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.

Aquatic and Crop Resource Development National Research Council Saskatoon Saskatchewan Canada

Canadian Grain Commission Winnipeg Manitoba Canada

Chinese Academy of Agricultural Sciences Beijing China

Earlham Institute Norwich UK

ETH Zürich Zürich Switzerland

Federal University of Pernambuco Pernambuco Brazil

Georg August Universität Göttingen Göttingen Germany

Harrow Research and Development Centre Agriculture and Agri Food Canada Saskatoon Saskatchewan Canada

Huazhong Agricultural University Wuhan China

HYBRO Saatzucht GmbH and Co KG Isernhagen Germany

Institute for Biosafety in Plant Biotechnology Julius Kühn Institut Quedlinburg Germany

Institute for Breeding Research on Agricultural Crops Julius Kühn Institut Sanitz Germany

Institute for Resistance Research and Stress Tolerance Julius Kühn Institute Quedlinburg Germany

Institute of Biotechnology and Viikki Plant Science Centre University of Helsinki Helsinki Finland

Institute of Experimental Botany of the Czech Academy of Sciences Olomouc Czech Republic

John Innes Centre Norwich UK

Kansas State University Manhattan KS USA

KWS SAAT SE and Co Einbeck Germany

Leibniz Institute of Plant Genetics and Crop Plant Research Seeland Germany

Lethbridge Research and Development Centre Agriculture and Agri Food Canada Lethbridge Alberta Canada

Montana BioAg Inc Durham NC USA

Noble Research Institute Ardmore OK USA

Plant Genome and Systems Biology Helmholtz Center Munich Neuherberg Germany

Production Systems Natural Resources Institute Finland Helsinki Finland

Sabanci University Tuzla Turkey

Saint Petersburg State University Saint Petersburg Russia

Technical University Munich Munich Germany

The University of Western Australia Crawley Western Australia Australia

TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany

University of Cukurova Cukurova Turkey

University of Maryland College Park MD USA

University of Saskatchewan Saskatoon Saskatchewan Canada

University of Zürich Zurich Switzerland

Vavilov Institute of General Genetics Russian Academy of Sciences Saint Petersburg Russia

Warsaw University of Life Sciences SGGW Warsaw Poland

West Pomeranian University of Technology Szczecin Szczecin Poland

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The genetic mechanism of B chromosome drive in rye illuminated by chromosome-scale assembly

DArTseq genotyping facilitates the transfer of "exotic" chromatin from a Secale cereale × S. strictum hybrid into wheat

Flow Cytometric Analysis and Sorting of Plant Chromosomes

Flow Sorting-Assisted Optical Mapping

An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

A DUF3494 ice-binding protein with a root cap domain in a streptophyte glacier ice alga

Isolation and Sequencing of Chromosome Arm 7RS of Rye, Secale cereale

Long-read sequence assembly: a technical evaluation in barley

A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes