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Chromosomal Genomics of Barley

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The Barley Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

Barley (Hordeum vulgare L.) genome has been difficult to analyze, map, and sequence due to its size (~5 Gb/1C) and high repeat content (over 80%). Flow cytometric sorting of plant mitotic chromosomes, which was first reported in 1984, provided an approach for reduction of complexity to simplify genome analysis and laid the basis of a new discipline—chromosomal genomics. Chromosome flow sorting in barley was established in 1999 and since that time played an important role in genomics of this crop. Initially, flow-sorted chromosomes facilitated assignment of DNA markers to chromosomes or their regions, providing a complement and validation to genetic mapping. A protocol for multiple displacement amplification of chromosomal DNA, established for mapping on Illumina genotyping platform, was shown compatible with next-generation sequencing. This enabled identification of gene content of individual barley chromosomes and establishment of their putative order by an innovative approach, which was later followed also in wheat and rye. Preparation of high-molecular-weight DNA from flow-sorted chromosomes, while developed in barley, opened avenues to constructing chromosome-specific BAC libraries in bread wheat and, more recently, generating optical maps in several cereal species. Thus, the development of a chromosome genomics toolbox contributed to the advances in genomics of other important crops, in addition to barley. Chromosomal genomics plays an important role also in the post-sequencing era by enabling cost-efficient gene cloning, analyzing chromatin structure by chromatin conformation capture approaches, and characterizing the proteome of mitotic chromosomes.

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Abbreviations

BAC:

Bacterial artificial chromosome

HMW DNA:

High-molecular-weight DNA

FISH:

Fluorescence in situ hybridization

FISHIS:

Fluorescence in situ hybridization in suspension

MDA:

Multiple displacement amplification

NGS:

Next-generation sequencing

OPA:

Oligonucleotide Pool Assay

RFLP:

Restriction fragment length polymorphism

STS:

Sequence-tagged site

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Acknowledgements

We thank our colleagues Helena Toegelová, Tomáš Beseda, and Beáta Petrovská for sharing their unpublished results. This work was supported by the Czech Ministry of Education, Youth and Sports (award LO1204 from the National Program of Sustainability I).

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Authors and Affiliations

  1. Institute of Experimental Botany, Šlechtitelů 31, Olomouc, Czech Republic

    Hana Šimková, Marie Kubaláková, Jan Vrána, Petr Cápal & Jaroslav Doležel

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  1. Hana Šimková
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  2. Marie Kubaláková
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  3. Jan Vrána
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  4. Petr Cápal
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  5. Jaroslav Doležel
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Correspondence to Hana Šimková .

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Editors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Sachsen-Anhalt, Germany

    Nils Stein

  2. Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, USA

    Gary J. Muehlbauer

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Šimková, H., Kubaláková, M., Vrána, J., Cápal, P., Doležel, J. (2018). Chromosomal Genomics of Barley. In: Stein, N., Muehlbauer, G. (eds) The Barley Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-92528-8_4

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