Abstract
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.
Keywords
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
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 84:385–394
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):231–242
Allshire RC, Karpen GH (2008) Epigenetic regulation of centromeric chromatin: old dogs, new tricks? Nat Rev Genet 9:923–937
Ashida T, Nasuda S, Sato K, Endo TR (2007) Dissection of barley chromosome 5H in common wheat. Genes Genet Syst 82:123–133
Bai YW, Zhou Z, Feng HQ, Zhou BR (2011) Recognition of centromeric histone variant CenH3s by their chaperones Structurally conserved or not. Cell Cycle 10:3217–3218
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 84:111–124
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 22:749–762
Birchler JA, Krishnaswamy L, Gaeta RT et al (2010) Engineered minichromosomes in plants. Crit Rev Plant Sci 29:135–147
Brandes A, Roder MS, Ganal MW (1995) Barley telomeres are associated with two different types of satellite DNA sequences. Chromosome Res 3:315–320
Busch W, Martin R, Herrmann RG, Hohmann U (1995) Repeated DNA sequences isolated by microdissection. 1. Karyotyping of barley (Hordeum vulgare L.). Genome 38:1082–1090
Costa JM, Singh RJ (2006) Chromosome mapping in barley (Hordeum vulgare L.). In: Genetic resources, chromosome engineering, and crop improvement, vol 2, pp 257–280
Cuacos M, Franklin FCH, Heckmann S (2015) Atypical centromeres in plants—what they can tell us. Front Plant Sci 6
Cuadrado A, Jouve N (2007) The nonrandom distribution of long clusters of all possible classes of trinucleotide repeats in barley chromosomes. Chromosome Res 15:711–720
Dong FG, Jiang JM (1998) Non-rabl patterns of centromere and telomere distribution in the interphase nuclei of plant cells. Chromosome Res 6:551–558
Earnshaw WC, Allshire RC, Black BE et al (2013) Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant. Chromosome Res 21:101–106
Endo TR (1988) Induction of chromosomal structural changes by a chromosome of Aegilops cylindrical L. in common wheat. J Hered 79:366–370
Endo TR (1990) Gametocidal chromosomes and their induction of chromosome mutations in wheat. Jpn J Genet 65:135–152
Endo TR (2007) The gametocidal chromosome as a tool for chromosome manipulation in wheat. Chromosome Res 15:67–75
Endo TR (2011) Cytological dissection of the triticeae chromosomes by the gametocidal system. Methods Mol Biol 701:247–257
Endo TR, Gill BS (1996) The deletion stocks of common wheat. J Hered 87:295–307
Farr C, Fantes J, Goodfellow P et al (1991) Functional reintroduction of human telomeres into mammalian cells. Proc Natl Acad Sci USA 88:7006–7010
Foltz DR, Jansen LET, Bailey AO et al (2009) Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell 137:472–484
Fuchs J, Demidov D, Houben A (2006) Chromosomal histone modification patterns—from conservation to diversity. Trends Plant Sci 11:199–208
Fukui K, Kamisugi Y, Sakai F (1994) Physical mapping of 5S rDNA loci by direct cloned biotinylated probes in barley chromosomes. Genome 37:105–111
Gill BS, Kimber G (1974) Giemsa C-banding and the evolution of wheat. Proc Natl Acad Sci USA 71:4086–4090
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 2:258
Hagberg A (1995) Coordinator’s report: duplication of chromosome segments. Barley Genet Newsl 25:114
Higgins JD, Osman K, Jones GH et al (2014) Factors underlying restricted crossover localization in barley meiosis. Annu Rev Genet 48:29–47
Houben A, Pickering R (2009) Applying cytogenetics and genomics to wide hybridisations in the genus Hordeum. In: Genetics and genomics of the triticeae. Springer
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 18:675–679
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 33:967–973
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 116:275–283
Hudakova S, Michalek W, Presting GG (2001) Sequence organization of barley centromeres. Nucleic Acids Res 29:5029–5035
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 491:711–716
Ishihara A, Mizuno N, Islam AKMR et al (2014) Dissection of barley chromosomes 1H and 6H by the gametocidal system. Genes Genet Syst 89:203–214
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 23:277–284
Ishii T, Karimi-Ashtiyani R, Houben A (2016) Haploidization via chromosome elimination: means and mechanisms. Annu Rev Plant Biol
Islam AKMR (1980) Identification of wheat-barley addition lines with N-banding of chromosomes. Chromosoma 76:365–373
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 233–238
Islam AKMR, Shepherd KW (2000) Isolation of a fertile wheat-barley addition line carrying the entire barley chromosome 1H. Euphytica 111:145–149
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 260–270
Islam AKMR, Shepherd KW, Sparrow DHB (1981) Isolation and characterization of euplasmic wheat-barley chromosome addition lines. Heredity 46:161–174
Jiang J, Friebe B, Gill BS (1994) Recent advances in alien gene transfer in wheat. Euphytica 73:199–212
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 86:231–248
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 126:2381–2390
Kakeda K, Yamagata H (1992) Immunological analysis of chromosome replication in barley, rye and durum wheat by using anti-BrdU antibody. Hereditas 116:67–70
Kakeda K, Fukui K, Yamagata H (1991) Heterochromatic differentiation in barley chromosomes revealed by C- and N-banding techniques. Theor Appl Genet 81:144–150
Kapusi E, Ma L, Teo CH et al (2012) Telomere-mediated truncation of barley chromosomes. Chromosoma 121:181–190
Karafiatova M, Bartos J, Kopecky D et al (2013) Mapping nonrecombining regions in barley using multicolor FISH. Chromosome Res 21:739–751
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 112:11211–11216
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 54:151–159
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 81:71–78
Kilian A, Stiff C, Kleinhofs A (1995) Barley telomeres shorten during differentiation but grow in callus culture. Proc Natl Acad Sci USA 92:9555–9559
Kruse A (1973) Hordeum × Triticum hybrids. Hereditas 73:157–161
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 285–318
Künzel G (1992) Coordinator’s report: translocation sand balanced tertiary trisomics. Barley Genet Newsl 22:80–102
Künzel G, Waugh R (2002) Integration of microsatellite markers into the translocation-based physical RFLP map of barley chromosome 3H. Theor Appl Genet 105:660–665
Künzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154:397–412
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 44:128–132
Leitch IJ, Heslop-Harrison JS (1992) Physical mapping of the 18s-5.8s-26s ribosomal-rna genes in barley by in situ hybridization. Genome 35:1013–1018
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 36:517–523
Linde-Laursen I (1975) Giemsa C-banding of the chromosomes of ‘Emir’ barley. Hereditas 81:285–289
Linde-Laursen L (1991) Giemsa C-banded karyotypes of cultivated and wild barley. Barley Genet Newsl 20:47–52
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 126:1–16
Ma L, Vu GTH, Schubert V et al (2010) Synteny between Brachypodium distachyon and Hordeum vulgare as revealed by FISH. Chromosome Res 18:841–850
Marthe F, Künzel G (1994) Localization of translocation breakpoints in somatic metaphase chromosomes of barley. Theor Appl Genet 89:240–248
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 274:589–594
Mayer KFX, Taudien S, Maris M, Šimková et al (2009) Gene content and virtual gene order of barley chromosome 1H. Plant Physiol 151:496–505
Mette MF, Houben A (2015) Engineering of plant chromosomes. Chromosome Res 23:69–76
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 315–345
Molnár-Láng M, Linc G, Szakács E´ (2014) Wheat–barley hybridization: the last 40 years. Euphytica 195:315–329
Mukai Y, Gill BS (1991) Detection of barley chromatin added to wheat by genomic in situ hybridization. Genome 34:448–452
Nasuda S, Hudakova S, Schubert I et al (2005a) Stable barley chromosomes without centromeric repeats. Proc Natl Acad Sci USA 102:9842–9847
Nasuda S, Kikkawa Y, Ashida T et al (2005b) Chromosomal assignment and deletion mapping of barley EST markers. Genes Genet Syst 80:357–366
Oliver C, Pradillo M, Corredor E et al (2013) The dynamics of histone H3 modifications is species-specific in plant meiosis. Planta 238:23–33
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 39:93–104
Phillips D, Nibau C, Ramsay L et al (2010) Development of a molecular cytogenetic recombination assay for barley. Cytogenet Genome Res 129:154–161
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 16:721–728
Puchta H (2015) Using CRISPR/Cas in three dimensions: towards synthetic plant genomes, transcriptomes and epigenomes. Plant J
Ravi M, Chan SW (2010) Haploid plants produced by centromere-mediated genome elimination. Nature 464:615–618
Ravi M, Marimuthu MPA, Tan EH et al (2014) A haploid genetics toolbox for Arabidopsis thaliana. Nat Commun 5
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 84:25–34
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 85:19–29
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–E505
Sato K, Nankaku N, Takeda K (2009) A high-density transcript linkage map of barley derived from a single population. Heredity 103:110–117
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 142:66–78
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 246:96–106
Schubert I, Künzel G (1990) Position-dependent NOR activity in barley. Chromosoma 99:352–359
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 14:489–495
Sears ER (1954) The aneuploids of common wheat. Missouri Agric Exp Stat Res Bull 572:1–59
Sears ER (1966) Nullisomic-tetrasomic combinations in hexaploid wheat. In: Riley R, Lewis KR (eds) Chromosome manipulations and plant genetics. Oliver & Boyd, Edinburgh, pp 29–45
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 389–407
Serizawa N, Nasuda S, Endo TR (2001a) Barley chromosome addition lines of wheat for screening of AFLP markers on barley chromosomes. Genes Genet Syst 76:107–110
Serizawa N, Nasuda S, Shi F et al (2001b) Deletion-based physical mapping of barley chromosome 7H. Theor Appl Genet 103:827–834
Shi F, Endo TR (1997) Production of wheat-barley disomic addition lines possessing an Aegilops cylindrica gametocidal chromosome. Genes Genet Syst 72:243–248
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 74:49–54
Sorokin A, Marthe F, Houben A et al (1994) Polymerase chain reaction mediated localization of RFLP clones to microisolated translocation chromosomes of barley. Genome 37:550–555
Stephens JL, Brown SE, Lapitan NLV et al (2004) Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique. Genome 47:179–189
Suchánková P, Kubaláková M, Kovárová P et al (2006) Dissection of the nuclear genome of barley by chromosome flow sorting. Theor Appl Genet 113:651–659
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 51:199–206
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. https://doi.org/10.1139/g02-024
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 97–119
Tsuchiya T (1969) Status of studies of primary trisomics and other aneuploids in barley. Genetica 40:216
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 361–384
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 72:303–309
Valarik M, Bartos J, Kovarova P et al (2004) High-resolution FISH on super-stretched flow-sorted plant chromosomes. Plant J 37:940–950
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 149:258–270
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG, part of Springer Nature
About this chapter
Cite this chapter
Houben, A., Aliyeva-Schnorr, L., Joshi, G.P., Endo, T.R. (2018). Cytogenetics and Genetic Stocks for Physical Mapping and Sequencing. 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_3
Download citation
DOI: https://doi.org/10.1007/978-3-319-92528-8_3
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-92527-1
Online ISBN: 978-3-319-92528-8
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)