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 Baez; Andreas Houben; Klaus F.X. Mayer; Liangliang Guo; Jesse Poland; Curtis J. Pozniak; Sean Walkowiak; Joanna Melonek; Coraline R. Praz; Mona Schreiber; Hikmet Budak; Matthias Heuberger; Burkhard Steuernagel; Brande Wulff; Andreas Börner; Brook Byrns; Jana Čížková; D. Brian Fowler; Allan 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; Natalia Tsvetkova; Anatoly V. Voylokov; Jan Vrána; Eva Bauer; Hanna Bolibok-Bragoszewska; Jaroslav Doležel; Anthony Hall; Jizeng Jia; Viktor Korzun; André Laroche; Xue Feng Ma; Frank Ordon; Hakan Özkan; Monika Rakoczy-Trojanowska; Uwe Scholz; Alan H. Schulman; Dörthe Siekmann; Stefan Stojałowski; Vijay K. Tiwari; Manuel Spannagl; Nils Stein

doi:10.1038/s41588-021-00807-0

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 Baez, Andreas Houben, Klaus F.X. Mayer, Liangliang Guo, Jesse Poland, Curtis J. Pozniak, Sean Walkowiak, Joanna Melonek, Coraline R. Praz, Mona Schreiber, Hikmet Budak, Matthias Heuberger, Burkhard Steuernagel, Brande WulffAndreas Börner, Brook Byrns, Jana Čížková, D. Brian Fowler, Allan 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, Natalia Tsvetkova, Anatoly V. Voylokov, Jan Vrána, Eva Bauer, Hanna Bolibok-Bragoszewska, Jaroslav Doležel, Anthony Hall, Jizeng Jia, Viktor Korzun, André Laroche, Xue Feng Ma, Frank Ordon, Hakan Özkan, Monika Rakoczy-Trojanowska, Uwe Scholz, Alan H. Schulman, Dörthe Siekmann, Stefan Stojałowski, Vijay K. Tiwari, Manuel Spannagl, Nils Stein

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139 Scopus citations

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 (US)
Pages (from-to)	564-573
Number of pages	10
Journal	Nature Genetics
Volume	53
Issue number	4
DOIs	https://doi.org/10.1038/s41588-021-00807-0
State	Published - Apr 1 2021
Externally published	Yes

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10.1038/s41588-021-00807-0

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Rabanus-Wallace, M. T., Hackauf, B., Mascher, M., Lux, T., Wicker, T., Gundlach, H., Baez, M., Houben, A., Mayer, K. F. X., Guo, L., Poland, J., Pozniak, C. J., Walkowiak, S., Melonek, J., Praz, C. R., Schreiber, M., Budak, H., Heuberger, M., Steuernagel, B., ... Stein, N. (2021). Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential. Nature Genetics, 53(4), 564-573. https://doi.org/10.1038/s41588-021-00807-0

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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{\textquoteright}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.",

author = "Rabanus-Wallace, {M. Timothy} and Bernd Hackauf and Martin Mascher and Thomas Lux and Thomas Wicker and Heidrun Gundlach and Mariana Baez and Andreas Houben and Mayer, {Klaus F.X.} and Liangliang Guo and Jesse Poland and Pozniak, {Curtis J.} and Sean Walkowiak and Joanna Melonek and Praz, {Coraline R.} and Mona Schreiber and Hikmet Budak and Matthias Heuberger and Burkhard Steuernagel and Brande Wulff and Andreas B{\"o}rner and Brook Byrns and Jana {\v C}{\'i}{\v z}kov{\'a} and Fowler, {D. Brian} and Allan Fritz and Axel Himmelbach and Gemy Kaithakottil and Jens Keilwagen and Beat Keller and David Konkin and Jamie Larsen and Qiang Li and Beata My{\'s}k{\'o}w and Sudharsan Padmarasu and Nidhi Rawat and Uğur Sesiz and Sezgi Biyiklioglu-Kaya and Andy Sharpe and Hana {\v S}imkov{\'a} and Ian Small and David Swarbreck and Helena Toegelov{\'a} and Natalia Tsvetkova and Voylokov, {Anatoly V.} and Jan Vr{\'a}na and Eva Bauer and Hanna Bolibok-Bragoszewska and Jaroslav Dole{\v z}el and Anthony Hall and Jizeng Jia and Viktor Korzun and Andr{\'e} Laroche and Ma, {Xue Feng} and Frank Ordon and Hakan {\"O}zkan and Monika Rakoczy-Trojanowska and Uwe Scholz and Schulman, {Alan H.} and D{\"o}rthe Siekmann and Stefan Stoja{\l}owski and Tiwari, {Vijay K.} and Manuel Spannagl and Nils Stein",

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doi = "10.1038/s41588-021-00807-0",

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Rabanus-Wallace, MT, Hackauf, B, Mascher, M, Lux, T, Wicker, T, Gundlach, H, Baez, M, Houben, A, Mayer, KFX, Guo, L, Poland, J, Pozniak, CJ, Walkowiak, S, Melonek, J, Praz, CR, Schreiber, M, Budak, H, Heuberger, M, Steuernagel, B, Wulff, B, Börner, A, Byrns, B, Čížková, J, Fowler, DB, Fritz, A, Himmelbach, A, Kaithakottil, G, Keilwagen, J, Keller, B, Konkin, D, Larsen, J, Li, Q, Myśków, B, Padmarasu, S, Rawat, N, Sesiz, U, Biyiklioglu-Kaya, S, Sharpe, A, Šimková, H, Small, I, Swarbreck, D, Toegelová, H, Tsvetkova, N, Voylokov, AV, Vrána, J, Bauer, E, Bolibok-Bragoszewska, H, Doležel, J, Hall, A, Jia, J, Korzun, V, Laroche, A, Ma, XF, Ordon, F, Özkan, H, Rakoczy-Trojanowska, M, Scholz, U, Schulman, AH, Siekmann, D, Stojałowski, S, Tiwari, VK, Spannagl, M & Stein, N 2021, 'Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential', Nature Genetics, vol. 53, no. 4, pp. 564-573. https://doi.org/10.1038/s41588-021-00807-0

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 - Generated from Scopus record by KAUST IRTS on 2022-09-13

PY - 2021/4/1

Y1 - 2021/4/1

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.

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SN - 1546-1718

VL - 53

SP - 564

EP - 573

JO - Nature Genetics

JF - Nature Genetics

IS - 4

ER -

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

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