. Radiant, M. Feldman for help with delimiting the Fertile Crescent in Fig. 1, H. Cherry Guo for managing Illumina sequencing, T. Olsson for Illumina data handling, C. Michael Smith for maintenance of wheat curl mite colonies, H. Ahlers for creating graphics, M. Buttner for helpful discussions, A. Galvin and A. Lawn for OWWC communications, A. Meldrum for drafting the OWWC research agreement, the JIC NBI Computing Infrastructure for Science group and the Kansas State University (KSU) BEOCAT for HPC access and maintenance and S. Krattinger for reviewing the draft manuscript. This research was financed by the UK Biotechnology and Biological Sciences Research Council (BBSRC) Wheat Improvement Strategic Programme BB/I002561/1 to R.H. and A.R.B.; BBSRC Designing Future Wheat Institute Strategic Programme BB/P016855/1 to R.H., A.R.B., P.N., S.A.B., X.B., R.P.D., C.U. and B.B.H.W.; BBSRC Earlham Institute Strategic Programme BBS/E/T/000PR9817 to R.P.D.; BBSRC-Embrapa Newton Fund BB/ N019113/1 to P.N.; BBSRC grant BB/PPR1740/1 to W.H.; BBSRC National Capability award BBS/E/T/000PR9814 to R.P.D.; UK Research and Innovation-BBSRC National Capability grant BBS/E/J/000PR8000 to N.C.; a UKRI BBSRC Norwich Research Park Biosciences Doctoral Training Partnership scholarship (BB/M011216/1) to A.N.H.; US National Science Foundation (NSF) Industry-University Cooperative Research Center (IUCRC) Award 1822162 to J.P.; Phase II IUCRC at the KSU Center for Wheat Genetic Resources to J.P.; US-NSF award grant/FAIN 1339389 to J.P.; Kansas Wheat Commission award B65336 to J.P.; US-NSF award IOS-1238231 to J.D. and M.-C.L.; United States Department of Agriculture (USDA) to G.B.-G., S.X. and J.F.; National Institute of Food and Agriculture-USDA awards to V.K.T. (2020-67013-31460) and L.G.; a Fulbright Scholars Program to P.S.; Swiss National Science Foundation award 310030B_182833 to B.K.; Newton-Mosharafa Fund award 332408563 to A.F.E. and B.B.H.W.; a JIC Institute Development Grant to B.B.H.W; Agriculture Development Fund of the Saskatchewan Ministry of Agriculture project 20180095 to G.S.B. and H.R.K.; Saskatchewan Wheat Development Commission to G.S.B. and H.R.K.; Alberta Wheat Development Commission to G.S.B. and H.R.K.; Manitoba Crop Alliance to G.S.B. and H.R.K.; Government of Saskatchewan Ministry of Agriculture to P.H.; European Research Council award ERC-2016-STG-716233-MIREDI to K.K.; a Consejo Nacional de Ciencia y Tecnología scholarship to J.Q.-C.; JIC International Scholarships to J.Q.-C. and S.G.; Monsanto’s (now Bayer) Beachell-Borlaug International Scholars’ Program fellowship to S.G.; 2Blades Foundation to S.G. and B.B.H.W.; John Innes Foundation to J.W.; European Union’s Horizon 2020 research and innovation programme Marie Skłodowska-Curie grant agreement 674964 to N.K., B.B.H.W. and C.U.; JIC Science For Africa Initiative to N.K.; The Royal Society award UF150081 to S.A.B.; Australian Research Council award DP210103744 to S.A.B.; a Università di Bologna scholarship to A.P.; Innovation Fund Denmark award 4105-00022B to M.P. and A.F.J.; Jewish National Fund of Australia to R.A. and A.S.; Ministry of Education and Culture of the Republic of Indonesia and the Austrian Agency for International Cooperation in Education and Research (OeAD-GmbH) in cooperation with ASEA-UNINET to R.P.K.; Department of Biotechnology, India award BT/PR30871/BIC/101/1159/2018 to N. Sandhu and award BT/IN/Indo-UK/CGAT/14/PC/2014-15 to P.C.; Science and Technology Development Fund, Egypt-UK Newton-Mosharafa Institutional Links award 30718 to A.F.E. and B.B.H.W. National Science Foundation of China grants 91731305 and 31661143007 to L.M.; Knowledge Innovation Program of Chinese Academy of Agricultural Sciences award CAAS-DRW202002 to LM and the breeding companies KWS, Limagrain, Syngenta and Bayer to the Open Wild Wheat Consortium.

Funding Information:
We are grateful to the germplasm banks at Kansas State University Wheat Genetics Resource Center, International Center for Agricultural Research in the Dry Areas, USDA-ARS National Small Grains Collection, Leibniz Institute of Plant Genetics and Crop Plant Research, Ilam University, Tajikistan Academy of Sciences and the N. I. Vavilov Research Institute of Plant Industry for providing seed and/or collection data of Ae. tauschii. We thank our colleagues Y. Yue, P. Crane and S. Burrows and John Innes Centre (JIC) Horticultural Services for plant husbandry, M. Ambrose for help with public distribution of germplasm, M. Craze and S. Bowden for help with creation of synthetic wheats, H. Jones for help with elucidating provenance of Ae. tauschii donors used for synthetic wheats, C. Kling for developing and making available the durum wheat line Hoh-501 used for generating synthetic wheats, R. Graf for supplying wheat cv. Radiant, M. Feldman for help with delimiting the Fertile Crescent in Fig. 1 , H. Cherry Guo for managing Illumina sequencing, T. Olsson for Illumina data handling, C. Michael Smith for maintenance of wheat curl mite colonies, H. Ahlers for creating graphics, M. Buttner for helpful discussions, A. Galvin and A. Lawn for OWWC communications, A. Meldrum for drafting the OWWC research agreement, the JIC NBI Computing Infrastructure for Science group and the Kansas State University (KSU) BEOCAT for HPC access and maintenance and S. Krattinger for reviewing the draft manuscript. This research was financed by the UK Biotechnology and Biological Sciences Research Council (BBSRC) Wheat Improvement Strategic Programme BB/I002561/1 to R.H. and A.R.B.

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