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Chromosome-based genomics in the cereals

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Abstract

The cereals are of enormous importance to mankind. Many of the major cereal species – specifically, wheat, barley, oat, rye, and maize – have large genomes. Early cytogenetics, genome analysis and genetic mapping in the cereals benefited greatly from their large chromosomes, and the allopolyploidy of wheat and oats that has allowed for the development of many precise cytogenetic stocks. In the genomics era, however, large genomes are disadvantageous. Sequencing large and complex genomes is expensive, and the assembly of genome sequence is hampered by a significant content of repetitive DNA and, in allopolyploids, by the presence of homoeologous genomes. Dissection of the genome into its component chromosomes and chromosome arms provides an elegant solution to these problems. In this review we illustrate how this can be achieved by flow cytometric sorting. We describe the development of methods for the preparation of intact chromosome suspensions from the major cereals, and their analysis and sorting using flow cytometry. We explain how difficulties in the discrimination of specific chromosomes and their arms can be overcome by exploiting extant cytogenetic stocks of polyploid wheat and oats, in particular chromosome deletion and alien addition lines. Finally, we discuss some of the applications of flow-sorted chromosomes, and present some examples demonstrating that a chromosome-based approach is advantageous for the analysis of the complex genomes of cereals, and that it can offer significant potential for the delivery of genome sequencing and gene cloning in these crops.

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References

  • Allouis S, Moore G, Bellec A et al. (2003) Construction and characterisation of a hexaploid wheat (Triticum aestivum L.) BAC library from the reference germplasm ‘Chinese Spring’. Cereal Res Commun 31: 331–338.

    CAS  Google Scholar 

  • Arumuganathan K, Martin GB, Telenius H, Tanksley SD, Earle ED (1994) Chromosome 2-specific DNA clones from flow-sorted chromosomes of tomato. Mol Gen Genet 242: 551–558.

    Article  PubMed  CAS  Google Scholar 

  • Aston C, Mishra B, Schwartz DC (1999) Optical mapping and its potential for large-scale sequencing projects. Trends Biotech 17: 297–302.

    Article  CAS  Google Scholar 

  • Bennett MD, Smith J (1976) Nuclear DNA amounts in angiosperms. Phil Trans R Soc B 274: 227–274.

    PubMed  CAS  Google Scholar 

  • Chalhoub B, Belcram H, Caboche M (2004) Efficient cloning of plant genomes into bacterial artificial chromosome (BAC) libraries with larger and more uniform insert size. Plant Biotechnol J 2: 181–188.

    Article  PubMed  CAS  Google Scholar 

  • Dean FB, Nelson JR, Giesler TL, Lasken RS (2001) Rapid amplification of plasmid and phage DNA using phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 11: 1095–1099.

    Article  PubMed  CAS  Google Scholar 

  • de Jong JH, Fransz P, Zabel P (1999) High resolution FISH in plants – techniques and applications. Trends Plant Sci 4: 258–263.

    Article  Google Scholar 

  • Doležel J, Lucretti S (1995) High-resolution flow karyotyping and chromosome sorting in Vicia faba lines with standard and reconstructed karyotypes. Theor Appl Genet 90: 797–802.

    Google Scholar 

  • 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: 93–98.

    Article  Google Scholar 

  • Doležel J, Greilhuber J, Lucretti S, et al. (1998) Plant genome size estimation by flow cytometry: Inter-laboratory comparison. Ann Bot 82 (Suppl. A): 17–26.

    Article  Google Scholar 

  • Doležel J, Lucretti S, Schubert I (1994) Plant chromosome analysis and sorting by flow cytometry. Crit Rev Plant Sci 13: 275–309.

    Google Scholar 

  • Doležel J, Kubaláková M, Bartoš J, Macas J (2004) Flow cytogenetics and plant genome mapping. Chromosome Res 12: 77–91.

    Article  PubMed  Google Scholar 

  • Doležel J, Kubaláková M, Bartoš J, Macas J (2005a) Chromosome flow sorting and physical mapping. In Meksem K, Kahl G, eds., The Handbook of Plant Genome Mapping. Genetic and Physical Mapping. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA, pp. 151–171.

    Chapter  Google Scholar 

  • Doležel J, Kubaláková M, Suchánková P et al. (2005b) Flow cytogenetic analysis of the wheat genome. In Tsunewaki K, ed., Frontiers of Wheat Bioscience. Hundredth Memorial Issue of Wheat Information Service. Yokohama: Kihara Memorial Yokohama Foundation for the Advancement of Life Sciences, pp. 3–15.

    Google Scholar 

  • Endo TR, Gill BS (1996) The deletion stocks of common wheat. J Hered 87: 295–307.

    CAS  Google Scholar 

  • Feldman M, Levy AA (2005) Allopolyploidy – a shaping force in the evolution of wheat genomes. Cytogenet Genome Res 109: 250–258.

    Article  PubMed  CAS  Google Scholar 

  • Fuchs J, Houben A, Brandes A, Schubert I (1996) Chromosome ‘painting’ in plants – A feasible technique? Chromosoma 104: 315–320.

    PubMed  CAS  Google Scholar 

  • Gill BS, Friebe B, Endo TR (1991) Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat (Triticum aestivum L.). Genome 34: 830–839.

    Google Scholar 

  • Gill KS, Arumuganathan K, Le JH (1999) Isolating individual wheat (Triticum aestivum) chromosome arm by flow cytometric analysis of ditelosomic lines. Theor Appl Genet 98: 1248–1252.

    Article  Google Scholar 

  • Goff SA, Ricke D, Lan TH et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science 296: 92–100.

    Article  PubMed  CAS  Google Scholar 

  • International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793–800.

    Article  CAS  Google Scholar 

  • Isidore E, Scherrer B, Bellec A et al. (2005) Direct targeting and rapid isolation of BAC clones spanning a defined chromosome region. Func Integr Genomics 5: 97–103.

    Article  CAS  Google Scholar 

  • Islam AKMR, Shepherd KW, Sparrow DHB (1981) Isolation and characterization of euplasmic wheat–barley chromosome addition lines. Heredity 46: 161–174.

    Google Scholar 

  • Islam AKMR, Shepherd KW (1990) Incorporation of barley chromosomes into wheat. In Bajaj YPS, ed., Biotechnology in Agriculture and Forestry 13: Wheat. Berlin: Springer-Verlag, pp. 128–151.

    Google Scholar 

  • Islam AKMR, Shepherd KW (2000) Isolation of a fertile wheat– barley addition line carrying the entire barley chromosome 1H. Euphytica 111: 145–149.

    Article  Google Scholar 

  • Janda J, Bartoš J, Šafář J et al. (2004) Construction of a subgenomic BAC library specific for chromosomes 1D, 4D and 6D of hexaploid wheat. Theor Appl Genet 109: 1337–1345.

    Article  PubMed  CAS  Google Scholar 

  • Janda J, Šafář J, Kubaláková M et al. (2006) Novel resources for wheat genomics: BAC library specific for the short arm of chromosome 1B. Plant J 47: 977–986.

    Article  PubMed  CAS  Google Scholar 

  • Jiang J, Friebe B, Gill BS (1994) Recent advances in alien gene transfer in wheat. Euphytica 73: 199–212.

    Article  Google Scholar 

  • Joppa LR (1993) Chromosome engineering in tetraploid wheat. Crop Sci 33: 908–913.

    Article  Google Scholar 

  • Kovářová P, Navrátilová A, Macas J, Doležel J (2007) Chromosome analysis and sorting in common vetch (Vicia sativa L.) using flow cytometry. Biol Plant 51: 43–48.

    Google Scholar 

  • Kubaláková M, Vrána J, Číhalíková J, Lysák MA, Doležel J (2001) Localisation of DNA sequences on plant chromosomes using PRINS and C-PRINS. Methods Cell Sci 23: 71–82.

    Article  PubMed  Google Scholar 

  • Kubaláková M, Vrána J, Číhalíková J, Šimková H, Doležel J (2002) Flow karyotyping and chromosome sorting in bread wheat (Triticum aestivum L.). Theor Appl Genet 104: 1362–1372.

    Article  PubMed  Google Scholar 

  • Kubaláková M, Valárik M, Bartoš J (2003) Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry. Genome 46: 893–905.

    Article  PubMed  Google Scholar 

  • Kubaláková M, Kovářová P, Suchánková P (2005) Chromosome sorting in tetraploid wheat and its potential for genome analysis. Genetics 170: 823–829.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  Google Scholar 

  • Kynast RG, Okagaki RJ, Galatowitsch MW (2004) Dissecting the maize genome by using chromosome addition and radiation hybrid lines. Proc Natl Acad Sci USA 101: 9921–9926.

    Article  PubMed  CAS  Google Scholar 

  • Laurie DA, Bennett MD (1985). Nuclear DNA content in the genera Zea and Sorghum Intergeneric, interspecific and intraspecific variation. Heredity 55: 307.

    Google Scholar 

  • Lee JH, Arumuganathan K (1999) Metaphase chromosome accumulation and flow karyotypes in rice (Oryza sativa L.) root tip meristem cells. Mol Cells 9: 436–439.

    PubMed  CAS  Google Scholar 

  • Lee JH, Arumuganathan K, Kaeppler SM, Kaeppler HF, Papa CM (1996) Cell synchronization and isolation of metaphase chromosomes from maize (Zea mays L) root tips for flow cytometric analysis and sorting. Genome 39: 697–703.

    CAS  PubMed  Google Scholar 

  • Lee JH, Arumuganathan K, Yen Y, Kaeppler S, Kaeppler H, Baenziger PS (1997) Root tip cell cycle synchronization and metaphase-chromosome isolation suitable for flow sorting in common wheat (Triticum aestivum L.). Genome 40: 633–638.

    CAS  PubMed  Google Scholar 

  • Lee JH, Arumuganathan K, Chung YS et al. (2000) Flow cytometric analysis and chromosome sorting of barley (Hordeum vulgare L.). Mol Cells 10: 619–625.

    Article  PubMed  CAS  Google Scholar 

  • Lee JH, Arumuganathan K, Kaeppler SM et al. (2002) Variability of chromosomal DNA contents in maize (Zea mays L.) inbred and hybrid lines. Planta 215: 666–671.

    Article  PubMed  CAS  Google Scholar 

  • Li L, Arumuganathan K (2001) Physical mapping of 45S and 5S rDNA on maize metaphase and sorted chromosomes by FISH. Hereditas 134: 141–145.

    Article  PubMed  CAS  Google Scholar 

  • Linde-Laursen I (1988) Giemsa C-banding of barley chromosomes. VI. Localization of breakpoints in 70 reciprocal translocations. Hereditas 108: 65–76.

    Google Scholar 

  • Lucretti S, Doležel J (1997) Bivariate flow karyotyping in broad bean (Vicia faba). Cytometry 28: 236–242.

    Article  PubMed  CAS  Google Scholar 

  • Lucretti S, Doležel J, Schubert I, Fuchs J (1993) Flow karyotyping and sorting of Vicia faba chromosomes. Theor Appl Genet 85: 665–672.

    Article  Google Scholar 

  • Luo MC, Thomas C, You FM et al. (2003) High-throughput fingerprinting of bacterial artificial chromosomes using the SNaPshot labeling kit and sizing of restriction fragments by capillary electrophoresis. Genomics 82: 378–389.

    Article  PubMed  CAS  Google Scholar 

  • 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.). Chrom Res 7: 431–444.

    Article  PubMed  Google Scholar 

  • Macas J, Doležel J, Gualberti G, Pich U, Schubert I, Lucretti S (1995) Primer-induced labeling of pea and field bean chromosomes in situ and in suspension. BioTechniques 19: 402–408.

    PubMed  CAS  Google Scholar 

  • Marthe F, Künzel G (1994) Localization of translocation breakpoints in somatic metaphase chromosomes of barley. Theor Appl Genet 89: 240–248.

    Article  CAS  Google Scholar 

  • Messing J, Bharti AK, Karlowski WM et al. (2004) Sequence composition and genome organization of maize. Proc Natl Acad Sci USA 101: 14349–14354.

    Article  PubMed  CAS  Google Scholar 

  • Meyers BC, Scalabrin S, Morgante M (2004) Mapping and sequencing complex genomes: let’s get physical! Nature Rev Genet 5: 578–581.

    Article  CAS  PubMed  Google Scholar 

  • Nasuda S, Hudakova S, Schubert I, Houben A, Endo TR (2005) Stable barley chromosomes without centromeric repeats. Proc Natl Acad Sci USA 102: 9842–9847.

    Article  PubMed  CAS  Google Scholar 

  • Paterson AH (2006) Leafing through the genomes of our major crop plants: strategies for capturing unique information. Nat Rev Genet 7: 174–184.

    Article  PubMed  CAS  Google Scholar 

  • Paux E, Roger D, Badaeva E et al. (2006) Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J 48: 463–474.

    Article  PubMed  CAS  Google Scholar 

  • Pedersen C, Langridge P (1997) Identification of the entire chromosome complement of bread wheat by two-colour FISH. Genome 40: 589–593.

    CAS  PubMed  Google Scholar 

  • Potz H, Schubert V, Houben A, Schubert I, Weber WE (1996) Aneuploids as a key for new molecular cloning strategies: development of DNA markers by microdissection using Triticum aestivum–Aegilops markgrafii chromosome addition line B. Euphytica 89: 41–47.

    Article  CAS  Google Scholar 

  • Požárková D, Koblížková A, Román B (2002) Development and characterization of microsatellite markers from chromosome 1-specific DNA libraries of Vicia faba. Biol Plant 45: 337–345.

    Article  Google Scholar 

  • Qi LL, Echalier B, Chao SA et al. (2004) Chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168: 701–712.

    Article  PubMed  CAS  Google Scholar 

  • Riera-Lizarazu O, Rines HW, Phillips RL (1996) Cytological and molecular characterization of oat × maize partial hybrids. Theor Appl Genet 93: 123–135.

    Article  Google Scholar 

  • Román B, Šatovič Z, Požárková D et al. (2004) Development of a composite map in Vicia faba, breeding applications and future prospects. Theor Appl Genet 108: 1079–1088.

    Article  PubMed  CAS  Google Scholar 

  • Röder MS, Korzun V, Gill BS, Ganal MW (1998) The physical mapping of microsatellite markers in wheat. Genome 41: 278–283.

    Article  Google Scholar 

  • Šafář J, Bartoš J, Janda J et al. (2004) Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J 39: 960–968.

    Article  PubMed  CAS  Google Scholar 

  • Šafář J, Šimková H, Suchánková P et al. (2006) A novel resource for genomics of rye and wheat: BAC library specific for the short arm of chromosome 1R (1RS). In: Abstracts of the International Conference ‘Plant and Animal Genome XIV’. San Diego: Sherago International, p. 115.

  • Schlegel R, Melz G, Nestrowicz R (1987) A universal reference karyotype in rye, Secale cereale L. Theor Appl Genet 74: 820–826.

    Article  Google Scholar 

  • Schubert I, Doležel J, Houben A, Scherthan H, Wanner G (1993) Refined examination of plant metaphase chromosome structure at different levels made feasible by new isolation methods. Chromosoma 102: 96–101.

    Article  Google Scholar 

  • Schwarzacher T, Wang ML, Leitch AR, Miller N, Moore G, Heslop-Harrison JS (1997) Flow cytometric analysis of the chromosomes and stability of a wheat cell-culture line. Theor Appl Genet 94: 91–97.

    Article  CAS  PubMed  Google Scholar 

  • Sears ER (1954) The aneuploids of common wheat. Missouri Agric Exp Stn Res Bull 572: 1–58.

    Google Scholar 

  • Shi F, Endo TR (1997) Production of wheat–barley disomic addition lines possessing an Aegilops cylindrica gametocidal chromosome. Genes Genet Syst 72: 243–248.

    Article  Google Scholar 

  • Šimková H, Číhalíková J, Vrána J, Lysák MA, Doležel J (2003) Preparation of high molecular weight DNA from plant nuclei and chromosomes isolated from root tips. Biol Plantarum 46: 369–373.

    Article  Google Scholar 

  • Stein N, Ponelies N, Musket T, McMullen M, Weber G (1998) Chromosome micro-dissection and region-specific libraries from pachytene chromosomes of maize (Zea mays L.). Plant J 13: 281–289.

    Article  CAS  Google Scholar 

  • Suchánková P, Kubaláková M, Kovářová P et al. (2006) Dissection of the nuclear genome of barley by chromosome flow sorting. Theor Appl Genet 113: 651–659.

    Article  PubMed  CAS  Google Scholar 

  • Telenius H, Carter NP, Bebb CE, Nordenskjöld M, Ponder BAJ, Tunnacliffe A (1992) Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13: 718–725.

    Article  PubMed  CAS  Google Scholar 

  • ten Hoopen R, Manteuffel R, Doležel J, Malysheva L, Schubert I (2000) Evolutionary conservation of kinetochore protein sequences in plants. Chromosoma 109: 482–489.

    PubMed  Google Scholar 

  • Thangavelu M, James AB, Bankier A, Bryan GJ, Dear PH, Waugh R (2003) HAPPY mapping in a plant genome: reconstruction and analysis of a high-resolution physical map of a 1.9 Mbp region of Arabidopsis thaliana chromosome 4. Plant Biotech J 1: 23–31.

    Article  CAS  Google Scholar 

  • Valárik M, Bartoš J, Kovářová P, Kubaláková M, de Jong H, Doležel J (2004) High-resolution FISH on super-stretched flow-sorted plant chromosomes. Plant J 37: 940–950.

    Article  PubMed  CAS  Google Scholar 

  • Venora GS, Blangiforti MR, Castiglione D et al. (2002) Chromatin organisation and computer aided karyotyping of Triticum durum Desf. cv. Timilia. Caryologia 55: 91–98.

    Google Scholar 

  • Vrána J, Kubaláková M, Šimková H, Číhalíková J, Lysák MA, Doležel J (2000) Flow-sorting of mitotic chromosomes in common wheat (Triticum aestivum L.). Genetics 156: 2033–2041.

    PubMed  Google Scholar 

  • Wang ML, Leitch AR, Schwarzacher T, Heslop-Harrison JS, Moore G (1992) Construction of a chromosome-enriched HpaII library from flow-sorted wheat chromosomes. Nucleic Acids Res 20: 1897–1901.

    Article  PubMed  CAS  Google Scholar 

  • Wenzl P, Carling J, Kudrna D et al. (2004) Diversity arrays technology (DArT) for whole-genome profiling of barely. Proc Natl Acad Sci USA 101: 9915–9920.

    Article  PubMed  CAS  Google Scholar 

  • Xu YB, McCouch SR, Zhang QF (2005) How can we use genomics to improve cereals with rice as a reference genome? Plant Mol Biol 59(1): 7–26.

    Article  PubMed  CAS  Google Scholar 

  • Yoshino M, Nasuda S, Endo TR (1998) Detection of terminal deletions in barley chromosomes by the PCR-based method. Genes Genet Syst 73: 163–168.

    Article  CAS  Google Scholar 

  • Yu J, Hu SN, Wang J et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296: 79–92.

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, CZ-77200, Olomouc, Czech Republic

    Jaroslav Doležel, Marie Kubaláková & Jan Bartoš

  2. Department of Cell Biology and Genetics, Palacký University, Šlechtitelů 11, CZ-78371, Olomouc, Czech Republic

    Jaroslav Doležel & Marie Kubaláková

  3. UMR ASP 1095, INRA-Université Blaise Pascal, 63100, Clermont-Ferrand, France

    Etienne Paux & Catherine Feuillet

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  1. Jaroslav Doležel
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  2. Marie Kubaláková
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  3. Etienne Paux
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  4. Jan Bartoš
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  5. Catherine Feuillet
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Correspondence to Jaroslav Doležel.

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Doležel, J., Kubaláková, M., Paux, E. et al. Chromosome-based genomics in the cereals. Chromosome Res 15, 51–66 (2007). https://doi.org/10.1007/s10577-006-1106-x

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