Skip to main content
SpringerLink
Log in

Development and Characterization of Microsatellite Markers from Chromosome 1-Specific DNA Libraries of Vicia Faba

  • Published:
Biologia Plantarum

Abstract

An integrated approach has been developed for targeted retrieval of microsatellite markers from selected regions of the field bean (Vicia faba L.) genome. The procedure is based on a combination of advanced physical and genetic mapping techniques and includes the following steps: 1) flow-sorting of metaphase chromosomes, 2) construction of microsatellite-enriched chromosome-specific DNA libraries, 3) isolation of polymorphic microsatellite sequences from the libraries, 4) testing chromosome specificity of the microsatellites using polymerase chain reaction with purified fractions of individual chromosome types, and 5) integration of chromosome-specific markers into a genetic map. Several strategies for isolation of microsatellite clones were tested, including direct screening of non-enriched libraries with single or mixed probes and screening of the libraries after one or two rounds of enrichment. Finally, the usefulness of this approach was demonstrated by the retrieval of novel markers from a selected portion of the largest field been chromosome (No. 1).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.-Nucleic Acids Res. 25: 3389–3402, 1997.

    Google Scholar 

  • Armour, J.A.L., Neumann, R., Gobert, S., Jeffreys, A.J.: Isolation of human simple repeat loci by hybridization selection.-Hum. mol. Genet. 4: 599–605, 1994.

    Google Scholar 

  • Arumuganathan, K., Martin, G.B., Telenius, H., Tanksley, S.D., Earle, E.D.: Chromosome 2-specific DNA clones from flow-sorted chromosomes of tomato.-Mol. gen. Genet. 242: 551–558, 1994.

    Google Scholar 

  • Aydin, A.: How to map a gene.-J. mol. Med. 77: 691–694, 1999.

    Google Scholar 

  • Barreneche, T., Bodenes, C., Lexer, C., Trontin, J.F., Fluch, S., Streiff, R., Plomion, C., Roussel, G., Steinkellner, H., Burg, K., Favre, J.M., Glossl, J., Kremer, A.: A genetic linkage map of Quercus robur L. (pedunculate oak) based on RAPD, SCAR, microsatellite, minisatellite, isozyme and 5S rDNA markers.-Theor. appl. Genet. 97: 1090–1103, 1998.

    Google Scholar 

  • Beckmann, J.S., Weber, J.L.: Survey of human and rat microsatellites.-Genomics 12: 627–631, 1992.

    Google Scholar 

  • Bennett, M.D., Leitch, I.: Nuclear DNA amounts in angiosperms.-Ann. Bot. 76: 113–176, 1995.

    Google Scholar 

  • Brondani, R.P.V., Brondani, C., Tarchini, R., Grattapaglia, D.: Development, characterization and mappping of microsatellite markers in Eucalyptus grandis and E. urophylla.-Theor. appl. Genet. 97: 816–827, 1998.

    Google Scholar 

  • Cabrera, A., Cubero, J.I., Martín, A.: Genetic mapping using trisomics in Vicia faba L.-FABIS Newslett. 23: 5–7, 1989.

    Google Scholar 

  • Cregan, P.B., Bhagwat, A.A., Akkaya, M.S., Rongwen, J.: Microsatellite fingerprinting and mapping of soybean.-Methods mol. Cell Biol. 5: 49–61, 1994.

    Google Scholar 

  • Dellaporta, S.L., Wood, J., Hicks, J.B.: A plant molecular DNA minipreparation. Version II.-Plant mol. Biol. Rep. 1: 19–21, 1983.

    Google Scholar 

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

    Google Scholar 

  • Doležel, J., Lysák, M.A., Kubaláková, M., Šimková, H., Macas, J., Lucretti, S.: Sorting of Plant Chromosomes.-In: Darzynkiewicz, Z., Crissman, H.A., Robinson, J.P. (ed.): Methods in Cell Biology. Vol. 64. Part B. Pp. 3–31. Academic Press, San Diego 2001.

    Google Scholar 

  • Don, R.H., Cox, P.T., Wainwright, B.J., Baker, K., Mattick, J.S.: ‘Touchdown’ PCR to circumvent spurious priming during gene amplification.-Nucleic Acids Res. 19: 4008, 1991.

    Google Scholar 

  • Ellegren, H.: Abundant (A)n/(T)n mononucleotide repeats in the pig genome-linkage mapping of the porcine APOB, FSA, ALOX12, PEPN and RLN loci.-Animal Genet. 24: 367–372, 1993.

    Google Scholar 

  • Grimm, D.R., Goldman, T., Holley-Shanks, R., Buoen, L., Mendiola, J., Schook, L.B., Louis, C., Rohrer, G.A., Lunney, J.K.: Mapping of microsatellite markers developed from a flow-sorted swine Chromosome 6 library.-Mammal. Genome 8: 193–199, 1997.

    Google Scholar 

  • Hamada, H., Petrino, M.C., Takugana, T.: A novel repeated element with Z-DNA forming potential is widely found in diverse eucaryotic genomes.-Proc. nat. Acad. Sci. USA 79: 6465–6469, 1982.

    Google Scholar 

  • Hamilton, M.B., Pincus, E.L., DiFiore, A., Fleischer, R.C.: Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites.-BioTechniques 27: 500–507, 1999.

    Google Scholar 

  • Hicks, M., Adams, D., O'Keefe, S., Macdonald, E., Hodgetts, R.: The development of RAPD and microsatellite markers in lodgepole pine (Pinus contorta var. latifolia).-Genome 41: 797–805, 1998.

    Google Scholar 

  • Huang, W.G., Cipriani, G., Morgante, M., Testolin, R.: Microsatellite DNA in Actinidia chinensis: isolation characterisation, and homology in related species.-Theor. appl. Genet. 97: 1269–1278, 1998.

    Google Scholar 

  • Kijas, J.M.H., Fowler, J.C.S., Garbett, C.A., Thomas, M.R.: Enrichment of microsatellites from the citrus genome using biotinylated oligonucleotide sequences bound to streptavidin-coated magnetic particles.-BioTechniques 4: 657–662, 1994.

    Google Scholar 

  • Kijas, J.M.H., Thomas, M.R., Fowler, J.C.S., Roose, M.L.: Integration of trinucleotide microsatellites into a linkage map of Citrus.-Theor. appl. Genet. 94: 701–706, 1997.

    Google Scholar 

  • Koblížková, A., Doležel, J., Macas, J.: Subtraction with 3'modified oligonucleotides eliminates amplification artifacts in DNA libraries enriched for microsatellites.-BioTechniques 25: 32–38, 1998.

    Google Scholar 

  • Korzun, V., Roder, M.S., Wendehake, K., Pasqualone, A., Lotti, C., Ganal, M.W., Blanco, A.: Integration of dinucleotide microsatellites from hexaploid bread wheat into a genetic linkage map of durum wheat.-Theor. appl. Genet. 98: 1202–1207, 1999.

    Google Scholar 

  • Kosambi, D.D.: The estimation of map distance from recombination values.-Ann. Eugen. 12: 172–175, 1944.

    Google Scholar 

  • Kostia, S., Varvio, S.L., Vakkari, P., Pulkkinen, P.: Microsatellite sequences in a conifer Pinus sylvestris.-Genome 38: 1244–1248, 1995.

    Google Scholar 

  • Lagercrantz, U., Ellegren, H., Andersson, L.: The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates.-Nucleic Acids Res. 21: 1111–1115, 1993.

    Google Scholar 

  • Lander, E.S., Green, P., Abrahamson, J., Barlow, A., Daly, M.J., Lincoln, S.E., Newburg, L.: MAPMAKER: an interactive computer program for constructing genetic linkage maps of experimental and natural populations.-Genomics 1: 174–181, 1987.

    Google Scholar 

  • Lassner, M.W., Peterson, P., Yoder, J.I.: Simultaneous amplification of multiple DNA fragments by polymerase chain reaction in the analysis of transgenic plants and their progeny.-Plant mol. Biol. Rep. 7: 116–128, 1989.

    Google Scholar 

  • Lench, N.J., Norris, A., Bailey, A., Booth, A., Markham, A.F.: Vectorette PCR isolation of microsatellite repeat sequences using anchored dinucleotide repeat primers.-Nucleic Acids Res. 24: 2190–2191, 1996.

    Google Scholar 

  • Lincoln, S.E., Daly, M.J., Lander, E.S.: PRIMER Version 0.5: A Computer Program for Automatically Selecting PCR Primers.-Whitehead Institute, Cambridge 1991.

    Google Scholar 

  • Litt, M., Luty, J.A.: A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle action gene.-Amer. J. hum. Genet. 44: 391–401, 1989.

    Google Scholar 

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

    Google Scholar 

  • Lunt, D.H., Hutchinson, W.F., Carvalho, G.R.: An efficient method for PCR-based isolation of microsatellite arrays (PIMA).-Mol. Ecol. 8: 891–893, 1999.

    Google Scholar 

  • Lyall, J.E.W., Brown, G.M., Furlong, R.A., Ferguson-Smith, M.A., Affara, N.A.: A method for creating chromosome-specific plasmid libraries enriched in clones containing [CA]n microsatellite repeat sequences directly from flow-sorted chromosomes.-Nucleic Acids Res. 19: 4641–4642, 1993.

    Google Scholar 

  • Macas, J., Doležel, J., Lucretti, S., Pich, U., Meister, A., Fuchs, J., Schubert, I.: Localization of seed protein genes on flow-sorted field bean chromosomes.-Chromosome Res. 1: 107–115, 1993.

    Google Scholar 

  • Macas, J., Gualberti, G., Nouzová, M., Samec, P., Lucretti, S., Doležel, J.: Construction of chromosome-specific DNA libraries covering the whole genome of field bean (Vicia faba L.).-Chromosome Res. 4: 531–539, 1996.

    Google Scholar 

  • Morgante, M., Olivieri, A.M.: PCR-amplified microsatellites as markers in plant genetics.-Plant J. 1: 175–182, 1993.

    Google Scholar 

  • Paetkau, D.: Microsatellites obtained using strand extension: An enrichment protocol.-BioTechniques 26: 690–697, 1999.

    Google Scholar 

  • Pearson, W.R., Lipman, D.J.: Improved tools for biological sequence comparison.-Proc. nat. Acad. Sci. USA 85: 2444–2448, 1988.

    Google Scholar 

  • Pfeiffer, A., Olivieri, A.M., Morgante, M.: Identification and characterization of microsatellites in Norway spruce (Picea abies K.).-Genome 40: 411–419, 1997.

    Google Scholar 

  • Ponce, M.R., Robles, P., Micol, J.L.: High-throughput genetic mapping in Arabidopsis thaliana.-Mol. gen. Genet. 261: 408–415, 1999.

    Google Scholar 

  • Powell, W., Machray, G.C., Provan, J.: Polymorphism revealed by simple sequence repeats.-Trends Plant Sci. 1: 215–222, 1996.

    Google Scholar 

  • Saal, B., Wricke, G.: Development of simple sequence repeat markers in rye (Secale cereale L.).-Genome 42: 964–972, 1999.

    Google Scholar 

  • Sanger, F., Nicklen, D., Coulson, A.R.: DNA sequencing with chain terminating inhibitors.-Proc. nat. Acad. Sci. USA 74: 5463–5467, 1977.

    Google Scholar 

  • Satovic, Z., Torres, A.M., Cubero, J.I.: Genetic mapping of new morphological, isozyme and RAPD markers in Vicia faba L. using trisomics.-Theor. appl. Genet. 93: 1130–1138, 1996.

    Google Scholar 

  • Schubert, I., Rieger, R., Michaelis, A.: Structural and numerical manipulation of the Vicia faba karyotype: results and perspectives.-Biol. Zentralbl. 105: 9–17, 1986.

    Google Scholar 

  • Smulders, M.J.M., Bredemeijer, G., Rus-Kortekaas, W., Arens, P., Vosman, B.: Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species.-Theor. appl. Genet. 97: 264–272, 1997.

    Google Scholar 

  • Tautz, D., Renz, M.: Simple sequences are ubiquitous repetitive components of eukaryotic genomes.-Nucleic Acids Res. 12: 4127–4138, 1984.

    Google Scholar 

  • Telenius, H., Carter, N.P., Bebb, C.E., Nordenskjold, M., Ponder, B.A.J., Tunnacliffe, A.: Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer.-Genomics 13: 718–725, 1992.

    Google Scholar 

  • Torres, A.M., Weeden, N.F., Martin, A.: Linkage among isozyme, RFLP and RAPD markers in Vicia faba.-Theor. appl. Genet. 85: 937–945, 1993.

    Google Scholar 

  • Torres, A.M., Satovic, Z., Canovas, J., Cobos, S., Cubero, J.I.: Genetics and mapping of new isozyme loci in Vicia faba L. using trisomics.-Theor. appl. Genet. 91: 783–789, 1995.

    Google Scholar 

  • Torres, A.M., Vaz Patto, M.C., Satovic, Z., Cubero, J.I.: New isozyme loci in faba bean (Vicia faba L.): Genetic analysis and mapping using trisomics.-J. Hered. 89: 271–272, 1998.

    Google Scholar 

  • Vaiman, D., Pailhoux, E., Schmitz, A., Giraud-Delville, C., Cotinot, C., Cribiu, E.P.: Mass production of genetic markers from a limited number of sorted chromosomes.-Mammal. Genome 8: 153–156, 1997.

    Google Scholar 

  • Van Dilla, M.A., Deaven, L.L.: Construction of gene libraries for each human chromosome.-Cytometry 11: 208–218, 1990.

    Google Scholar 

  • Vaz Patto, M.C., Torres, A.M., Koblížková, A., Macas, J., Cubero, J.I.: Development of a genetic composite map of Vicia faba using F2 populations derived from trisomic plants.-Theor. appl. Genet. 98: 736–743, 1999.

    Google Scholar 

  • Wang, M.L., Leitch, A.R., Schwarzacher, T., Heslop-Harrison, J.S., Moore, G.: Construction of a chromosome-enriched HpaII library from flow-sorted wheat chromosomes.-Nucleic Acids Res. 20: 1897–1901, 1992.

    Google Scholar 

  • Wang, Z., Weber, J.L., Zhong, G., Tanksley, S.D.: Survey of plant short tandem DNA repeats.-Theor. appl. Genet. 88: 1–6, 1994.

    Google Scholar 

  • Wu, K.S., Tanksley, S.D.: Abundance, polymorphism and genetic mapping of microsatellites in rice.-Mol. gen. Genet. 241: 225–235, 1993.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Plant Molecular Biology, ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic

    D. Požárková & A. Koblížková

  2. Departamento de Mejora y Agronomía, C.I.F.A., Aptdo. 3092, E-14080, Córdoba, Spain

    B. Román & A.M. Torres

  3. Biotechnology and Agriculture Division, ENEA C.R. Casaccia, Via Anguillarese 301, S.M. di Galeria, I-00060, Rome, Italy

    S. Lucretti

  4. Institute of Experimental Botany, ASCR, Sokolovská 6, CZ-77200, Olomouc, Czech Republic

    M. Lysák & J. Doležel

  5. Institute of Plant Moelcular Biology, ASCR, Branišovská 31, České Budějovice, CZ-37005, Czech Republic

    J. Macas

Authors
  1. D. Požárková
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. Koblížková
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. B. Román
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. A.M. Torres
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. S. Lucretti
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. M. Lysák
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. J. Doležel
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. J. Macas
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Požárková, D., Koblížková, A., Román, B. et al. Development and Characterization of Microsatellite Markers from Chromosome 1-Specific DNA Libraries of Vicia Faba . Biologia Plantarum 45, 337–345 (2002). https://doi.org/10.1023/A:1016253214182

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1016253214182

Search

Navigation