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

Kumar Gaurav, Sanu Arora, Paula Silva, Javier Sánchez-Martín, Richard Horsnell, Liangliang Gao, Gurcharn S. Brar, Victoria Widrig, W. John Raupp, Narinder Singh, Shuangye Wu, Sandip M. Kale, Catherine Chinoy, Paul Nicholson, Jesús Quiroz-Chávez, James Simmonds, Sadiye Hayta, Mark A. Smedley, Wendy Harwood, Suzannah PearceDavid Gilbert, Ngonidzashe Kangara, Catherine Gardener, Macarena Forner-Martínez, Jiaqian Liu, Guotai Yu, Scott A. Boden, Attilio Pascucci, Sreya Ghosh, Amber Hafeez, Tom O’Hara, Joshua Waites, Jitender Cheema, Burkhard Steuernagel, Mehran Patpour, Annemarie Fejer Justesen, Shuyu Liu, Jackie C. Rudd, Raz Avni, Amir Sharon, Barbara Steiner, Rizky Pasthika Kirana, Hermann Buerstmayr, Ali A. Mehrabi, Firuza Y. Nasyrova, Noam Chayut, Oadi Matny, Brian J. Steffenson, Nitika Sandhu, Parveen Chhuneja, Evans Lagudah, Ahmed F. Elkot, Simon Tyrrell, Xingdong Bian, Robert P. Davey, Martin Simonsen, Leif Schauser, Vijay K. Tiwari, H. Randy Kutcher, Pierre Hucl, Aili Li, Deng-Cai Liu, Long Mao, Steven Xu, Gina Brown-Guedira, Justin Faris, Jan Dvorak, Ming-Cheng Luo, Ksenia Krasileva, Thomas Lux, Susanne Artmeier, Klaus F. X. Mayer, Cristobal Uauy, Martin Mascher, Alison R. Bentley, Beat Keller, Jesse Poland, Brande B. H. Wulff

Research output: Contribution to journalArticlepeer-review

78 Scopus citations

Abstract

Abstract$\textit{Aegilops tauschii}$, 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 $\textit{Ae. tauschii}$ accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of $\textit{Ae. tauschii}$ geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through $\textit{k}$-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 $\textit{Ae. tauschii}$ genomes. Exploiting the genomic diversity of the $\textit{Ae. tauschii}$ ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.
Original languageEnglish (US)
JournalNature Biotechnology
DOIs
StatePublished - Nov 1 2021

Bibliographical note

KAUST Repository Item: Exported on 2021-11-26
Acknowledgements: 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.

ASJC Scopus subject areas

  • Biomedical Engineering
  • Applied Microbiology and Biotechnology
  • Bioengineering
  • Molecular Medicine
  • Biotechnology

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