Unlocking the diversity of genebanks: whole-genome marker analysis of Swiss bread wheat and spelt

  • Thomas Müller
  • Beate Schierscher-Viret
  • Dario Fossati
  • Cécile Brabant
  • Arnold Schori
  • Beat Keller
  • Simon G. Krattinger
Original Article

Abstract

Key message

High-throughput genotyping of Swiss bread wheat and spelt accessions revealed differences in their gene pools and identified bread wheat landraces that were not used in breeding.

Abstract

Genebanks play a pivotal role in preserving the genetic diversity present among old landraces and wild progenitors of modern crops and they represent sources of agriculturally important genes that were lost during domestication and in modern breeding. However, undesirable genes that negatively affect crop performance are often co-introduced when landraces and wild crop progenitors are crossed with elite cultivars, which often limit the use of genebank material in modern breeding programs. A detailed genetic characterization is an important prerequisite to solve this problem and to make genebank material more accessible to breeding. Here, we genotyped 502 bread wheat and 293 spelt accessions held in the Swiss National Genebank using a 15K wheat SNP array. The material included both spring and winter wheats and consisted of old landraces and modern cultivars. Genome- and sub-genome-wide analyses revealed that spelt and bread wheat form two distinct gene pools. In addition, we identified bread wheat landraces that were genetically distinct from modern cultivars. Such accessions were possibly missed in the early Swiss wheat breeding program and are promising targets for the identification of novel genes. The genetic information obtained in this study is appropriate to perform genome-wide association studies, which will facilitate the identification and transfer of agriculturally important genes from the genebank into modern cultivars through marker-assisted selection.

Notes

Acknowledgements

We thank Simon Fluckiger and Helen Zbinden for technical assistance with DNA extraction and Prof. Eduard Akhunov for providing the genotypic data of the international wheat accessions. This work was supported by the Swiss Federal Office for Agriculture (BLW) in the framework of NAP-PGREL (national plan of action for the conservation and sustainable utilization of plant genetic resources). SGK is supported by an Ambizione fellowship of the Swiss National Science Foundation.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The authors declare that this study complies with the current laws of the countries in which the experiments were performed.

Supplementary material

122_2017_3010_MOESM1_ESM.csv (215 kb)
Supplementary material 1 (CSV 215 kb) Online resource 1—Accession and passport data Additional information about the accessions used in this study
122_2017_3010_MOESM2_ESM.csv (23.4 mb)
Supplementary material 2 (CSV 23999 kb) Online resource 2—Genotypes Genotypes of accessions
122_2017_3010_MOESM3_ESM.xlsx (19 kb)
Supplementary material 3 (XLSX 19 kb) Online resource 3—Similar accessions Additional information about highly similar accessions
122_2017_3010_MOESM4_ESM.csv (24 kb)
Supplementary material 4 (CSV 23 kb) Online resource 4—Winter bread wheat landraces with no overlap with cultivars Passport data of winter bread wheat landraces of circle A in Fig. 2
122_2017_3010_MOESM5_ESM.csv (15 kb)
Supplementary material 5 (CSV 14 kb) Online resource 5—Spring bread wheat landraces with only little overlap with cultivars Passport data of spring bread wheat landraces of circle B in Fig. 2
122_2017_3010_MOESM6_ESM.pdf (44 kb)
Supplementary material 6 (PDF 43 kb) Online resource 6—Phylogenetic tree Phylogenetic tree of all accessions. Tree was constructed using R packages adegenet and poppr. Color codes: purple: spring spelt, dark green: winter spelt, light green: wheat/spelt cross, yellow: wheat winter landrace, red: wheat winter cultivar, light blue: wheat spring landrace, dark blue: wheat spring cultivar
122_2017_3010_MOESM7_ESM.pdf (13.1 mb)
Supplementary material 7 (PDF 13424 kb) Online resource 7—Supporting figures and tables Supporting figures S1–S17 and supporting tables S1–S4

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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
  2. 2.Department of Plant Production SciencesAgroscope, ChanginsNyonSwitzerland
  3. 3.Biological and Environmental Sciences and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia

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