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 & 14 others 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

Research output: Contribution to journalArticleResearchpeer-review

9 Citations (Scopus)

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 languageEnglish
Pages (from-to)319-326
Number of pages8
JournalNature Genetics
Volume51
Issue number2
Early online date12 Nov 2018
DOIs
Publication statusPrint publication - 1 Feb 2019
Externally publishedYes

Fingerprint

Hordeum
Genomics
Potyviridae
Genome-Wide Association Study
Sample Size
Genome
Food
Infection
Population

Keywords

  • Crops
  • Genetic variation
  • Genomics
  • Genotype
  • Hordeum
  • Oryza
  • Phenotype
  • Polymorphism

Cite this

Milner, S. G., Jost, M., Taketa, S., Mazón, E. R., Himmelbach, A., Oppermann, M., ... Stein, N. (2019). 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
Milner, Sara G ; Jost, Matthias ; Taketa, Shin ; Mazón, Elena Rey ; Himmelbach, Axel ; Oppermann, Markus ; Weise, Stephan ; Knüpffer, Helmut ; Basterrechea, Martín ; König, Patrick ; Schüler, Danuta ; Sharma, Rajiv ; Pasam, Raj K ; Rutten, Twan ; Guo, Ganggang ; Xu, Dongdong ; Zhang, Jing ; Herren, Gerhard ; Müller, Thomas ; Krattinger, Simon G ; Keller, Beat ; Jiang, Yong ; González, Maria Y ; Zhao, Yusheng ; Habekuß, Antje ; Färber, Sandra ; Ordon, Frank ; Lange, Matthias ; Börner, Andreas ; Graner, Andreas ; Reif, Jochen C ; Scholz, Uwe ; Mascher, Martin ; Stein, Nils. / Genebank genomics highlights the diversity of a global barley collection. In: Nature Genetics. 2019 ; Vol. 51, No. 2. pp. 319-326.
@article{82df68e975004d02971bf49ed296e776,
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'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.",
keywords = "Crops, Genetic variation, Genomics, Genotype, Hordeum, Oryza, Phenotype, Polymorphism",
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",
year = "2019",
month = "2",
day = "1",
doi = "10.1038/s41588-018-0266-x",
language = "English",
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 2019, '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

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

In: Nature Genetics, Vol. 51, No. 2, 01.02.2019, p. 319-326.

Research output: Contribution to journalArticleResearchpeer-review

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

PY - 2019/2/1

Y1 - 2019/2/1

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.

KW - Crops

KW - Genetic variation

KW - Genomics

KW - Genotype

KW - Hordeum

KW - Oryza

KW - Phenotype

KW - Polymorphism

U2 - 10.1038/s41588-018-0266-x

DO - 10.1038/s41588-018-0266-x

M3 - Article

VL - 51

SP - 319

EP - 326

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

IS - 2

ER -

Milner SG, Jost M, Taketa S, Mazón ER, Himmelbach A, Oppermann M et al. Genebank genomics highlights the diversity of a global barley collection. Nature Genetics. 2019 Feb 1;51(2):319-326. https://doi.org/10.1038/s41588-018-0266-x