Chromosomal Genomics of Barley

  • Hana ŠimkováEmail author
  • Marie Kubaláková
  • Jan Vrána
  • Petr Cápal
  • Jaroslav Doležel
Part of the Compendium of Plant Genomes book series (CPG)


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.


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



Bacterial artificial chromosome


High-molecular-weight DNA


Fluorescence in situ hybridization


Fluorescence in situ hybridization in suspension


Multiple displacement amplification


Next-generation sequencing


Oligonucleotide Pool Assay


Restriction fragment length polymorphism


Sequence-tagged site



We thank our colleagues Helena Toegelová, Tomáš Beseda, and Beáta Petrovská for sharing their unpublished results.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).


  1. Beier S, Himmelbach A, Colmsee C, Zhang X-Q, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Sampath D, Heavens D, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Houben A, Doležel J, Ayling S, Lonardi S, Langridge P, Muehlbauer GJ, Kersey P, Clark MD, Caccamo M, Schulman AH, Platzer M, Close TJ, Hansson M, Zhang G, Braumann I, Li C, Waugh R, Scholz U, Stein N, Mascher M (2017) Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Sci Data 4:170044CrossRefPubMedPubMedCentralGoogle Scholar
  2. Belova T, Zhan BJ, Wright J, Caccamo M, Asp T, Šimková H, Kent M, Bendixen C, Panitz F, Lien S, Doležel J, Olsen OA, Sandve SR (2013) Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat. BMC Genomics 14:222CrossRefPubMedPubMedCentralGoogle Scholar
  3. Blavet N, Uřinovská J, Jeřábková H, Chamrád I, Vrána J, Lenobel R, Beinhauer J, Šebela M, Doležel J, Petrovská B (2017) UNcleProt (Universal Nuclear Protein database of barley): the first nuclear protein database that distinguishes proteins from different phases of the cell cycle. Nucleus 8:70–80CrossRefPubMedGoogle Scholar
  4. Busch W, Martin R, Herrmann RG, Hohmann U (1995) Repeated DNA sequences isolated by microdissection. I. Karyotyping of barley (Hordeum vulgare L.). Genome 38:1082–1090CrossRefPubMedGoogle Scholar
  5. Cápal P, Blavet N, Vrána J, Kubaláková M, Doležel J (2015) Multiple displacement amplification of the DNA from single flow-sorted plant chromosome. Plant J 84:838–844CrossRefPubMedGoogle Scholar
  6. Close TJ, Wanamaker S, Roose ML, Lyon M (2006) HarvEST. Methods Mol Biol 406:161–177Google Scholar
  7. Close TJ, Bhat PR, Lonardi S, Wu YH, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao SAM, Varshney RK, Szucs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582CrossRefPubMedPubMedCentralGoogle Scholar
  8. Datta S, Malhotra L, Dickerson R, Chaffee S, Sen CK et al (2015) Laser capture microdissection: big data from small samples. Histol Histopathol 30:1255–1269PubMedPubMedCentralGoogle Scholar
  9. De Laat AMM, Blaas J (1984) Flow cytometric characterization and sorting of plant chromosomes. Theor Appl Genet 67:463–467CrossRefPubMedGoogle Scholar
  10. Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, Sun Z, Zong Q, Du Y, Du J, Driscoll M, Song W, Kingsmore SF, Egholm M, Lasken RS (2002) Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci USA 99:5261–5266CrossRefPubMedGoogle Scholar
  11. Doležel J, Číhalíková J, Lucretti S (1992) A high-yield procedure for isolation of metaphase chromosomes from root tips of Vicia faba L. Planta 188:93–98CrossRefPubMedGoogle Scholar
  12. Doležel J, Vrána J, Cápal P, Kubaláková M, Burešová V, Šimková H (2014) Advances in plant chromosome genomics. Biotechnol Adv 32:122–136CrossRefPubMedGoogle Scholar
  13. Fominaya A, Linares C, Loarce Y, Ferrer E (2005) Microdissection and microcloning of plant chromosomes. Cytogenet Genome Res 109:8–14CrossRefPubMedGoogle Scholar
  14. Fukui K, Minezawa M, Kamisugi Y, Ishikawa M, Ohmido N, Yanagisawa T, Fujishita M, Sakai F (1992) Microdissection of plant chromosomes by argon-ion laser-beam. Theor Appl Genet 84:787–791PubMedGoogle Scholar
  15. Giorgi D, Farina A, Grosso V, Gennaro A, Ceoloni C, Lucretti S (2013) FISHIS: fluorescence in situ hybridization in suspension and chromosome flow sorting made easy. PLoS One 8:e57994CrossRefPubMedPubMedCentralGoogle Scholar
  16. Gualberti G, Doležel J, Macas J, Lucretti S (1996) Preparation of pea (Pisum sativum L.) chromosome and nucleus suspensions from single root tips. Theor Appl Genet 92:744–751CrossRefPubMedGoogle Scholar
  17. Hobza R, Vyskot B (2007) Laser microdissection-based analysis of plant sex chromosomes. Methods Cell Biol 82:433–453CrossRefPubMedGoogle Scholar
  18. International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid wheat (Triticum aestivum) genome. Science 345:1251788CrossRefGoogle Scholar
  19. Islam AKMR (1983) Ditelosomic additions of barley chromosomes to wheat. In: Sakamoto S (ed) Proceedings of 6th international wheat genetics symposium, Kyoto University Press, Kyoto, Japan, pp 233–238Google Scholar
  20. Islam AKMR, Shepherd KW (2000) Isolation of a fertile wheat–barley addition line carrying the entire barley chromosome 1H. Euphytica 111:145–149CrossRefGoogle Scholar
  21. Islam AKMR, Shepherd KW, Sparrow DHB (1981) Isolation and characterization of euplasmic wheat–barley chromosome addition lines. Heredity 46:161–174CrossRefGoogle Scholar
  22. Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucl Acids Res 29:e25CrossRefPubMedGoogle Scholar
  23. Kopecký D, Martis M, Číhalíková J, Hřibová E, Vrána J, Bartoš J, Kopecká J, Cattonaro F, Stočes Š, Novák P, Neumann P, Macas J, Šimková H, Studer B, Asp T, Baird JH, Navrátil P, Karafiátová M, Kubaláková M, Šafář J, Mayer KFX, Doležel J (2013) Flow sorting and sequencing meadow fescue chromosome 4F. Plant Physiol 163:1323–1337CrossRefPubMedPubMedCentralGoogle Scholar
  24. Künzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154:397–412PubMedPubMedCentralGoogle Scholar
  25. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293CrossRefPubMedPubMedCentralGoogle Scholar
  26. Lysák MA, Číhalíková J, Kubaláková M, Šimková H, Künzel G, Doležel J (1999) Flow karyotyping and sorting of mitotic chromosomes of barley (Hordeum vulgare L.). Chromosome Res 7:431–444CrossRefPubMedGoogle Scholar
  27. Martis MM, Zhou R, Haseneyer G, Schmutzer T, Vrána J, Kubaláková M, König S, Kugler KG, Scholz U, Hackauf B, Korzun V, Schön CC, Doležel J, Bauer E, Mayer KFX, Stein N (2013) Reticulate evolution of the rye genome. Plant Cell 25:3685–3698CrossRefPubMedPubMedCentralGoogle Scholar
  28. Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang X-Q, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature 544:427–433CrossRefPubMedGoogle Scholar
  29. Mayer KFX, Taudien S, Martis M, Šimková H, Suchánková P, Gundlach H, Wicker T, Petzold A, Felder M, Steuernagel B, Scholz U, Graner A, Platzer M, Doležel J, Stein N (2009) Gene content and virtual gene order of barley chromosome 1H. Plant Physiol 151:496–505CrossRefPubMedPubMedCentralGoogle Scholar
  30. Mayer KFX, Martis M, Hedley PE, Šimková H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo TR, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Doležel J, Waugh R, Stein N (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23:1249–1263CrossRefPubMedPubMedCentralGoogle Scholar
  31. Muñoz-Amatriaín M, Moscou MJ, Bhat PR, Svensson JT, Bartoš J, Suchánková P, Šimková H, Endo TR, Fenton RD, Lonardi S, Castillo AM, Chao S, Cistué L, Cuesta-Marcos A, Forrest KL, Hayden MJ, Hayes PM, Horsley RD, Makoto K, Moody D, Sato K, Vallés MP, Wulff BBH, Muehlbauer GJ, Doležel J, Close TJ (2011) An improved consensus linkage map of barley based on flow-sorted chromosomes and single nucleotide polymorphism markers. Plant Genome 4:238–249CrossRefGoogle Scholar
  32. Muñoz-Amatriaín M, Lonardi S, Luo M-C, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Šimková H, Doležel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ (2015) Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant J 84:216–227CrossRefPubMedPubMedCentralGoogle Scholar
  33. Ounit R, Wanamaker S, Close TJ, Lonardi S (2015) CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics 16:236CrossRefPubMedPubMedCentralGoogle Scholar
  34. Rostoks N, Ramsay L, Mackenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, Graner A, Close TJ, Waugh R (2006) Recent history of artificial outcrossing facilitate whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103:18656–18661CrossRefPubMedGoogle Scholar
  35. Šafář J, Šimková H, Kubaláková M, Číhalíková J, Suchánková P, Bartoš J, Doležel J (2010) Development of chromosome-specific BAC resources for genomics of bread wheat. Cytogenet Genome Res 129:211–223CrossRefPubMedGoogle Scholar
  36. Sánchez-Martín J, Steuernagel B, Ghosh S, Herren G, Hurni S, Adamski N, Vrána J, Kubaláková M, Krattinger SG, Wicker T, Doležel J, Keller B, Wulff BBH (2016) Rapid gene isolation in barley and wheat by mutant chromosome sequencing. Genome Biol 17:221CrossRefPubMedPubMedCentralGoogle Scholar
  37. Schondelmaier J, Martin R, Jahoor A, Houben A, Graner A, Koop HU, Herrmann RH, Jung C (1993) Microdissection and microcloning of the barley (Hordeum vulgare L) chromosome 1HS. Theor Appl Genet 86:629–636CrossRefPubMedGoogle Scholar
  38. Šimková H, Číhalíková J, Vrána J, Lysák MA, Doležel J (2003) Preparation of HMW DNA from plant nuclei and chromosomes isolated from root tips. Biol Plant 46:369–373CrossRefGoogle Scholar
  39. Šimková H, Svensson JT, Condamine P, Hřibová E, Suchánková P, Bhat PR, Bartoš J, Šafář J, Close TJ, Doležel J (2008) Coupling amplified DNA from flow-sorted chromosomes to high-density SNP mapping in barley. BMC Genomics 9:294CrossRefPubMedPubMedCentralGoogle Scholar
  40. Sorokin A, Marthe F, Houben A, Pich U, Graner A, Kunzel G (1994) Polymerase chain-reaction mediated localization of RFLP clones to microisolated translocation chromosomes of barley. Genome 37:550–555CrossRefPubMedGoogle Scholar
  41. Staňková H, Hastie AR, Chan S, Vrána J, Tulpová Z, Kubaláková M, Visendi P, Hayashi S, Luo M, Batley J, Edwards D, Doležel J, Šimková H (2016) BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnol J 14:1523–1531CrossRefPubMedPubMedCentralGoogle Scholar
  42. Suchánková P, Kubaláková M, Kovářová P, Bartoš J, Číhalíková J, Molnár-Láng M, Endo TR, Doležel J (2006) Dissection of the nuclear genome of barley by chromosome flow sorting. Theor Appl Genet 113:651–659CrossRefPubMedGoogle Scholar
  43. Vrána J, Cápal P, Šimková H, Karafiátová M, Čížková J, Doležel J (2016) Flow analysis and sorting of plant chromosomes. Curr Protoc Cytom 78:5.3.1–5.3.43CrossRefGoogle Scholar
  44. Zhou R-N, Hu Z-M (2007) The development of chromosome microdissection and microcloning technique and its applications in genomic research. Curr Genomics 8:67–72CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

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

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