Russian Journal of Genetics

, Volume 41, Issue 4, pp 378–388 | Cite as

Studying plant genome variation using molecular markers

  • S. A. Gostimsky
  • Z. G. Kokaeva
  • F. A. Konovalov
Theoretical Papers and Reviews
Received:

Abstract

The authors’ studies on the organization and variation of plant genome with the use of molecular markers are briefly reviewed with special emphasis on random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR), sequence characterized amplified region (SCAR), and cleaved amplified polymorphic sequence (CAPS) markers detected with the use of polymerase chain reaction (PCR). These markers have been demonstrated to be promising for identifying cultivars and determining the purity of genetic strains of pea. Genetic relationships between strains, cultivars, and mutants of pea have been studied. The role of molecular markers in molecular genetic mapping and localizing the genes of commercially important characters of pea has been shown. The possibility of the use of molecular markers for studying somaclonal variation and detecting mutagenic factors in plants during long-term spaceflights is considered. The prospects of using DNA markers for understanding the organization and variability of higher plant genomes are discussed.

Keywords

Polymerase Chain Reaction Molecular Marker Genetic Mapping Sequence Repeat Genetic Relationship 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in to check access.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

REFERENCES

  1. 1.
    Welsh, J. and McClelland, M., Fingerprinting Genomes Using PCR with Arbitrary Primers, Nucleic Acids Res., 1991, vol. 18, pp. 7213–7218.Google Scholar
  2. 2.
    Williams, J.G.K., Kubelik, A.R., Livak, K.J., et al., DNA Polymorphisms Amplified by Arbitrary Primers Are Useful As Genetic Markers, Nucleic Acids Res., 1990, vol. 18, pp. 6531–6535.PubMedGoogle Scholar
  3. 3.
    Weeden, N.F., Timmerman, G.M., Hemmat, M., et al., Inheritance and Reliability of RAPD Markers, Appl. RAPD Tech. Plant Breed. (Minneapolis, United States), 1992, pp. 12–17.Google Scholar
  4. 4.
    Karp, A., Kresovich, S., Bhat, K.V., et al., Molecular Tools in Plant Genetic Resources Conservation: A Guide to the Technologies, IPGRI Technical Bull., Rome: Int. Plant Genet. Resources Inst., 1997, no. 2.Google Scholar
  5. 5.
    Virk, P.S., Zhu, J., Newbury, H.J., et al., Effectiveness of Different Classes of Molecular Markers for Classifying and Revealing Variations in Rice (Oryza sativa) Germplasm, Euphytica, 2000, vol. 112, pp. 275–284.CrossRefGoogle Scholar
  6. 6.
    Waugh, R. and Powell, W., Using RAPD Markers for Crop Improvement, Trends Biotechnol., 1992, vol. 10, pp. 186–191.CrossRefGoogle Scholar
  7. 7.
    Zietkiewicz, E., Rafalski, A., and Labuda, D., Genome Fingerprinting by Simple Sequence Repeat (SSR)-Anchored Polymerase Chain Reaction Amplification, Genomics, 1994, vol. 20, pp. 176–183.CrossRefPubMedGoogle Scholar
  8. 8.
    Bornet, B. and Branchard, M., Nonanchored Inter Simple Sequence Repeat (ISSR) Markers: Reproducible and Specific Tools for Genome Fingerprinting, Plant Mol. Biol. Rep., 2001, vol. 19, pp. 209–215.Google Scholar
  9. 9.
    Malyshev, S.V. and Kartel’, N.A., Molecular Markers in Genetic Mapping in Plants, Mol. Biol. (Moscow), 1997, vol. 31, no.2, pp. 197–208.Google Scholar
  10. 10.
    Galande, A.A., Tiwari, R., Ammiraju, J.S.S., et al., Genetic Analysis of Kernel Hardness in Bread Wheat Using PCR-Based Markers, Theor. Appl. Genet., 2001, vol. 103, pp. 601–606.Google Scholar
  11. 11.
    Irzykowska, L., Wolko, B., and Swikcicki, W.K., Interval Mapping of QTLs Controlling Some Morphological Traits in Pea, Cell. Mol. Biol. Lett., 2002, vol. 7, pp. 417–422.PubMedGoogle Scholar
  12. 12.
    Kesseli, R.V., Paran, J., and Michelmore, R.W., Efficient Mapping of Specifically Targeted Genomic Regions and the Tagging of These Regions with Reliable PCR-Based Genetic Markers, in Application of RAPD Technology to Plant Breeding: Joint Plant Breeding Symposia Series, Minneapolis, Minn., 1993, pp. 31–36.Google Scholar
  13. 13.
    Tiwari, K.R., Penner, G.A., and Warkentin, T.D., Inheritance of Powdery Mildew Resistance in Pea, Can. J. Plant Sci., 1997, vol. 77, pp. 307–310.Google Scholar
  14. 14.
    Zijlstra, C., Identification of Meloidogyne chitwoodi, M. fallax and M. hapla Based on SCAR-PCR: A Powerful Way of Enabling Reliable Identification of Population or Individuals That Share Common Traits, Eur. J. Plant Physiol., 2000, vol. 106, pp. 283–290.CrossRefGoogle Scholar
  15. 15.
    Deng, Z., Huang, S., Xiao, S.Y., and Gmitter, F.G., Jr., Development and Characterization of SCAR Markers Linked to the Citrus Tristeza Virus Resistance Gene from Poncirus trifoliate, Genome, 1997, vol. 40, pp. 697–704.Google Scholar
  16. 16.
    Dax, E., Livneh, O., Auskevicius, E., et al., A SCAR Marker Linked to the ToMV Resistance Gene, Tm22, in Tomato, Euphytica, 1998, vol. 101, pp. 73–77.CrossRefGoogle Scholar
  17. 17.
    Laroche, A., Demeke, T., Gaudet, D.A., et al., Development of a PCR Marker for Rapid Identification of the Bt-10 Gene for Common Bunt Resistance in Wheat, Genome, 2000, vol. 43, pp. 217–223.CrossRefPubMedGoogle Scholar
  18. 18.
    Konieczny, A. and Ausubel, F.M., A Procedure for Mapping Arabidopsis Mutations Using Co-Dominant Ecotype-Specific PCR-Based Markers, Plant J., 1993, vol. 4, pp. 403–410.CrossRefPubMedGoogle Scholar
  19. 19.
    Whitkus, R., Doebley, J., and Lee, M., Comparative Genome Mapping of Sorghum and Maize, Genetics, 1992, vol. 132, pp. 119–1130.Google Scholar
  20. 20.
    Sivolap, Yu.M. and Kalendar’, R.N., Genetic Polymorphism of Barley As Revealed by PCR with Arbitrary Primers, Russ. J. Genet., 1995, vol. 31, no.10, pp. 1155–1161.Google Scholar
  21. 21.
    Oganisyan, A.S., Kochieva, E.Z., and Ryskov, A.P., Fingerprinting of Potato Species and Cultivars by the RAPD-PCR Method, Russ. J. Genet., 1996, vol. 32, no.3, pp. 391–394.Google Scholar
  22. 22.
    Weising, K., Nybom, H., Wolff, K., and Meyer, W., DNA Fingerprinting in Plants and Fungi, Boca Raton, FL: CRC, 1995.Google Scholar
  23. 23.
    Ispol’zovanie PTsR-analiza v genetiko-selektsionnykh issledovaniyakh. Nauchno-metodicheskoe rukovodstvo (Use of PCR Analysis in Genetics and Breeding: A Theoretical and Methodical Handbook), Sivolap, Yu.M., Ed., Kiev: Agrarna Nauka, 1998.Google Scholar
  24. 24.
    Ellis, T.H.N., Hellens, R.P., Turner, L., et al., On the Pea Linkage Map, Pisum Genet., 1993, vol. 25, pp. 5–12.Google Scholar
  25. 25.
    Kokaeva, Z.G., Valiejo-Roman, K.M., Bobrova, V.K., et al., Application of Random Amplified Polymorphic DNA Technique for Detection of Polymorphism among Somaclonal Variants of Pea, Plant Genome IV: The Int. Conf. of the Status of Plant Genome Research, San Diego, 1996, p. 41.Google Scholar
  26. 26.
    Kokaeva, Z.G., Bobrova, V.K., Petrova, T.V., et al., Genetic Polymorphism of Pea Cultivars, Lines, and Mutants Detected by RAPD Analysis, Rus. J. Genet., 1998, vol. 34, no.6, pp. 632–637.Google Scholar
  27. 27.
    Kokaeva, Z.G., Koveza, O.V., Bobrova, V.K., et al., Use of RAPD Analysis for Genotype Identification in Pea, Tezisy dokladov 2-i mezhdunarodnoi nauchnoi konferentsii “Biotekhnologiya v rastenievodstve, zhivotnovodstve i veterinarii” (Proc. 2nd Int. Conf. Biotechnology in Plant Industry, Animal Breeding, and Veterinary), Moscow, 2000, pp. 80–81.Google Scholar
  28. 28.
    Kokaeva, Z.G., Koveza, O.V., Chegamirza, K., et al., Detection of DNA Polymorphism in Various Genotypes of Pea with the Use of the Polymerase Chain Reaction, in 2nd Int. Iran and Russia Conf. “Agriculture and Natural Resources,” Moscow, 2001, pp. 8–9.Google Scholar
  29. 29.
    Koveza, O.V., Identification, Cloning, and Analysis of Molecular Markers of the Pea Genome, Cand. Sci. (Biol.) Dissertation, Moscow: Inst. Gen. Genet., 2003.Google Scholar
  30. 30.
    Koveza, O.V., Kokaeva, Z.G., Konovalov, F.A., and Gostimsky, S.A., Detection and Mapping of Polymorphic Markers of the Genome of Pea Pisum sativum L., Rus. J. Genet., 2005, vol. 41, no.3, pp. 341–348.Google Scholar
  31. 31.
    Konovalov, F.A., SARS Markers with Degenerate Primers and Their Potential in Mapping Plant Genomes, Tezizy dokladov 11-i mezhdunarodnoi konferentsii studentov, aspirantov i molodykh uchenykh “Lomonosov-2004” (Proc. 11th Int. Conf. of Undergraduate and Postgraduate Students and Young Researchers “ Lomonosov-2004”), Moscow, 2004, pp. 69–70.Google Scholar
  32. 32.
    Nouzova, M., Neumann, P., Navratilova, A., et al., Microarray-Based Survey of Repetitive Genomic Sequences in Vicia spp., Plant. Mol. Biol., 2001, vol. 45, pp. 229–244.CrossRefPubMedGoogle Scholar
  33. 33.
    Ko, J.-M., Do, G.-S., Suh, D.-Y., et al., Identification and Chromosomal Organization of Two Rye Genome-Specific RAPD Products Useful As Introgression Markers in Wheat, Genome, 2002, vol. 45, pp. 157–164.CrossRefPubMedGoogle Scholar
  34. 34.
    Kato, A., Sriprasetsak, P., Seki, H., et al., Functional Analysis of Retrotransposons in Pea, Plant Cell Physiol., 1999, vol. 40, pp. 933–941.PubMedGoogle Scholar
  35. 35.
    Pearce, S.R., Knox, M.R., Ellis, T.H.N., et al., Pea Ty1-copia Group Retrotransposon: Transpositional Activity and Use As Markers to Study Genetic Diversity in Pisum, Mol. Gen. Genet., 2000, vol. 263, pp. 898–907.CrossRefPubMedGoogle Scholar
  36. 36.
    Neumann, P., Nouzova, M., and Macas, J., Molecular and Cytogenetic Analysis of Repetitive DNA in Pea (Pisum sativum L.), Genome, 2001, vol. 44, pp. 716–728.CrossRefPubMedGoogle Scholar
  37. 37.
    Tanksley, S.D., Ganal, M.W., and Martin, G.B., Chromosome Landing: A Paradigm for Map-Based Gene Cloning in Plants with Large Genomes, Trends Genet., 1995, vol. 11, no.2, pp. 63–68.CrossRefPubMedGoogle Scholar
  38. 38.
    Weeden, N.F., Ellis, T.H.N., Timmerman-Vaughan, G.M., et al., A Consensus Linkage Map for Pisum sativum, Pisum Genet., 1998, vol. 30, pp. 1–4.Google Scholar
  39. 39.
    Laucou, V., Haurogne, K., Ellis, N., and Rameau, C., Genetic Mapping in Pea: 1. RAPD-Based Genetic Linkage Map of Pisum sativum, Theor. Appl. Genet., 1998, vol. 97, pp. 905–915.CrossRefGoogle Scholar
  40. 40.
    Brauner, S., Murphy, R.L., Przyborowski, J., et al., STS Markers for Comparative Mapping in Legumes, J. Am. Soc. Hort. Sci., 2002, vol. 127, pp. 616–622.Google Scholar
  41. 41.
    Cheghamirza, K., Koveza, O.V., Konovalov, F.A., and Gostimsky, S.A., Identification and Mapping of chi115 Gene and DNA Markers Linked to It in Pea (Pisum sativum L.), Rus. J. Genet., 2004, vol. 40, no.7, pp. 737–742.CrossRefGoogle Scholar
  42. 42.
    Cheghamirza, K., Molecular Genetic Mapping of Qualitative and Quantitative Trait Loci in Pea, Cand. Sci. (Biol.) Dissertation, Moscow: Inst. Gen. Genet., 2004.Google Scholar
  43. 43.
    Flavell, A.J., Bolshakov, V.N., Booth, A., et al., A Microarray-Based High Throughput Molecular Marker Genotyping Method: The Tagged Microarray Marker (TAM) Approach, Nucleic Acids Res., 2003, vol. 31, e115 (electronic version).Google Scholar
  44. 44.
    Michelmore, R.W., Paran, J., and Kesseli, R.V., Identification of Markers Linked to Disease Resistance Genes by Bulk Segregant Analysis: A Rapid Method to Detect Markers in Specific Genomic Regions Using Segregating Populations, Proc. Natl. Acad. Sci. USA, 1991, vol. 88, pp. 9828–9832.PubMedGoogle Scholar
  45. 45.
    Giovannoni, J.J., Wing, R.A., Ganal, M.W., and Tanksley, S.D., Isolation of Molecular Markers from Specific Chromosomal Intervals Using DNA Pools from Existing Mapping Populations, Nucleic Acid Res., 1991, vol. 19, pp. 6553–6558.PubMedGoogle Scholar
  46. 46.
    Timmerman, D.M., Frew, T.J., Miller, A.L., et al., Linkage Mapping of sbm-1, a Gene Conferring Resistance to a Pea Seed-Borne Mosaic Virus, Using Molecular Markers in Pisum sativum, Teor. Appl. Genet., 1993, vol. 95, pp. 609–615.Google Scholar
  47. 47.
    Temnykh, S.V., Mapping of Genes That Control Symbiotic Nitrogen Fixation in Pea, Cand. Sci. (Biol.) Dissertation, Novosibirsk: Inst. Cytol. Genet., 1994.Google Scholar
  48. 48.
    Kokaeva, Z.G., Bobrova, V.K., Gostimsky, S.A., and Troitskii, A.V., Inheritance and Characterization of RAPD Markers Revealed in Somaclonal Variants of Pea, Dokl. Akad. Nauk, 2000, vol. 372, no.4, pp. 565–567.Google Scholar
  49. 49.
    Cheghamirza, K., Koveza, O.V., Konovalov, F.A., and Gostimsky, S.A., Identification of RAPD-Markers and Their Use for Molecular Mapping in Pea, Cell. Mol. Biol. Lett., 2002, vol. 7, pp. 649–655.PubMedGoogle Scholar
  50. 50.
    Penner, G.A., Bezte, L.J., and Leisle, D., Identification of RAPD Markers Linked to a Gene Governing Cadmium Uptake in Durum Wheat, Genome, 1995, vol. 38, pp. 543–547.Google Scholar
  51. 51.
    Subudhi, P.K., Borkakati, R.P., Virmani, S.S., and Huang, N., Molecular Mapping of a Thermosensitive Genetic Male Sterility Gene in Rice Using Bulked Segregant Analyses, Genome, 1997, vol. 40, pp. 188–194.Google Scholar
  52. 52.
    Larkin, P.J. and Scowcroft, W.R., Somaclonal Variation—A Novel Source of Variability from Cell Cultures for Plant Improvement, Theor. Appl. Genet., 1981, vol. 60, pp. 197–241.Google Scholar
  53. 53.
    Skaukroft, U.R., in Mobil’nost’ genoma rastenii (Mobility of the Plant Genome), Moscow: Agropromizdat, 1990, pp. 228–260.Google Scholar
  54. 54.
    Gostimsky, S.A., Bagrova, A.M., and Ezhova, T.A., Detection and Cytogenetic Analysis of the Variation Arising during Regeneration of Plants from Cultured Tissues of Pisum sativum, Dokl. Akad. Nauk SSSR, 1985, vol. 283, no.4, pp. 1007–1011.Google Scholar
  55. 55.
    Ezhova, T.A., Bagrova, A.M., and Gostimsky, S.A., Study of the Heritability of Somaclonal Changes in Pisum sativum Regenerants, Genetika (Moscow), 1989, vol. 25, no.5, pp. 878–885.Google Scholar
  56. 56.
    Bagrova, A.M., Ezhova, T.A., Khartina, G.A., and Gostimsky, S.A., Generation of Long-Term Morphogenic Callus Cultures and Analysis of the Somaclonal Variation in Regenerants of Grain and Vegetable Cultivars of Pea, Vestn. Mosk. Univ., Ser. 16: Biol., 1991, no. 1, pp. 28–33.Google Scholar
  57. 57.
    Frenkel’-Konrat, Kh., Geizen, G., Diz, P., et al., Mobil’nost’ genoma rastenii (Mobility of the Plant Genome), Moscow: Agropromizdat, 1990.Google Scholar
  58. 58.
    Kokaeva, Z.G., Bobrova, V.K., Valiejo-Roman, K.M., et al., RARD Analysis of the Somaclonal and Among-Cultivar Variations in Pea, Dokl. Akad. Nauk, 1997, vol. 355, no.1, pp. 134–136.Google Scholar
  59. 59.
    Kuznetsova, O.I., Ash, O.A., Khartina, G.A., and Gostimsky, S.A., RARD Analysis of Somaclones in Pea Pisum sativum L., Biotekhnologiya ovoshchnykh, tsvetochnykh i malorasprostranennykh kul’tur. Sbornik nauchykh trudov mezhdunarodnoi nauchno-prakticheskoi konferentsii (Biotechnology of Vegetables, Flowers, and Rare Cultivated Plants: Proc. Int. Conf.), Moscow, 2004, pp. 161–169.Google Scholar
  60. 60.
    Kuznetsova, O.I., Ash, O.A., Khartina, G.A., and Gostimsky, S.A., RAPD and ISSR Analyses of Regenerated Pea Pisum sativum L. Plants, Rus. J. Genet., 2005, vol. 41, no.1, pp. 60–65.Google Scholar
  61. 61.
    Osipova, E.S., Troitskii, A.V., Dolgikh, Yu.I., et al., Molecular Genetic Analysis of Maize Somaclones, Tezisy konferentsii “Gorizonty fiziko-khimicheskoi biologii” (Proc. Conf. “Frontiers in Physico-Chemical Biology), Pushchino, 2000, p. 132.Google Scholar
  62. 62.
    Osipova, E.S., Koveza, O.V., Troitskii, A.V., et al., Analysis of Specific RAPD and ISSR Fragments in Maize (Zea mays L.) Somaclones and Development of SCAR Markers on Their Basis, Rus. J. Genet., 2003, vol. 39, no.12, pp. 1412–1419.CrossRefGoogle Scholar
  63. 63.
    Osipova, E.S., Kokaeva, Z.G., Troitskii, A.V., et al., RARD Analysis of Maize Somaclones, Rus. J. Genet., 2001, vol. 37, no.1, pp. 80–84.CrossRefGoogle Scholar
  64. 64.
    Osipova, E.S., Changes of DNA Markers (RARD, ISSR) in Somaclonal Variation in Maize, Cand. Sci. (Biol.) Dissertation, Moscow: Inst. Plant Physiol., 2004.Google Scholar
  65. 65.
    Brown, P.T.H., Lange, F.D., Kranz, E., and Lorz, H., Analysis of Single Protoplasts and Regenerated Plants by PCR and RAPD Technology, Mol. Gen. Genet., 1993, vol. 237, pp. 311–317.PubMedGoogle Scholar
  66. 66.
    Bogani, P., Simoni, A., Lio, P., et al., Genome Flux in Tomato Cell Clones Cultured in Vitro in Different Physiological Equilibria: II. A RAPD Analysis of Variability, Genome, 1996, vol. 39, pp. 846–853.Google Scholar
  67. 67.
    Osipova, E.C., Troitskij, A.V., Dolgikh, Yu.I., et al., SCAR-Marker Creation for Maize Somaclones Using Some Specific RAPD and ISSR Fragments, Maize Genet. Cooperation Newslett., 2003, vol. 77, pp. 53–55.Google Scholar

Copyright information

© MAIK “Nauka/Interperiodica” 2005

Authors and Affiliations

  • S. A. Gostimsky
    • 1
  • Z. G. Kokaeva
    • 1
  • F. A. Konovalov
    • 1
  1. 1.Department of Genetics, Biological FacultyMoscow State UniversityMoscowRussia

Personalised recommendations