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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Plant Sci. | doi: 10.3389/fpls.2019.01133

Detecting large chromosomal modifications using short read data from genotyping-by-sequencing

  • 1Julius Kühn-Institut, Germany
  • 2Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Germany
  • 3Vavilov Institute of General Genetics, Russian Academy of Sciences, Russia
  • 4Helmholtz Center Munich, Germany
  • 5Global Crop Diversity Trust, Germany
  • 6Institute for Breeding Research on Agricultural Crops, Federal Research Center for Cultivated Plants, Julius Kühn Institute, Germany

Markers linked to agronomic traits are of the prerequisite for molecular breeding. Genotyping-by-sequencing (GBS) data enables to detect small polymorphisms including single nucleotide polymorphisms (SNPs) and short insertions or deletions (InDels) that can be used, for instance, for marker-assisted selection, population genetics, and genome-wide association studies.

Here, we aim at detecting large chromosomal modifications in barley and wheat based on GBS data. These modifications could be duplications, deletions, substitutions including introgressions as well as alterations of DNA methylation. We demonstrate that GBS coverage analysis is capable to detect Hordeum vulgare/Hordeum bulbosum introgression lines. Furthermore, we identify large chromosomal modifications in barley and wheat collections.

Hence, large chromosomal modifications, including introgressions and copy number variations (CNV), can be detected easily and can be used as markers in research and breeding without additional wet-lab experiments.

Keywords: Crop wild relatives, characterization and utilization of plant genetic resources, translocation, Methylation-sensitive restriction enzyme, coverage, bioinformatics, Breeding, Genebank, Copy number variation (CNV )

Received: 31 Jan 2019; Accepted: 16 Aug 2019.

Edited by:

Guijun Yan, University of Western Australia, Australia

Reviewed by:

Songlin Hu, Monsanto Company, United States
Thomas Nussbaumer, Institut für Umweltmedizin (IEM), Helmholtz Zentrum München, Helmholtz-Gemeinschaft Deutscher Forschungszentren (HZ), Germany  

Copyright: © 2019 Keilwagen, Lehnert, Berner, Beier, Scholz, Himmelbach, Stein, Badaeva, Lang, Kilian, Hackauf and Perovic. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Jens Keilwagen, Julius Kühn-Institut, Quedlinburg, Germany, jens.keilwagen@julius-kuehn.de
Dr. Bernd Hackauf, Institute for Breeding Research on Agricultural Crops, Federal Research Center for Cultivated Plants, Julius Kühn Institute, Sanitz, Germany, bernd.hackauf@julius-kuehn.de