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Chromosomal Genomics of Barley

  • Hana Šimková
  • Marie Kubaláková
  • Jan Vrána
  • Petr Cápal
  • Jaroslav Doležel
Chapter
Part of the Compendium of Plant Genomes book series (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.

Keywords

Flow-cytometric sorting Gene cloning High-molecular-weight DNA Multiple displacement amplification Next-generation sequencing DNA arrays 

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

Notes

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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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Hana Šimková
    • 1
  • Marie Kubaláková
    • 1
  • Jan Vrána
    • 1
  • Petr Cápal
    • 1
  • Jaroslav Doležel
    • 1
  1. 1.Institute of Experimental BotanyOlomoucCzech Republic

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