Cytogenetics and Genetic Stocks for Physical Mapping and Sequencing

  • Andreas Houben
  • Lala Aliyeva-Schnorr
  • Giri Prasad Joshi
  • Takashi R. Endo
Part of the Compendium of Plant Genomes book series (CPG)


Barley is a model for other Triticeae genomes and is frequently used for cytological studies. In this chapter, we focus on cytogenetic approaches helping to improve physical mapping of the barley genome and describe the previous utilization of repetitive and low-copy probes successfully applied to barley. We demonstrate how the analysis of barley centromeres provided a better understanding of the process of uniparental chromosome elimination resulting in haploid plants. In addition, we describe how the downsizing of barley chromosomes was achieved by the production of aneuploids, and the application of the gametocidal system and telomere seeding.


Cytogenetic stocks Physical mapping Cytological mapping Telomere seeding Haploids FISH 


  1. Aliyeva-Schnorr L, Beier S, Karafiatova M et al (2015) Cytogenetic mapping with centromeric bacterial artificial chromosomes contigs shows that this recombination-poor region comprises more than half of barley chromosome 3H. Plant J 84:385–394CrossRefPubMedGoogle Scholar
  2. Aliyeva-Schnorr L, Stein N, Houben A (2016) Collinearity of homoeologous group 3 chromosomes in the genus Hordeum and Secale cereale as revealed by 3H-derived FISH analysis. Chromosome Res 24(2):231–242Google Scholar
  3. Allshire RC, Karpen GH (2008) Epigenetic regulation of centromeric chromatin: old dogs, new tricks? Nat Rev Genet 9:923–937CrossRefPubMedPubMedCentralGoogle Scholar
  4. Ashida T, Nasuda S, Sato K, Endo TR (2007) Dissection of barley chromosome 5H in common wheat. Genes Genet Syst 82:123–133CrossRefPubMedGoogle Scholar
  5. Bai YW, Zhou Z, Feng HQ, Zhou BR (2011) Recognition of centromeric histone variant CenH3s by their chaperones Structurally conserved or not. Cell Cycle 10:3217–3218CrossRefPubMedPubMedCentralGoogle Scholar
  6. Baker K, Dhillon T, Colas I et al (2015) Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance. Plant J 84:111–124CrossRefPubMedPubMedCentralGoogle Scholar
  7. Bassett EA, DeNizio J, Barnhart-Dailey MC et al (2012) HJURP uses distinct CENP-A surfaces to recognize and to stabilize CENP-A/histone H4 for centromere assembly. Dev Cell 22:749–762CrossRefPubMedPubMedCentralGoogle Scholar
  8. Birchler JA, Krishnaswamy L, Gaeta RT et al (2010) Engineered minichromosomes in plants. Crit Rev Plant Sci 29:135–147CrossRefGoogle Scholar
  9. Brandes A, Roder MS, Ganal MW (1995) Barley telomeres are associated with two different types of satellite DNA sequences. Chromosome Res 3:315–320CrossRefPubMedGoogle Scholar
  10. Busch W, Martin R, Herrmann RG, Hohmann U (1995) Repeated DNA sequences isolated by microdissection. 1. Karyotyping of barley (Hordeum vulgare L.). Genome 38:1082–1090CrossRefPubMedGoogle Scholar
  11. Costa JM, Singh RJ (2006) Chromosome mapping in barley (Hordeum vulgare L.). In: Genetic resources, chromosome engineering, and crop improvement, vol 2, pp 257–280Google Scholar
  12. Cuacos M, Franklin FCH, Heckmann S (2015) Atypical centromeres in plants—what they can tell us. Front Plant Sci 6Google Scholar
  13. Cuadrado A, Jouve N (2007) The nonrandom distribution of long clusters of all possible classes of trinucleotide repeats in barley chromosomes. Chromosome Res 15:711–720CrossRefPubMedGoogle Scholar
  14. Dong FG, Jiang JM (1998) Non-rabl patterns of centromere and telomere distribution in the interphase nuclei of plant cells. Chromosome Res 6:551–558CrossRefPubMedGoogle Scholar
  15. Earnshaw WC, Allshire RC, Black BE et al (2013) Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant. Chromosome Res 21:101–106CrossRefPubMedPubMedCentralGoogle Scholar
  16. Endo TR (1988) Induction of chromosomal structural changes by a chromosome of Aegilops cylindrical L. in common wheat. J Hered 79:366–370CrossRefGoogle Scholar
  17. Endo TR (1990) Gametocidal chromosomes and their induction of chromosome mutations in wheat. Jpn J Genet 65:135–152CrossRefGoogle Scholar
  18. Endo TR (2007) The gametocidal chromosome as a tool for chromosome manipulation in wheat. Chromosome Res 15:67–75CrossRefPubMedGoogle Scholar
  19. Endo TR (2011) Cytological dissection of the triticeae chromosomes by the gametocidal system. Methods Mol Biol 701:247–257CrossRefPubMedGoogle Scholar
  20. Endo TR, Gill BS (1996) The deletion stocks of common wheat. J Hered 87:295–307CrossRefGoogle Scholar
  21. Farr C, Fantes J, Goodfellow P et al (1991) Functional reintroduction of human telomeres into mammalian cells. Proc Natl Acad Sci USA 88:7006–7010CrossRefPubMedGoogle Scholar
  22. Foltz DR, Jansen LET, Bailey AO et al (2009) Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell 137:472–484CrossRefPubMedPubMedCentralGoogle Scholar
  23. Fuchs J, Demidov D, Houben A (2006) Chromosomal histone modification patterns—from conservation to diversity. Trends Plant Sci 11:199–208CrossRefPubMedGoogle Scholar
  24. Fukui K, Kamisugi Y, Sakai F (1994) Physical mapping of 5S rDNA loci by direct cloned biotinylated probes in barley chromosomes. Genome 37:105–111CrossRefPubMedGoogle Scholar
  25. Gill BS, Kimber G (1974) Giemsa C-banding and the evolution of wheat. Proc Natl Acad Sci USA 71:4086–4090CrossRefPubMedGoogle Scholar
  26. Gottwald S, Bauer P, Komatsuda T et al (2009) TILLING in the two-rowed barley cultivar ‘Barke’ reveals preferred sites of functional diversity in the gene HvHox1. BMC Res Notes 2:258CrossRefPubMedPubMedCentralGoogle Scholar
  27. Hagberg A (1995) Coordinator’s report: duplication of chromosome segments. Barley Genet Newsl 25:114Google Scholar
  28. Higgins JD, Osman K, Jones GH et al (2014) Factors underlying restricted crossover localization in barley meiosis. Annu Rev Genet 48:29–47CrossRefPubMedGoogle Scholar
  29. Houben A, Pickering R (2009) Applying cytogenetics and genomics to wide hybridisations in the genus Hordeum. In: Genetics and genomics of the triticeae. SpringerGoogle Scholar
  30. Houben A, Wako T, Furushima-Shimogawara R, Fukui K (1999) The cell cycle dependent phosphorylation of histone H3 is correlated with the condensation of plant mitotic chromosomes. Plant J 18:675–679CrossRefPubMedGoogle Scholar
  31. Houben A, Demidov D, Gernand D, Meister A et al (2003) Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content. Plant J 33:967–973CrossRefPubMedGoogle Scholar
  32. Houben A, Schroeder-Reiter E, Nagaki K et al (2007) CENH3 interacts with the centromeric retrotransposon cereba and GC-rich satellites and locates to centromeric substructures in barley. Chromosoma 116:275–283CrossRefPubMedGoogle Scholar
  33. Hudakova S, Michalek W, Presting GG (2001) Sequence organization of barley centromeres. Nucleic Acids Res 29:5029–5035CrossRefPubMedPubMedCentralGoogle Scholar
  34. International Barley Genome Sequencing C, Mayer KF, Waugh R, Brown JW et al (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–716Google Scholar
  35. Ishihara A, Mizuno N, Islam AKMR et al (2014) Dissection of barley chromosomes 1H and 6H by the gametocidal system. Genes Genet Syst 89:203–214CrossRefPubMedGoogle Scholar
  36. Ishii T, Karimi-Ashtiyani R, Banaei-Moghaddam AM et al (2015) The differential loading of two barley CENH3 variants into distinct centromeric substructures is cell type- and development-specific. Chromosome Res 23:277–284CrossRefPubMedGoogle Scholar
  37. Ishii T, Karimi-Ashtiyani R, Houben A (2016) Haploidization via chromosome elimination: means and mechanisms. Annu Rev Plant BiolGoogle Scholar
  38. Islam AKMR (1980) Identification of wheat-barley addition lines with N-banding of chromosomes. Chromosoma 76:365–373CrossRefGoogle Scholar
  39. Islam AKMR (1983) Ditelosomic additions of barley chromosomes to wheat. In: Sakamoto S (ed) Proceedings of the sixth international wheat genetics symposium, Kyoto University Press, Kyoto, Japan, 28 Nov–3 Dec 1983, pp 233–238Google Scholar
  40. Islam AKMR, Shepherd KW (2000) Isolation of a fertile wheat-barley addition line carrying the entire barley chromosome 1H. Euphytica 111:145–149CrossRefGoogle Scholar
  41. Islam AKMR, Shepherd KW, Sparrow DHB (1975) Addition of individual barley chromosomes to wheat. In: Proceedings of 3rd international barley genetics symposium (Garching, BRD), pp 260–270Google Scholar
  42. Islam AKMR, Shepherd KW, Sparrow DHB (1981) Isolation and characterization of euplasmic wheat-barley chromosome addition lines. Heredity 46:161–174CrossRefGoogle Scholar
  43. Jiang J, Friebe B, Gill BS (1994) Recent advances in alien gene transfer in wheat. Euphytica 73:199–212CrossRefGoogle Scholar
  44. Joshi GP, Nasuda S, Endo TR (2011) Dissection and cytological mapping of barley chromosome 2H in the genetic background of common wheat. Genes Genet Syst 86:231–248CrossRefPubMedGoogle Scholar
  45. Joshi GP, Endo TR, Nasuda S (2013) PCR and sequence analysis of barley chromosome 2H subjected to the gametocidal action of chromosome 2C. Theor Appl Genet 126:2381–2390CrossRefPubMedGoogle Scholar
  46. Kakeda K, Yamagata H (1992) Immunological analysis of chromosome replication in barley, rye and durum wheat by using anti-BrdU antibody. Hereditas 116:67–70CrossRefGoogle Scholar
  47. Kakeda K, Fukui K, Yamagata H (1991) Heterochromatic differentiation in barley chromosomes revealed by C- and N-banding techniques. Theor Appl Genet 81:144–150CrossRefPubMedGoogle Scholar
  48. Kapusi E, Ma L, Teo CH et al (2012) Telomere-mediated truncation of barley chromosomes. Chromosoma 121:181–190CrossRefPubMedGoogle Scholar
  49. Karafiatova M, Bartos J, Kopecky D et al (2013) Mapping nonrecombining regions in barley using multicolor FISH. Chromosome Res 21:739–751CrossRefPubMedGoogle Scholar
  50. Karimi-Ashtiyani R, Ishii T, Niessen M et al (2015) Point mutation impairs centromeric CENH3 loading and induces haploid plants. Proc Natl Acad Sci USA 112:11211–11216CrossRefPubMedGoogle Scholar
  51. Kato A (2011) High-density fluorescence in situ hybridization signal detection on barley (Hordeum vulgare L.) chromosomes with improved probe screening and reprobing procedures. Genome 54:151–159CrossRefPubMedGoogle Scholar
  52. Kato A, Albert P, Vega J et al (2006) Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation. Biotech Histochem 81:71–78CrossRefPubMedGoogle Scholar
  53. Kilian A, Stiff C, Kleinhofs A (1995) Barley telomeres shorten during differentiation but grow in callus culture. Proc Natl Acad Sci USA 92:9555–9559CrossRefPubMedGoogle Scholar
  54. Kruse A (1973) Hordeum × Triticum hybrids. Hereditas 73:157–161CrossRefGoogle Scholar
  55. Kumar A, Bassi FM, de Jimenez MKM et al (2014) Radiation hybrids: a valuable tool for genetic, genomic and functional analysis of plant genomes. In: Genomics of plant genetic resources. Springer, Netherlands, pp 285–318Google Scholar
  56. Künzel G (1992) Coordinator’s report: translocation sand balanced tertiary trisomics. Barley Genet Newsl 22:80–102Google Scholar
  57. Künzel G, Waugh R (2002) Integration of microsatellite markers into the translocation-based physical RFLP map of barley chromosome 3H. Theor Appl Genet 105:660–665CrossRefPubMedGoogle Scholar
  58. 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
  59. Künzel G, Gecheff KI, Schubert I (2001) Different chromosomal distribution patterns of radiation-induced interchange breakpoints in barley: first post-treatment mitosis versus viable offspring. Genome 44:128–132CrossRefPubMedGoogle Scholar
  60. Leitch IJ, Heslop-Harrison JS (1992) Physical mapping of the 18s-5.8s-26s ribosomal-rna genes in barley by in situ hybridization. Genome 35:1013–1018CrossRefGoogle Scholar
  61. Leitch IJ, Heslop-Harrison JS (1993) Physical mapping of four sites of 5S rDNA sequences and one site of the α-amylase-2 gene in barley (Hordeum vulgare). Genome 36:517–523CrossRefPubMedGoogle Scholar
  62. Linde-Laursen I (1975) Giemsa C-banding of the chromosomes of ‘Emir’ barley. Hereditas 81:285–289CrossRefGoogle Scholar
  63. Linde-Laursen L (1991) Giemsa C-banded karyotypes of cultivated and wild barley. Barley Genet Newsl 20:47–52Google Scholar
  64. Linde-Laursen I, Heslop-Harrison J, Shepherd K et al (1997) The barley genome and its relationship with the wheat genomes. A survey with an internationally agreed recommendation for barley chromosome nomenclature. Hereditas 126:1–16Google Scholar
  65. Ma L, Vu GTH, Schubert V et al (2010) Synteny between Brachypodium distachyon and Hordeum vulgare as revealed by FISH. Chromosome Res 18:841–850CrossRefPubMedGoogle Scholar
  66. Marthe F, Künzel G (1994) Localization of translocation breakpoints in somatic metaphase chromosomes of barley. Theor Appl Genet 89:240–248PubMedGoogle Scholar
  67. Masoudi-Nejad A, Nasuda S, Bihoreau MT et al (2005) An alternative to radiation hybrid mapping for large-scale genome analysis in barley. Mol Genet Genomics 274:589–594CrossRefPubMedGoogle Scholar
  68. Mayer KFX, Taudien S, Maris M, Šimková et al (2009) Gene content and virtual gene order of barley chromosome 1H. Plant Physiol 151:496–505Google Scholar
  69. Mette MF, Houben A (2015) Engineering of plant chromosomes. Chromosome Res 23:69–76CrossRefPubMedGoogle Scholar
  70. Molnár-Láng M, Linc G (2015) Wheat-barley hybrids and introgression lines. In: Molnár-Láng M, Ceoloni C, Doležel, J (eds) Alien introgression in wheat, pp 315–345Google Scholar
  71. Molnár-Láng M, Linc G, Szakács E´ (2014) Wheat–barley hybridization: the last 40 years. Euphytica 195:315–329Google Scholar
  72. Mukai Y, Gill BS (1991) Detection of barley chromatin added to wheat by genomic in situ hybridization. Genome 34:448–452CrossRefGoogle Scholar
  73. Nasuda S, Hudakova S, Schubert I et al (2005a) Stable barley chromosomes without centromeric repeats. Proc Natl Acad Sci USA 102:9842–9847CrossRefPubMedGoogle Scholar
  74. Nasuda S, Kikkawa Y, Ashida T et al (2005b) Chromosomal assignment and deletion mapping of barley EST markers. Genes Genet Syst 80:357–366CrossRefPubMedGoogle Scholar
  75. Oliver C, Pradillo M, Corredor E et al (2013) The dynamics of histone H3 modifications is species-specific in plant meiosis. Planta 238:23–33CrossRefPubMedGoogle Scholar
  76. Pedersen C, Rasmussen SK, Linde-Laursen I (1996) Genome and chromosome identification in cultivated barley and related species of the Triticeae (Poaceae) by in situ hybridization with the GAA-satellite sequence. Genome 39:93–104CrossRefPubMedGoogle Scholar
  77. Phillips D, Nibau C, Ramsay L et al (2010) Development of a molecular cytogenetic recombination assay for barley. Cytogenet Genome Res 129:154–161CrossRefPubMedGoogle Scholar
  78. Presting GG, Malysheva L, Fuchs J et al (1998) A Ty3/gypsy retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J 16:721–728CrossRefPubMedGoogle Scholar
  79. Puchta H (2015) Using CRISPR/Cas in three dimensions: towards synthetic plant genomes, transcriptomes and epigenomes. Plant JGoogle Scholar
  80. Ravi M, Chan SW (2010) Haploid plants produced by centromere-mediated genome elimination. Nature 464:615–618CrossRefPubMedGoogle Scholar
  81. Ravi M, Marimuthu MPA, Tan EH et al (2014) A haploid genetics toolbox for Arabidopsis thaliana. Nat Commun 5Google Scholar
  82. Sakai K, Nasuda S, Sato K, Endo TR (2009) Dissection of barley chromosome 3H in common wheat and a comparison of 3H physical and genetic maps. Genes Genet Syst 84:25–34CrossRefPubMedGoogle Scholar
  83. Sakata M, Nasuda S, Endo TR (2010) Dissection of barley chromosome 4H in common wheat by the gametocidal system and cytological mapping of chromosome 4H with EST markers. Genes Genet Syst 85:19–29CrossRefPubMedGoogle Scholar
  84. Sanei M, Pickering R, Kumke K et al (2011) Loss of centromeric histone H3 (CENH3) from centromeres precedes uniparental chromosome elimination in interspecific barley hybrids. Proc Natl Acad Sci USA 108:E498–E505CrossRefPubMedGoogle Scholar
  85. Sato K, Nankaku N, Takeda K (2009) A high-density transcript linkage map of barley derived from a single population. Heredity 103:110–117CrossRefPubMedGoogle Scholar
  86. Schmutzer T, Ma L, Pousarebani N et al (2014) Kmasker-a tool for in silico prediction of single-copy FISH probes for the large-genome species Hordeum vulgare. Cytogenet Genome Res 142:66–78CrossRefPubMedGoogle Scholar
  87. Schroeder-Reiter E, Sanei M, Houben A et al (2012) Current SEM techniques for de- and re-construction of centromeres to determine 3D CENH3 distribution in barley mitotic chromosomes. J Microsc 246:96–106CrossRefPubMedGoogle Scholar
  88. Schubert I, Künzel G (1990) Position-dependent NOR activity in barley. Chromosoma 99:352–359CrossRefGoogle Scholar
  89. Schubert I, Shi F, Fuchs J et al (1998) An efficient screening for terminal deletions and translocations of barley chromosomes added to common wheat. Plant J 14:489–495CrossRefGoogle Scholar
  90. Sears ER (1954) The aneuploids of common wheat. Missouri Agric Exp Stat Res Bull 572:1–59Google Scholar
  91. Sears ER (1966) Nullisomic-tetrasomic combinations in hexaploid wheat. In: Riley R, Lewis KR (eds) Chromosome manipulations and plant genetics. Oliver & Boyd, Edinburgh, pp 29–45Google Scholar
  92. Sears ER, Sears LMS (1978) The telocentric chromosomes of common wheat. In: Ramanujam RS (ed) Proceedings of 5th international wheat genetics symposium, New Delhi, India, pp 389–407Google Scholar
  93. Serizawa N, Nasuda S, Endo TR (2001a) Barley chromosome addition lines of wheat for screening of AFLP markers on barley chromosomes. Genes Genet Syst 76:107–110CrossRefPubMedGoogle Scholar
  94. Serizawa N, Nasuda S, Shi F et al (2001b) Deletion-based physical mapping of barley chromosome 7H. Theor Appl Genet 103:827–834CrossRefGoogle Scholar
  95. Shi F, Endo TR (1997) Production of wheat-barley disomic addition lines possessing an Aegilops cylindrica gametocidal chromosome. Genes Genet Syst 72:243–248CrossRefGoogle Scholar
  96. Shi F, Endo TR (1999) Genetic induction of structural changes in barley chromosomes added to common wheat by a gametocidal chromosome derived from Aegilops cylindrica. Genes Genet Syst 74:49–54CrossRefGoogle Scholar
  97. Sorokin A, Marthe F, Houben A et al (1994) Polymerase chain reaction mediated localization of RFLP clones to microisolated translocation chromosomes of barley. Genome 37:550–555CrossRefPubMedGoogle Scholar
  98. Stephens JL, Brown SE, Lapitan NLV et al (2004) Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique. Genome 47:179–189CrossRefPubMedGoogle Scholar
  99. Suchánková P, Kubaláková M, Kovárová P et al (2006) Dissection of the nuclear genome of barley by chromosome flow sorting. Theor Appl Genet 113:651–659CrossRefPubMedGoogle Scholar
  100. Taketa S, Takeda K (2001) Production and characterization of a complete set of wheat-wild barley (Hordeum vulgare ssp. spontaneum) chromosome addition lines. Breed Sci 51:199–206CrossRefGoogle Scholar
  101. Taketa S, Choda M, Ohashi R et al (2002) Molecular and physical mapping of a barley gene on chromosome arm 1HL that causes sterility in hybrids with wheat. Genome 45:617–625. Scholar
  102. Taketa S, Linde-Laursen I, Künzel G (2003) Cytogenetic diversity. In: von Bothmer R, van Hintum Th, Knüppffer H, Sato K (eds) Diversity in barley (Hordeum vulgare). Elsevier Science BV, Amsterdam, The Netherlands, pp 97–119Google Scholar
  103. Tsuchiya T (1969) Status of studies of primary trisomics and other aneuploids in barley. Genetica 40:216CrossRefGoogle Scholar
  104. Tsuchiya T (1991) Chromosome mapping by means of aneuploid analysis in barley. In: Gupta PK, Tsuchiya T (eds) Chromosome engineering in plants: genetics, breeding, evolution part A. Elsevier, pp 361–384Google Scholar
  105. Tsujimoto H, Mukai Y, Akagawa K et al (1997) Identification of individual barley chromosomes based on repetitive sequences: conservative distribution of Afa-family repetitive sequences on the chromosomes of barley and wheat. Genes Genet Syst 72:303–309CrossRefPubMedGoogle Scholar
  106. Valarik M, Bartos J, Kovarova P et al (2004) High-resolution FISH on super-stretched flow-sorted plant chromosomes. Plant J 37:940–950CrossRefPubMedGoogle Scholar
  107. Wicker T, Krattinger SG, Lagudah ES et al (2009) Analysis of intraspecies diversity in wheat and barley genomes identifies breakpoints of ancient haplotypes and provides insight into the structure of diploid and hexaploid triticeae gene pools. Plant Physiol 149:258–270CrossRefPubMedPubMedCentralGoogle Scholar

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© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Andreas Houben
    • 1
  • Lala Aliyeva-Schnorr
    • 1
  • Giri Prasad Joshi
    • 2
  • Takashi R. Endo
    • 3
  1. 1.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
  2. 2.Central Department of BotanyTribhuvan UniversityKathmanduNepal
  3. 3.Faculty of AgricultureRyukoku UniversityOtsuJapan

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