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

Affiliation
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
Rabanus-Wallace, M. Timothy;
GND
121322327
Affiliation
Julius Kühn-Institute (JKI), Institute for Breeding Research on Agricultural Crops, Germany
Hackauf, Bernd;
GND
1052596703
Affiliation
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
Mascher, Martin;
Affiliation
Plant Genome and Systems Biology (PGSB), Helmholtz-Center Munich, Neuherberg, Germany
Lux, Thomas;
GND
1188437925
Affiliation
University of Zürich, Zurich, Switzerland
Wicker, Thomas;
GND
172569370
Affiliation
Plant Genome and Systems Biology (PGSB), Helmholtz-Center Munich, Neuherberg, Germany
Gundlach, Heidrun;
Affiliation
Federal University of Pernambuco, Pernambuco, Brazil
Baez, Mariana;
Affiliation
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
Houben, Andreas;
GND
120210363
Affiliation
Plant Genome and Systems Biology (PGSB), Helmholtz-Center Munich, Neuherberg, Germany; Technical University Munich, Munich, Germany
Mayer, Klaus F. X.;
Affiliation
Kansas State University, Manhattan, KS, USA
Guo, Liangliang;
Affiliation
Kansas State University, Manhattan, KS, USA
Poland, Jesse;
Affiliation
University of Saskatchewan, Saskatoon, Saskatchewan, Canada
Pozniak, Curtis J.;
Affiliation
University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Canadian Grain Commission, Winnipeg, Manitoba, Canada
Walkowiak, Sean;
GND
143744461
Affiliation
The University of Western Australia, Crawley, Western Australia, Australia
Melonek, Joanna;
GND
1194064825
Affiliation
University of Zürich, Zurich, Switzerland
Praz, Coraline R.;
Affiliation
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
Schreiber, Mona;
Affiliation
Montana BioAg Inc, Durham, NC, USA
Budak, Hikmet;
Affiliation
ETH Zürich, Zürich, Switzerland
Heuberger, Matthias;
Affiliation
John Innes Centre, Norwich, UK
Steuernagel, Burkhard;
Affiliation
John Innes Centre, Norwich, UK
Wulff, Brande;
Affiliation
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
Börner, Andreas;
Affiliation
University of Saskatchewan, Saskatoon, Saskatchewan, Canada
Byrns, Brook;
Affiliation
Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
Čížková, Jana;
Affiliation
University of Saskatchewan, Saskatoon, Saskatchewan, Canada
Fowler, D. Brian;
Affiliation
Kansas State University, Manhattan, KS, USA
Fritz, Allan;
Affiliation
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
Himmelbach, Axel;
Affiliation
Earlham Institute, Norwich, UK
Kaithakottil, Gemy;
GND
1013858662
Affiliation
Julius Kühn-Institute (JKI), Institute for Biosafety in Plant Biotechnology, Germany
Keilwagen, Jens;
GND
171508513
Affiliation
University of Zürich, Zurich, Switzerland
Keller, Beat;
Affiliation
Aquatic and Crop Resource Development, National Research Council, Saskatoon, Saskatchewan, Canada
Konkin, David;
Affiliation
Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
Larsen, Jamie;
Affiliation
Huazhong Agricultural University, Wuhan, China
Li, Qiang;
Affiliation
West Pomeranian University of Technology Szczecin, Szczecin, Poland
Myśków, Beata;
Affiliation
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
Padmarasu, Sudharsan;
Affiliation
University of Maryland, College Park, MD, USA
Rawat, Nidhi;
Affiliation
University of Cukurova, Cukurova, Turkey
Sesiz, Uğur;
Affiliation
Sabanci University, Tuzla, Turkey
Biyiklioglu-Kaya, Sezgi;
Affiliation
University of Saskatchewan, Saskatoon, Saskatchewan, Canada
Sharpe, Andy;
Affiliation
Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
Šimková, Hana;
Affiliation
The University of Western Australia, Crawley, Western Australia, Australia
Small, Ian;
Affiliation
Earlham Institute, Norwich, UK
Swarbreck, David;
Affiliation
Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
Toegelová, Helena;
Affiliation
Saint Petersburg State University, Saint Petersburg, Russia
Tsvetkova, Natalia;
Affiliation
Vavilov Institute of General Genetics, Russian Academy of Sciences, Saint Petersburg, Russia
Voylokov, Anatoly V.;
Affiliation
Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
Vrána, Jan;
Affiliation
TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
Bauer, Eva;
Affiliation
Warsaw University of Life Sciences-SGGW, Warsaw, Poland
Bolibok-Bragoszewska, Hanna;
GND
132721090
Affiliation
Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
Doležel, Jaroslav;
Affiliation
Earlham Institute, Norwich, UK
Hall, Anthony;
Affiliation
Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
Jia, Jizeng;
GND
1177839385
Affiliation
KWS SAAT SE & Co, Einbeck, Germany
Korzun, Viktor;
Affiliation
Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada
Laroche, André;
Affiliation
Noble Research Institute, Ardmore, OK, USA
Ma, Xue-Feng;
GND
172295300
Affiliation
Julius Kühn-Institute (JKI), Institute for Resistance Research and Stress Tolerance, Germany
Ordon, Frank;
Affiliation
University of Cukurova, Cukurova, Turkey
Özkan, Hakan;
Affiliation
Warsaw University of Life Sciences-SGGW, Warsaw, Poland
Rakoczy-Trojanowska, Monika;
Affiliation
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
Scholz, Uwe;
Affiliation
Production Systems, Natural Resources Institute Finland (LUKE), Helsinki, Finland; Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
Schulman, Alan H.;
GND
1175588393
Affiliation
HYBRO Saatzucht GmbH & Co. KG, Isernhagen, Germany
Siekmann, Dörthe;
Affiliation
West Pomeranian University of Technology Szczecin, Szczecin, Poland
Stojałowski, Stefan;
Affiliation
University of Maryland, College Park, MD, USA
Tiwari, Vijay K.;
Affiliation
Plant Genome and Systems Biology (PGSB), Helmholtz-Center Munich, Neuherberg, Germany
Spannagl, Manuel;
GND
120077000
Affiliation
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany; Georg-August-Universität Göttingen, Göttingen, Germany
Stein, Nils

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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