Genebank genomics highlights the diversity of a global barley collection

Sara G. Milner; Matthias Jost; Shin Taketa; Elena Rey Mazón; Axel Himmelbach; Markus Oppermann; Stephan Weise; Helmut Knüpffer; Martín Basterrechea; Patrick König; Danuta Schüler; Rajiv Sharma; Raj K. Pasam; Twan Rutten; Ganggang Guo; Dongdong Xu; Jing Zhang; Gerhard Herren; Thomas Müller; Simon G. Krattinger; Beat Keller; Yong Jiang; Maria Y. González; Yusheng Zhao; Antje Habekuß; Sandra Färber; Frank Ordon; Matthias Lange; Andreas Börner; Andreas Graner; Jochen C. Reif; Uwe Scholz; Martin Mascher; Nils Stein

doi:10.1038/s41588-018-0266-x

Genebank genomics highlights the diversity of a global barley collection

Sara G. Milner, Matthias Jost, Shin Taketa, Elena Rey Mazón, Axel Himmelbach, Markus Oppermann, Stephan Weise, Helmut Knüpffer, Martín Basterrechea, Patrick König, Danuta Schüler, Rajiv Sharma, Raj K. Pasam, Twan Rutten, Ganggang Guo, Dongdong Xu, Jing Zhang, Gerhard Herren, Thomas Müller, Simon G. KrattingerBeat Keller, Yong Jiang, Maria Y. González, Yusheng Zhao, Antje Habekuß, Sandra Färber, Frank Ordon, Matthias Lange, Andreas Börner, Andreas Graner, Jochen C. Reif, Uwe Scholz, Martin Mascher, Nils Stein

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Abstract

Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world’s major genebanks. Our large sample size and dense marker data afford great power for genome-wide association scans. We detect known and novel loci underlying morphological traits differentiating barley genepools, find evidence for convergent selection for barbless awns in barley and rice and show that a major-effect resistance locus conferring resistance to bymovirus infection has been favored by traditional farmers. This study outlines future directions for genomics-assisted genebank management and the utilization of germplasm collections for linking natural variation to human selection during crop evolution.

Original language	English (US)
Pages (from-to)	319-326
Number of pages	8
Journal	Nature Genetics
Volume	51
Issue number	2
DOIs	https://doi.org/10.1038/s41588-018-0266-x
State	Published - Nov 12 2018

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We thank G. Matzig, J. Pohl, M. Ziems, C. Fricke, M. Kretschmann, S. König, I. Walde, G. Schütze, A. Fiebig, J. Bauernfeind, T. Münch and D. Grau for technical assistance and G. Proeseler for initiating the long-term virus testing. We are grateful to H. de Beukelaer for Corehunter support. We thank B. Schierscher-Viret from the Swiss national genebank for providing seeds and K. Lipfert for artwork. This work was supported by a grant from the Leibniz Association to N.S., U.S., H.K., A.B., A.G. and J.C.R. (Pakt für Forschung und Innovation: SAW-2015-IPK-1 ‘BRIDGE’); by the German Ministry of Education and Research (BMBF; grant 031A536 ‘de.NBI’ to U.S.); by the Young Elite Scientists Sponsorship Program (2015QNRC001) from the China Association for Science and Technology (CAST); by a grant from the China Scholarship Council to G.G.; by funding from the China Agriculture Research System (CARS-05) and the Agricultural Science and Technology Innovation Program to J.Z.; and by the Swiss Federal Office for Agriculture in the framework of the National Plan of Action for the conservation and sustainable utilization of plant genetic resources (NAP-PGREL). S.G.M. acknowledges support from the German Academic Exchange service (DAAD) through a Leibniz-DAAD fellowship. Y.J. and M.Y.G. were supported by BMBF grants 031B0184A and 031B0190A, respectively. S.F. was supported by BMBF grants to F.O. and A.Habekuß (ViReCrop, FKZ: 0315708B; COBRA, FKZ: 031A323B).

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Milner, S. G., Jost, M., Taketa, S., Mazón, E. R., Himmelbach, A., Oppermann, M., Weise, S., Knüpffer, H., Basterrechea, M., König, P., Schüler, D., Sharma, R., Pasam, R. K., Rutten, T., Guo, G., Xu, D., Zhang, J., Herren, G., Müller, T., ... Stein, N. (2018). Genebank genomics highlights the diversity of a global barley collection. Nature Genetics, 51(2), 319-326. https://doi.org/10.1038/s41588-018-0266-x

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title = "Genebank genomics highlights the diversity of a global barley collection",

abstract = "Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world{\textquoteright}s major genebanks. Our large sample size and dense marker data afford great power for genome-wide association scans. We detect known and novel loci underlying morphological traits differentiating barley genepools, find evidence for convergent selection for barbless awns in barley and rice and show that a major-effect resistance locus conferring resistance to bymovirus infection has been favored by traditional farmers. This study outlines future directions for genomics-assisted genebank management and the utilization of germplasm collections for linking natural variation to human selection during crop evolution.",

author = "Milner, {Sara G.} and Matthias Jost and Shin Taketa and Maz{\'o}n, {Elena Rey} and Axel Himmelbach and Markus Oppermann and Stephan Weise and Helmut Kn{\"u}pffer and Mart{\'i}n Basterrechea and Patrick K{\"o}nig and Danuta Sch{\"u}ler and Rajiv Sharma and Pasam, {Raj K.} and Twan Rutten and Ganggang Guo and Dongdong Xu and Jing Zhang and Gerhard Herren and Thomas M{\"u}ller and Krattinger, {Simon G.} and Beat Keller and Yong Jiang and Gonz{\'a}lez, {Maria Y.} and Yusheng Zhao and Antje Habeku{\ss} and Sandra F{\"a}rber and Frank Ordon and Matthias Lange and Andreas B{\"o}rner and Andreas Graner and Reif, {Jochen C.} and Uwe Scholz and Martin Mascher and Nils Stein",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We thank G. Matzig, J. Pohl, M. Ziems, C. Fricke, M. Kretschmann, S. K{\"o}nig, I. Walde, G. Sch{\"u}tze, A. Fiebig, J. Bauernfeind, T. M{\"u}nch and D. Grau for technical assistance and G. Proeseler for initiating the long-term virus testing. We are grateful to H. de Beukelaer for Corehunter support. We thank B. Schierscher-Viret from the Swiss national genebank for providing seeds and K. Lipfert for artwork. This work was supported by a grant from the Leibniz Association to N.S., U.S., H.K., A.B., A.G. and J.C.R. (Pakt f{\"u}r Forschung und Innovation: SAW-2015-IPK-1 {\textquoteleft}BRIDGE{\textquoteright}); by the German Ministry of Education and Research (BMBF; grant 031A536 {\textquoteleft}de.NBI{\textquoteright} to U.S.); by the Young Elite Scientists Sponsorship Program (2015QNRC001) from the China Association for Science and Technology (CAST); by a grant from the China Scholarship Council to G.G.; by funding from the China Agriculture Research System (CARS-05) and the Agricultural Science and Technology Innovation Program to J.Z.; and by the Swiss Federal Office for Agriculture in the framework of the National Plan of Action for the conservation and sustainable utilization of plant genetic resources (NAP-PGREL). S.G.M. acknowledges support from the German Academic Exchange service (DAAD) through a Leibniz-DAAD fellowship. Y.J. and M.Y.G. were supported by BMBF grants 031B0184A and 031B0190A, respectively. S.F. was supported by BMBF grants to F.O. and A.Habeku{\ss} (ViReCrop, FKZ: 0315708B; COBRA, FKZ: 031A323B).",

year = "2018",

month = nov,

day = "12",

doi = "10.1038/s41588-018-0266-x",

language = "English (US)",

volume = "51",

pages = "319--326",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Research",

number = "2",

}

Milner, SG, Jost, M, Taketa, S, Mazón, ER, Himmelbach, A, Oppermann, M, Weise, S, Knüpffer, H, Basterrechea, M, König, P, Schüler, D, Sharma, R, Pasam, RK, Rutten, T, Guo, G, Xu, D, Zhang, J, Herren, G, Müller, T, Krattinger, SG, Keller, B, Jiang, Y, González, MY, Zhao, Y, Habekuß, A, Färber, S, Ordon, F, Lange, M, Börner, A, Graner, A, Reif, JC, Scholz, U, Mascher, M & Stein, N 2018, 'Genebank genomics highlights the diversity of a global barley collection', Nature Genetics, vol. 51, no. 2, pp. 319-326. https://doi.org/10.1038/s41588-018-0266-x

TY - JOUR

T1 - Genebank genomics highlights the diversity of a global barley collection

AU - Milner, Sara G.

AU - Jost, Matthias

AU - Taketa, Shin

AU - Mazón, Elena Rey

AU - Himmelbach, Axel

AU - Oppermann, Markus

AU - Weise, Stephan

AU - Knüpffer, Helmut

AU - Basterrechea, Martín

AU - König, Patrick

AU - Schüler, Danuta

AU - Sharma, Rajiv

AU - Pasam, Raj K.

AU - Rutten, Twan

AU - Guo, Ganggang

AU - Xu, Dongdong

AU - Zhang, Jing

AU - Herren, Gerhard

AU - Müller, Thomas

AU - Krattinger, Simon G.

AU - Keller, Beat

AU - Jiang, Yong

AU - González, Maria Y.

AU - Zhao, Yusheng

AU - Habekuß, Antje

AU - Färber, Sandra

AU - Ordon, Frank

AU - Lange, Matthias

AU - Börner, Andreas

AU - Graner, Andreas

AU - Reif, Jochen C.

AU - Scholz, Uwe

AU - Mascher, Martin

AU - Stein, Nils

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We thank G. Matzig, J. Pohl, M. Ziems, C. Fricke, M. Kretschmann, S. König, I. Walde, G. Schütze, A. Fiebig, J. Bauernfeind, T. Münch and D. Grau for technical assistance and G. Proeseler for initiating the long-term virus testing. We are grateful to H. de Beukelaer for Corehunter support. We thank B. Schierscher-Viret from the Swiss national genebank for providing seeds and K. Lipfert for artwork. This work was supported by a grant from the Leibniz Association to N.S., U.S., H.K., A.B., A.G. and J.C.R. (Pakt für Forschung und Innovation: SAW-2015-IPK-1 ‘BRIDGE’); by the German Ministry of Education and Research (BMBF; grant 031A536 ‘de.NBI’ to U.S.); by the Young Elite Scientists Sponsorship Program (2015QNRC001) from the China Association for Science and Technology (CAST); by a grant from the China Scholarship Council to G.G.; by funding from the China Agriculture Research System (CARS-05) and the Agricultural Science and Technology Innovation Program to J.Z.; and by the Swiss Federal Office for Agriculture in the framework of the National Plan of Action for the conservation and sustainable utilization of plant genetic resources (NAP-PGREL). S.G.M. acknowledges support from the German Academic Exchange service (DAAD) through a Leibniz-DAAD fellowship. Y.J. and M.Y.G. were supported by BMBF grants 031B0184A and 031B0190A, respectively. S.F. was supported by BMBF grants to F.O. and A.Habekuß (ViReCrop, FKZ: 0315708B; COBRA, FKZ: 031A323B).

PY - 2018/11/12

Y1 - 2018/11/12

N2 - Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world’s major genebanks. Our large sample size and dense marker data afford great power for genome-wide association scans. We detect known and novel loci underlying morphological traits differentiating barley genepools, find evidence for convergent selection for barbless awns in barley and rice and show that a major-effect resistance locus conferring resistance to bymovirus infection has been favored by traditional farmers. This study outlines future directions for genomics-assisted genebank management and the utilization of germplasm collections for linking natural variation to human selection during crop evolution.

AB - Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world’s major genebanks. Our large sample size and dense marker data afford great power for genome-wide association scans. We detect known and novel loci underlying morphological traits differentiating barley genepools, find evidence for convergent selection for barbless awns in barley and rice and show that a major-effect resistance locus conferring resistance to bymovirus infection has been favored by traditional farmers. This study outlines future directions for genomics-assisted genebank management and the utilization of germplasm collections for linking natural variation to human selection during crop evolution.

UR - http://hdl.handle.net/10754/629868

UR - https://www.nature.com/articles/s41588-018-0266-x

UR - http://www.scopus.com/inward/record.url?scp=85056617315&partnerID=8YFLogxK

U2 - 10.1038/s41588-018-0266-x

DO - 10.1038/s41588-018-0266-x

M3 - Article

SN - 1061-4036

VL - 51

SP - 319

EP - 326

JO - Nature Genetics

JF - Nature Genetics

IS - 2

ER -

Genebank genomics highlights the diversity of a global barley collection

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