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.
Original language | English |
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Pages (from-to) | 564-573 |
Number of pages | 10 |
Journal | Nature Genetics |
Volume | 53 |
Issue number | 4 |
Early online date | 18 Mar 2021 |
DOIs | |
Publication status | Published - Apr 2021 |
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In: Nature Genetics, Vol. 53, No. 4, 04.2021, p. 564-573.
Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential
AU - Rabanus-Wallace, M. Timothy
AU - Hackauf, Bernd
AU - Mascher, Martin
AU - Lux, Thomas
AU - Wicker, Thomas
AU - Gundlach, Heidrun
AU - Baez, Mariana
AU - Houben, Andreas
AU - Mayer, Klaus F.X.
AU - Guo, Liangliang
AU - Poland, Jesse
AU - Pozniak, Curtis J.
AU - Walkowiak, Sean
AU - Melonek, Joanna
AU - Praz, Coraline R.
AU - Schreiber, Mona
AU - Budak, Hikmet
AU - Heuberger, Matthias
AU - Steuernagel, Burkhard
AU - Wulff, Brande
AU - Börner, Andreas
AU - Byrns, Brook
AU - Čížková, Jana
AU - Fowler, D. Brian
AU - Fritz, Allan
AU - Himmelbach, Axel
AU - Kaithakottil, Gemy
AU - Keilwagen, Jens
AU - Keller, Beat
AU - Konkin, David
AU - Larsen, Jamie
AU - Li, Qiang
AU - Myśków, Beata
AU - Padmarasu, Sudharsan
AU - Rawat, Nidhi
AU - Sesiz, Uğur
AU - Biyiklioglu-Kaya, Sezgi
AU - Sharpe, Andy
AU - Šimková, Hana
AU - Small, Ian
AU - Swarbreck, David
AU - Toegelová, Helena
AU - Tsvetkova, Natalia
AU - Voylokov, Anatoly V.
AU - Vrána, Jan
AU - Bauer, Eva
AU - Bolibok-Bragoszewska, Hanna
AU - Doležel, Jaroslav
AU - Hall, Anthony
AU - Jia, Jizeng
AU - Korzun, Viktor
AU - Laroche, André
AU - Ma, Xue-Feng
AU - Ordon, Frank
AU - Özkan, Hakan
AU - Rakoczy-Trojanowska, Monika
AU - Scholz, Uwe
AU - Schulman, Alan H.
AU - Siekmann, Dörthe
AU - Stojałowski, Stefan
AU - Tiwari, Vijay K.
AU - Spannagl, Manuel
AU - Stein, Nils
N1 - 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.
PY - 2021/4
Y1 - 2021/4
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85102987124&partnerID=8YFLogxK
U2 - 10.1038/s41588-021-00807-0
DO - 10.1038/s41588-021-00807-0
M3 - Article
C2 - 33737754
AN - SCOPUS:85102987124
SN - 1061-4036
VL - 53
SP - 564
EP - 573
JO - Nature Genetics
JF - Nature Genetics
IS - 4
ER -