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Rabanus-Wallace, M. Timothy, Hackauf, Bernd, Mascher, Martin, Lux, Thomas, Wicker, Thomas, Gundlach, Heidrun, Baez, Mariana, Houben, Andreas, Mayer, Klaus F.X., Guo, Liangliang, Poland, Jesse, Pozniak, Curtis J., Walkowiak, Sean, Melonek, Joanna, Praz, Coraline R., Schreiber, Mona, Budak, Hikmet, Heuberger, Matthias, Steuernagel, Burkhard, Wulff, Brande, Börner, Andreas, Byrns, Brook, Čížková, Jana, Fowler, D. Brian, Fritz, Allan, Himmelbach, Axel, Kaithakottil, Gemy, Keilwagen, Jens, Keller, Beat, Konkin, David, Larsen, Jamie, Li, Qiang, Myśków, Beata, Padmarasu, Sudharsan, Rawat, Nidhi, Sesiz, Uğur, Biyiklioglu-Kaya, Sezgi, Sharpe, Andy, Šimková, Hana, Small, Ian, Swarbreck, David, Toegelová, Helena, Tsvetkova, Natalia, Voylokov, Anatoly V., Vrána, Jan, Bauer, Eva, Bolibok-Bragoszewska, Hanna, Doležel, Jaroslav, Hall, Anthony 
ORCID: https://orcid.org/0000-0002-1806-020X, Jia, Jizeng, Korzun, Viktor, Laroche, André, Ma, Xue-Feng, Ordon, Frank, Özkan, Hakan, Rakoczy-Trojanowska, Monika, Scholz, Uwe, Schulman, Alan H., Siekmann, Dörthe, Stojałowski, Stefan, Tiwari, Vijay K., Spannagl, Manuel and Stein, Nils
(2021)
Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential.
Nature Genetics, 53 (4).
pp. 564-573.
ISSN 1061-4036
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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.
| Item Type: | Article |
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| Additional Information: | Data availability statement: The ‘Lo7’ assembly and gene feature annotation data are available via e!DAL at https://doi.org/10.5447/ipk/2020/33 and https://doi.org/10.5447/ipk/2020/29. The visual suite of resources for assembly assessment are stored at https://doi.org/10.5447/ipk/2020/32. Raw sequence data generated in the course of the study are available at European Nucleotide Archive (ENA) with accession numbers PRJEB32636 (PE and MP data for assembly), PRJEB32574 and PRJEB34626 (Hi-C), PRJEB34439 (10x), PRJEB32587 (CSS), PRJEB35392 (GBS data) and PRJEB35461 (RNAseq and IsoSeq for annotation of ‘Lo7’). Chromium 10x and RNAseq data for ‘Puma’ and ‘Norstar’ are available at PRJNA564622. The SNP matrix used for rye population genetic analyses is available via e!DAL at https://doi.org/10.5447/ipk/2020/31. GBS and sequence data generated for the USDA and CIMMYT wheat diversity panels are available at ENA with accession numbers PRJNA566410, PRJNA566408 and PRJNA566409. Optical map data and alignments are available via e!DAL at https://doi.org/10.5447/ipk/2020/30. High-stringency transposable element annotations (used for evolutionary analyses) are given in Supplementary Table 10, while the larger, low-stringency annotations (used for assembly quality comparisons) are available via e!DAL at https://doi.org/10.5447/ipk/2020/34. Code availability: The custom miRNA manipulation scripts used in miRNA annotation (SumirFind.pl, SumirFold.pl, SumirLocate_v2.py and Sumircreen_v2.py) are available at https://github.com/hikmetbudak/miRNA-annotation. Two custom scripts used for parsing BLAST output (get_alleles_at_position.c and blast_to_snps.c) are available at https://github.com/mtrw/tim_bioinfo_tools and custom R functions extending or modifying functions of the TRITEX assembly pipeline (version corresponding to commit ID 2898e74) are available at https://github.com/mtrw/Sc_genome_assembly. The custom tool used to demultiplex wheat panel GBS data (splitgbs.c) is available at github.com/umngao/splitgbs. Funding information: Research for this project was supported by funding from: the Czech Science Foundation (grant no. 17-17564S) to H.S.; the Agriculture and Agri-Food Canada International Collaboration Agri-Innovation Program to A.L.; the Natural Resources Institute Finland Innofood Stategic Funds program to A.S.; the Biotechnology and Biological Sciences Research Council Designing Future Wheat program (grant no. BB/P016855/1) to A. Hall; the German Federal Ministry of Education and Research (BMBF) to K.F.X.M. and U.S. (project de.NBI no. FKZ 031A536) and E.B. (project RYE-SELECT no. FKZ 0315946A); the German Federal Ministry of Food and Agriculture (BMEL) (WHEATSEQ no. 2819103915) to K.F.X.M.; HYBRO Saatzucht GmbH & Co. KG to D.S.; the European Regional Development Fund’s plants as a tool for sustainable global development project (grant no. CZ.02.1.01/0.0/0.0/16_019/0000827) to J.D.; the 2Blades Foundation to B.W.; the Julius Kühn-Institute to B.H. and F.O.; KWS SAAT SE & Co. KGaA to V.K.; the Deutsche Forschungsgemeinschaft (grant no. HO 1779/30-1) to A. Houben; the Montana Wheat and Barley Committee to H.B.; the Noble Research Institute, LLC to X.-F. M.; the Australian Research Council (grant no. CE140100008) to I.S. and J.M.; Genome Canada and Genome Prairie (grant no. CTAG2) to C.J.P.; the National Research Council Canada’s Wheat Flagship Program to D.K. and A.S.; the Province of Saskatchewan Agriculture Development Fund to D.B.F.; the Bundesamt für Landwirtschaft, Bern (grant no. PGREL NN-0036) to B.K.; the Polish National Science Centre (grant nos. DEC-2015/19/B/NZ9/00921, DEC-2014/14/E/NZ9/00285 and 2015/17/B/NZ9/01694) to M.R.-T., H.B.-B., S.S. and B.M. |
| Uncontrolled Keywords: | genetics ,/dk/atira/pure/subjectarea/asjc/1300/1311 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 31 Oct 2024 17:30 |
| Last Modified: | 01 Nov 2024 12:31 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97403 |
| DOI: | 10.1038/s41588-021-00807-0 |
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