Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

M. Timothy Rabanus-Wallace; Bernd Hackauf; Martin Mascher; Thomas Lux; Thomas Wicker; Heidrun Gundlach; Mariana Baez; Andreas Houben; Klaus F. X. Mayer; Liangliang Guo; Jesse Poland; Curtis J. Pozniak; Sean Walkowiak; Joanna Melonek; Coraline R. Praz; Mona Schreiber; Hikmet Budak; Matthias Heuberger; Burkhard Steuernagel; Brande Wulff; Andreas Boerner; Brook Byrns; Jana Cizkova; D. Brian Fowler; Allan Fritz; Axel Himmelbach; Gemy Kaithakottil; Jens Keilwagen; Beat Keller; David Konkin; Jamie Larsen; Qiang Li; Beata Myskow; Sudharsan Padmarasu; Nidhi Rawat; Ugur Sesiz; Sezgi Biyiklioglu-Kaya; Andy Sharpe; Hana Simkova; Ian Small; David Swarbreck; Helena Toegelova; Natalia Tsvetkova; Anatoly V. Voylokov; Jan Vrana; Eva Bauer; Hanna Bolibok-Bragoszewska; Jaroslav Dolezel; Anthony Hall; Jizeng Jia; Viktor Korzun; Andre Laroche; Xue-Feng Ma; Frank Ordon; Hakan Ozkan; Monika Rakoczy-Trojanowska; Uwe Scholz; Alan H. Schulman; Dorthe Siekmann; Stefan Stojalowski; Vijay K. Tiwari; Manuel Spannagl; Nils Stein

doi:10.1038/s41588-021-00807-0

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Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

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Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential

M. Timothy Rabanus-Wallace, Bernd Hackauf, Martin Mascher, Thomas Lux, Thomas Wicker, Heidrun Gundlach, Mariana Baez, Andreas Houben, Klaus F. X. Mayer, Liangliang Guo, …

Nature genetics, Vol.53(4), pp.564-573

01/04/2021

DOI: https://doi.org/10.1038/s41588-021-00807-0

PMCID: 8035072

PMID: 33737754

Abstract

Genetics & Heredity

Life Sciences & Biomedicine

Science & Technology

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.

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Title: Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential
Creators - without role: M. Timothy Rabanus-Wallace - Leibniz Institute of Plant Genetics and Crop Plant Research
Bernd Hackauf - Julius Kühn-Institut
Martin Mascher - Leibniz Institute of Plant Genetics and Crop Plant Research
Thomas Lux - Helmholtz Zentrum München
Thomas Wicker - University of Zurich
Heidrun Gundlach - Helmholtz Zentrum München
Mariana Baez - Universidade Federal de Pernambuco
Andreas Houben - Leibniz Institute of Plant Genetics and Crop Plant Research
Klaus F. X. Mayer - Plant
Liangliang Guo - Kansas State University
Jesse Poland - Kansas State University
Curtis J. Pozniak - University of Saskatchewan
Sean Walkowiak - University of Saskatchewan
Joanna Melonek - University of Western Australia
Coraline R. Praz - University of Zurich
Mona Schreiber - Leibniz Institute of Plant Genetics and Crop Plant Research
Hikmet Budak - Montana BioAg Inc, Durham, NC USA
Matthias Heuberger - ETH Zurich
Burkhard Steuernagel - John Innes Centre
Brande Wulff - John Innes Ctr, Norwich, Norfolk, England
Andreas Boerner - Plant
Brook Byrns - University of Saskatchewan
Jana Cizkova - Czech Academy of Sciences, Institute of Experimental Botany
D. Brian Fowler - University of Saskatchewan
Allan Fritz - Kansas State University
Axel Himmelbach - Leibniz Institute of Plant Genetics and Crop Plant Research
Gemy Kaithakottil - Earlham Institute
Jens Keilwagen - Julius Kühn-Institut
Beat Keller - University of Zurich
David Konkin - Saskatchewan Research Council
Jamie Larsen - Agr & Agri Food Canada, Harrow Res & Dev Ctr, Saskatoon, SK, Canada
Qiang Li - Huazhong Agricultural University
Beata Myskow - West Pomeranian University of Technology
Sudharsan Padmarasu - Leibniz Institute of Plant Genetics and Crop Plant Research
Nidhi Rawat - University of Maryland, College Park
Ugur Sesiz - Cukurova University
Sezgi Biyiklioglu-Kaya - Sabancı Üniversitesi
Andy Sharpe - University of Saskatchewan
Hana Simkova - Czech Academy of Sciences, Institute of Experimental Botany
Ian Small - University of Western Australia
David Swarbreck - Earlham Institute
Helena Toegelova - Czech Academy of Sciences, Institute of Experimental Botany
Natalia Tsvetkova - St Petersburg University
Anatoly V. Voylokov - Vavilov Institute of General Genetics
Jan Vrana - Czech Academy of Sciences, Institute of Experimental Botany
Eva Bauer - Technical University of Munich
Hanna Bolibok-Bragoszewska - Warsaw University of Life Sciences
Jaroslav Dolezel - Czech Academy of Sciences, Institute of Experimental Botany
Anthony Hall - Earlham Institute
Jizeng Jia - Chinese Academy of Agricultural Sciences
Viktor Korzun - KWS Saat
Andre Laroche - Agriculture and Agri-Food Canada
Xue-Feng Ma - Noble Research Institute
Frank Ordon - Julius Kühn-Institut
Hakan Ozkan - Cukurova University
Monika Rakoczy-Trojanowska - Warsaw University of Life Sciences
Uwe Scholz - Leibniz Institute of Plant Genetics and Crop Plant Research
Alan H. Schulman - Natural Resources Institute Finland
Dorthe Siekmann - HYBRO Saatzucht GmbH & Co KG, Isernhagen, Germany
Stefan Stojalowski - West Pomeranian University of Technology
Vijay K. Tiwari - University of Maryland, College Park
Manuel Spannagl - Helmholtz Zentrum München
Nils Stein - Leibniz Institute of Plant Genetics and Crop Plant Research
Publication Details: Nature genetics, Vol.53(4), pp.564-573
Publisher: NATURE PORTFOLIO
Number of pages: 17
Grant note: Agriculture and Agri-Food Canada International Collaboration Agri-Innovation Program; Agriculture & Agri Food Canada 2819103915 / German Federal Ministry of Food and Agriculture (BMEL) (WHEATSEQ) CTAG2 / Genome Prairie HYBRO Saatzucht GmbH Co. KG German Federal Ministry of Education and Research (BMBF); Federal Ministry of Education & Research (BMBF) DEC-2015/19/B/NZ9/00921; DEC-2014/14/E/NZ9/00285; 2015/17/B/NZ9/01694 / Polish National Science Centre 17-17564S / Czech Science Foundation; Grant Agency of the Czech Republic Montana Wheat and Barley Committee PGREL NN-0036 / Bundesamt fur Landwirtschaft, Bern KWS SAAT SE Co. KGaA CTAG2 / Genome Canada 2Blades Foundation National Research Council Canada's Wheat Flagship Program Province of Saskatchewan Agriculture Development Fund FKZ 031A536 / U.S. (project de.NBI) FKZ 0315946A / U.S. (project RYE-SELECT) Natural Resources Institute Finland Innofood Stategic Funds program Noble Research Institute, LLC CZ.02.1.01/0.0/0.0/16_019/0000827 / European Regional Development Fund; European Union (EU) HO 1779/30-1 / Deutsche Forschungsgemeinschaft; German Research Foundation (DFG) Julius Kuhn-Institute CE140100008 / Australian Research Council BB/P016855/1 / Biotechnology and Biological Sciences Research Council Designing Future Wheat program
Identifiers: 9941340008331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article