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 Báez, Andreas Houben, Klaus Mayer, Liangliang Guo, Jesse Poland, Curtis Pozniak, Sean Walkowiak, Joanna Melonek, Coraline R. Praz, Mona Schreiber, Hikmet Budak, Matthias Heuberger, Burkhard Steuernagel, Brande B. H. Wulff, Andreas Börner, Brook Byrns, Jana Čížková, Brian Fowler, Allan K. Fritz, Axel Himmelbach, Gemy Kaithakottil, Jens Keilwagen, Beat Keller, David Konkin, Jamie Larsen, Qiang Li, Beata Myśków, Sudharsan Padmarasu, Nidhi Rawat, Uğur Sesiz, Sezgi Biyiklioglu-Kaya, Andy Sharpe, Hana Šimková, Ian Small, David Swarbreck, Helena Toegelová, Н. В. Цветкова, A. V. Voylokov, Jan Vrána, Eva Bauer, Hanna Bolibok-Brągoszewska, Jaroslav Doležel, Anthony Hall, Jizeng Jia, Viktor Korzun, André Laroche, Xuefeng Ma, Frank Ordon, Hakan Özkan, Monika Rakoczy‐Trojanowska, Uwe Scholz, Alan H. Schulman, Dörthe Siekmann, Stefan Stojałowski, Vijay Tiwari, M. Spannagl, Nils Stein
Abstract
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.