Skip to main content
SpringerLink
Log in

A new diagnostic SSR marker for selection of theRym4/Rym5 locus in barley breeding

  • Original Article
  • Published:
Journal of Applied Genetics Aims and scope Submit manuscript

Abstract

Genomic sequence AY661558, representing a part of the BAC contig of theRym4/Rym5 locus conferring resistance to the barley yellow mosaic virus complex (BaMMV/BaYMV), was exploited in order to develop SSR markers for practical barley breeding. Out of 57 SSR motifs found within this sequence, primers were designed and tested for the 5 SSRs with the highest repeat length. The polymorphic SSR marker QLB1 co-segregated withrym4 andrym5 phenotypes in respective high-resolution mapping populations developed for the construction of the original BAC contig. The primers targeted 2 sites located 756 bp and 5173 bp downstream of the translation initiation factor 4E (Hv-eIF4E). Physical linkage of the QLB1 marker to theRym4/Rym5 locus was confirmed experimentally on Morex BAC 519J14, a seed BAC ofHv-eIF4E, and BAC 801A11, which is located proximally toHv-eIF4E. QLB1 revealed 7 alleles in a set of 100 winter barley lines and cultivars. Five alleles were found within 673 advanced breeding lines derived from applied Polish winter barley breeding programmes, which corresponds to a PIC value of 0.684. No recombinants betweenRym4/5 and QLB1 were detected, suggesting that QLB1 can be used efficiently in marker-assisted selection of theHv-eIF4E-mediated bymovirus resistance.

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.

Institutional subscriptions

Similar content being viewed by others

References

  • Chalhoub BA, Thibault S, Laucou V, Rameau C, Höfte H, Cousin R, 1997. Silver staining and recovery of AFLP™ amplification products on large denaturing polyacrylamide gels. BioTechniques 22: 216–220.

    CAS  PubMed  Google Scholar 

  • Graner A, Bauer E, 1993. RFLP mapping of theym4 virus resistance gene in barley. Theor Appl Genet 86: 689–693.

    Article  CAS  Google Scholar 

  • Graner A, Streng S, Kellermann A, Proeseler G, Schiemann A, Peterka H, Ordon F, 1999a. Molecular mapping of genes conferring resistance to soil-borne viruses in barley: an approach to promote understanding of host-pathogen interactions. J Plant Dis Prot 106: 405–410.

    CAS  Google Scholar 

  • Graner A, Streng S, Kellermann A, Schemann A, Bauer E, Waugh R, et al. 1999b. Molecular mapping and genetic fine-structure of therym5 locus encoding resistance to different strains of the Barley Yellow Mosaic Virus Complex. Theor Appl Genet 98: 285–290.

    Article  CAS  Google Scholar 

  • Harding RM, Boyce AJ, Clegg JB, 1992. The evolution of tandemly repetitive DNA: recombination rules. Genetics 132: 847–859.

    CAS  PubMed  Google Scholar 

  • Kanyuka K, McGrann G, Alhudaib K, Hariri D, Adams MJ, 2004. Biological and sequence analysis of a novel European isolate ofBarley mild mosaic virus that overcomes the barleyrym5 resistance gene. Arch Virol 149: 1469–1480.

    Article  CAS  PubMed  Google Scholar 

  • Konishi T, Ordon F, Furusho M, 2002. Reactions of barley accessions carrying different rym genes to BaYMV and BaMMV in Japan and Germany. Barley Genet Newsl 32: 46–48.

    Google Scholar 

  • Le Gouis J, Ordon F, Friedt W, 1994. Isozyme-electrophoresis for chromosomal localization of barley mild mosaic virus resistance genes different fromym4. Barley Genet Newsl 23: 36–39.

    Google Scholar 

  • Li Y-C, Korol AB, Fahima T, Beiles A, Nevo E, 2002. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11: 2453–2465.

    Article  CAS  PubMed  Google Scholar 

  • McGrann GRD, Adams MJ, 2004. Investigating resistance toBarley mild mosaic virus. Plant Pathology 53: 161–169.

    Article  Google Scholar 

  • Milligan BG, 1992. Plant DNA isolation. In: Hoelzel AR, ed. Molecular analysis of populations: a practical approach. IRL Press, Oxford: 59–88.

    Google Scholar 

  • Morgante M, Hanafey M, Powell W, 2002. Microsatellites are preferentially associate with nonrepetitive DNA in plant genomes. Nature Genet 30: 194–200.

    Article  CAS  PubMed  Google Scholar 

  • Ordon F, Bauer E, Dehmer KJ, Graner A, Friedt W, 1995a. Identification of a RAPD-marker linked to the BaMMV/BaYMV resistance geneym4. Barley Genet Newsl 24: 123–126.

    Google Scholar 

  • Ordon F, Bauer E, Graner A, Friedt W, 1995b. Marker-based selection for the BaMMV-resistance gene in barley using RAPDs. Agronomie 15: 481–485.

    Article  Google Scholar 

  • Ordon F, Friedt W, Scheurer K, Pellio B, Werner K, Neuhaus G, et al. 2004. Molecular markers in breeding for virus resistance in barley. J Appl Genet 45: 145–159.

    PubMed  Google Scholar 

  • Pellio B, Friedt W, Graner A, Ordon F, 2004. Development of PCR-based markers closely linked torym5. J Plant Dis Prot 111: 30–38.

    CAS  Google Scholar 

  • Pellio B, Streng S, Bauer E, Stein N, Perovic D, Schiemann A, et al. 2005. High-resolution mapping of theRym4/Rym5 locus conferring resistance to the barley yellow mosaic virus complex (BaMMV, BaYMV, BaYMV-2) in barley (Hordeum vulgare ssp.vulgare L.). Theor Appl Genet 110: 283–293.

    Article  CAS  PubMed  Google Scholar 

  • Röder MS, Huang XQ, Ganal MW, 2004. Wheat microsatellites: potential and implications. In: Lörz H, Wenzel G, eds. Biotechnology in agriculture and forestry: molecular marker systems. Springer Verlag: 255–266.

  • Rozen S, Skaletsky H, 2000. Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S, eds. Bioinformatics Methods and Protocols: Methods in Molecular Biology, Humana Press, Totowa: 365–386.

    Google Scholar 

  • Ruge B, Linz A, Pickering R, Proeseler G, Greif P, Wehling P, 2003. Mapping of Rym14Hb, a gene introgressed fromHordeum bulbosum and conferring resistance to BaMMV and BaYMV in barley. Theor Appl Genet 107: 965–971.

    Article  CAS  PubMed  Google Scholar 

  • Ruge-Wehling B, Linz A, Habekuß A, Wehling P, 2006. Mapping ofRym16 (Hb), the second soil-borne virus-resistance gene introgressed fromHordeum bulbosum. Theor Appl Genet 113: 867–873.

    Article  CAS  PubMed  Google Scholar 

  • Schiemann A, Graner A, Friedt W, Ordon F, 1996. Specificity enhancement of a RAPD marker linked to the BaMMV/BaYMV resistance geneym4 by randomly added bases. Barley Genet Newsl 27: 63–65.

    Google Scholar 

  • Stein N, Perovic D, Kumlehn J, Pellio B, Stracke S, Streng S, et al. 2005. The eukaryotic translation initiation factor 4E confers multiallelic recessive Bymovirus resistance inHordeum vulgare (L.). Plant J 42: 912–922.

    Article  CAS  PubMed  Google Scholar 

  • Tachida H, Iizuka M, 1992. Persistence of repeated sequences that evolve by replication slippage. Genetics 131: 471–478.

    CAS  PubMed  Google Scholar 

  • Tatusova AT, Madden TL, 1999. Blast 2 sequences — a new tool for comparing protein and nucleotide sequences, FEMS Microbiol Lett 174: 247–250.

    Article  CAS  PubMed  Google Scholar 

  • Thiel T, Kota R, Grosse I, Stein N, Graner A, 2004. SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res 32: e5.

    Article  PubMed  Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A, 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106: 41–422.

    Google Scholar 

  • Weber JL, 1990. Informativeness of human (dC.dA) n(dG.dT)n polymorphisms. Genomics 7: 524–530.

    Article  CAS  PubMed  Google Scholar 

  • Werner K, Friedt W, Laubach E, Waugh R, Ordon F, 2003. Dissection of resistance to soil-borne yellow-mosaic-inducing viruses of barley (BaMMV, BaTMV, BaYMV-2) in a complex breeders’ cross by means of SSRs and simultaneous mapping of BaYMV/BaYMV-2 resistance of var. ‘Chikurin Ibaraki 1’. Theor Appl Genet 106: 1425–1432.

    CAS  PubMed  Google Scholar 

  • Werner K, Friedt W, Ordon F, 2005. Strategies for pyramiding resistance genes against the barley yellow mosaic virus complex (BaMMV, BaYMV, BaYMV-2). Mol Breed 16: 45–55.

    Article  CAS  Google Scholar 

  • Wicker T, Zimmermann W, Perovic D, Paterson AH, Ganal M, Graner A, Stein N, 2005. A detailed look at 7 million years of genome evolution in a 439-kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats. Plant J 41: 184–194.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Laboratory of Population Genetics, Polonia University, Częstochowa, Poland

    Mirosław Tyrka & Agnieszka Wardyńska

  2. Federal Centre for Breeding Research on Cultivated Plants, Institute of Epidemiology and Resistance Resources, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany

    Dragan Perovic & Frank Ordon

Authors
  1. Mirosław Tyrka
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dragan Perovic
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Agnieszka Wardyńska
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Frank Ordon
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Dragan Perovic.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tyrka, M., Perovic, D., Wardyńska, A. et al. A new diagnostic SSR marker for selection of theRym4/Rym5 locus in barley breeding. J Appl Genet 49, 127–134 (2008). https://doi.org/10.1007/BF03195605

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF03195605

Keywords

Search

Navigation