Skip to main content
SpringerLink
Log in

Fine-mapping of the leaf rust Lr34 locus in Triticum aestivum (L.) and characterization of large germplasm collections support the ABC transporter as essential for gene function

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Leaf rust resistance gene Lr34 is likely the most important leaf rust gene characterized to date. It has been characterized as an adult plant resistance gene and is known to enhance the resistance of other leaf rust resistance genes and to condition resistance to a number of other diseases. Located on chromosome 7D, this gene was identified to be one of six co-located genes of which, an ABC transporter was shown to be the only valid candidate. Ten new molecular markers were developed spanning the Lr34 locus, including six novel microsatellite markers (cam), one insertion site-based polymorphism marker (caISBP), two single nucleotide polymorphisms (caSNP), and one gene-specific marker (caIND). Using these new markers and others that were previously published, a comparative fine map of the locus was constructed from five segregating populations representing 1,742 lines. Identification of a susceptible line with a recombination in the 4.9 kb interval between caSNP4 located in the ABC transporter gene and cam8 located just upstream of this gene provided further evidence to support the identity of the ABC transporter as Lr34 by ruling out four of the adjacent genes. Originally, three mutations forming two haplotypes had been described for the ABC transporter gene. A third combination of the three mutations and an additional rare mutation in exon 22 were subsequently described. We identified an additional novel mutation in exon 10 that would cause a frameshift and is likely non-functional. This mutation was only found in Lr34− lines and constituted a novel molecular haplotype. Characterization of two germplasm collections of 700 Triticum aestivum lines permitted us to gain an understanding of the frequency of the ABC haplotypes characterized to date and their distribution in germplasm from and around the world. In addition to the four haplotypes previously described, a fifth haplotype was found in two of the 700 lines from the germplasm collections. These lines displayed the deletion in indel 11 characteristic of Lr34+ lines, but are likely susceptible to leaf rust. Mapping and haplotyping data suggest that of all the markers described herein, marker caIND11 is the best diagnostic marker for marker-assisted selection of Lr34 because it is co-dominant, robust and with the exception of 2/700 lines, it is highly diagnostic. Other markers are also described to provide alternatives for laboratories with different technologies.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Banks TW, Jordan MC, Somers DJ (2009) Single-feature polymorphism mapping in bread wheat. Plant Genome 2:157–178

    Article  Google Scholar 

  • Benham J, Jeung J-U, Jasieniul M, Kanazin V, Blake T (1999) Genographer: a graphical tool for automated fluorescent AFLP and microsatellite analysis. J Agric Genome 4 (http://wheat.pw.usda.gov/jag/)

  • Bossolini E, Krattinger SG, Keller B (2006) Development of simple sequence repeat markers specific for the Lr34 resistance region of wheat using sequence information from rice and Aegilops tauschii. Theor Appl Genet 113:1049–1062

    Article  PubMed  CAS  Google Scholar 

  • Chao S, Zhang W, Akhunov E, Sherman J, Ma Y, Luo M-C, Dubcovsky J (2009) Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars. Mol Breed 23:23–33

    Article  CAS  Google Scholar 

  • Cloutier S, Niu Z, Datla R, Duguid S (2009) Development and analysis of EST-SSRs for flax (Linum usitatissimum L.). Theor Appl Genet 119:53–63

    Article  PubMed  CAS  Google Scholar 

  • Dyck PL (1987) The association of a gene for leaf rust resistance with the chromosome 7D suppressor of stem rust resistance in common wheat. Genome 29:467–469

    Article  Google Scholar 

  • Dyck PL (1992) Inheritance of leaf rust and stem rust resistance in ‘Roblin’ wheat. Genome 36:289–293

    Article  Google Scholar 

  • Dyck PL, Samborski DJ, Anderson RG (1966) Inheritance of adult-plant leaf rust resistance derived from the common wheat varieties exchange and Frontana. Can J Genet Cytol 8:665–671

    Google Scholar 

  • Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8:175–185

    PubMed  CAS  Google Scholar 

  • German SE, Kolmer JA (1992) Effect of gene Lr34 in the enhancement of resistance to leaf rust of wheat. Theor Appl Genet 84:97–105

    Article  CAS  Google Scholar 

  • Huang XQ, Cloutier S (2008) Molecular characterization and genomic organization of low molecular weight glutenin subunit genes at the Glu-3 loci in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet 116:953–966

    Article  PubMed  CAS  Google Scholar 

  • Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877

    Article  PubMed  CAS  Google Scholar 

  • Huang XQ, Cloutier S, Lycar L, Radovanovic N, Humphreys DG, Noll JS, Somers DJ, Brown PD (2006) Molecular detection of QTLs for agronomic and quality traits in a doubled haploid population derived from two Canadian wheats (Triticum aestivum L.). Theor Appl Genet 113:753–766

    Article  PubMed  CAS  Google Scholar 

  • Kolmer JA (2005) Tracking wheat rust on a continental scale. Curr Opin Plant Biol 8:441–449

    Article  PubMed  Google Scholar 

  • Kolmer JA, Singh RP, Garvin DF, Viccars L, William HM, Huerta-Espino J, Ogbonnaya FC, Raman H, Orford S, Bariana HS, Lagudah ES (2008) Analysis of the Lr34/Yr18 rust resistance region in wheat germplasm. Crop Sci 48:1841–1852

    Article  CAS  Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Article  Google Scholar 

  • Krattinger SG, Lagudah ES, Spielmeyer W, Keller B (2008) Fine-mapping of the durable leaf rust resistance gene Lr34 using sequence information from Brachypodium and Aegilops tauschii. In: Proceedings of 11th international wheat genetics symposium, Brisbane, Australia, 24–29 Aug 2008, O32

  • Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller B (2009) A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323:1360–1363

    Article  PubMed  CAS  Google Scholar 

  • Lagudah ES, McFadden H, Singh RP, Huerta-Espino J, Bariana HS, Spielmeyer (2006) Molecular genetic characterization of the Lr34/Yr18 slow rusting resistance gene region in wheat. Theor Appl Genet 114:21–30

    Article  PubMed  CAS  Google Scholar 

  • Lagudah ES, Krattinger SG, Herrera-Foessel S, Singh RP, Huerta-Espino J, Spielmeyer W, Brown-Guedira G, Selter LL, Keller B (2009) Gene-specific markers for the wheat gene Lr34/Yr18/Pm38 which confers resistance to multiple fungal pathogens. Theor Appl Genet 119:889–898

    Article  PubMed  CAS  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  PubMed  CAS  Google Scholar 

  • Li W, Zhang P, Fellers JP, Friebe B, Gill BS (2004) Sequence composition, organization, and evolution of the core Triticeae genome. Plant J 40:500–511

    Article  PubMed  CAS  Google Scholar 

  • McCallum BD, Fetch T, Chong J (2007) Cereal rust control in Canada. Aust J Agric Res 58:639–647

    Article  Google Scholar 

  • McCallum BD, Somers DJ, Humphreys DG, Cloutier S (2008) Molecular marker analysis of Lr34 in Canada Western Red Spring wheat cultivars. In: Proceedings of 11th international wheat genetics symposium, Brisbane, Australia, 24–29 Aug 2008, P137

  • McCartney CA, Somers DJ, Humphreys DG, Lukow O, Ames N, Noll J, Cloutier S, McCallum BD (2005) Mapping quantitative trait loci controlling agronomic traits in the spring wheat cross RL4452 × ‘AC Domain’. Genome 48:870–883

    Article  PubMed  CAS  Google Scholar 

  • McCartney CA, Somers DJ, Lukow O, Ames N, Noll J, Cloutier S, Humphreys DG, McCallum BD (2006) QTL analysis of quality traits in the spring wheat cross RL4452 × ‘AC Domain’. Plant Breed 125:565–575

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Moxon ER, Wills C (1999) DNA microsatellites: agents of evolution? Sci Am 2870:94–99

    Article  Google Scholar 

  • Nilmalgoda SD, Cloutier S, Walichnowski AZ (2003) Construction and characterization of a bacterial artificial chromosome (BAC) library of hexaploid wheat (Triticum aestivum L.) and validation of genome coverage using locus-specific primers. Genome 46:870–878

    Article  PubMed  CAS  Google Scholar 

  • Peterson RF, Campbell AB, Hannah AE (1948) A diagrammatic scale for estimating rust intensity on leaves and stems of cereals. Can J Res 26:496–500

    Article  Google Scholar 

  • Phillips C (2007) Online resources for SNP analysis: a review and route map. Mol Biotechnol 35:65–97

    Article  PubMed  CAS  Google Scholar 

  • Piehler AP, Hellum M, Wenzel JJ, Kaminski E, Haug KBF, Kierfulf P, Kaminski WE (2008) The human ABC transporter pseudogene family: evidence for transcription and gene–pseudogene interference. BMC Genomics 9:165 (13 pages)

    Article  PubMed  Google Scholar 

  • Radovanovic N, Cloutier S (2003) Gene-assisted selection for high molecular weight glutenin subunits in wheat doubled haploid breeding programs. Mol Breed 12:51–59

    Google Scholar 

  • Rosewarne GM, Singh RP, Huerta-Espino J, William HM, Bouchet S, Cloutier S, McFadden H, Lagudah ES (2006) Leaf tip necrosis, molecular markers and β1-proteasome subunits associated with the slow rusting resistance genes Lr46/Yr29. Theor Appl Genet 112:500–508

    Article  PubMed  CAS  Google Scholar 

  • Samborski DJ (1985) Wheat leaf rust. In: Bushnell WR, Roelfs AP (eds) The cereal rusts, II. Academic Press, Orlando, pp 39–59

    Google Scholar 

  • Schuelke M (2000) An economic method for the fluorescent labelling of PCR fragments. Nat Biotechnol 18:233–234

    Article  PubMed  CAS  Google Scholar 

  • Singh RP (1992) Association between gene Lr34 for leaf rust resistance and leaf tip necrosis in wheat. Crop Sci 32:874–878

    Article  Google Scholar 

  • Singh RP (1993) Genetic association of gene Bdv1 for tolerance to barley yellow dwarf virus with genes Lr34 and Yr18 for adult plant resistance to rusts in bread wheat. Plant Dis 77:1103–1106

    Article  Google Scholar 

  • Singh D, Park RF, McIntosh RA (2007) Characterisation of wheat leaf rust resistance gene Lr34 in Australian wheats using components of partial resistance and molecular markers. Aust J Agric Res 58:1106–1114

    Article  CAS  Google Scholar 

  • Spielmeyer W, McIntosh RA, Kolmer J, Lagudah ES (2005) Powdery mildew resistance and Lr34/Yr18 genes for durable resistance to leaf and stripe rust cosegregate at a locus on the short arm of chromosome 7D of wheat. Theor Appl Genet 111:731–735

    Article  PubMed  CAS  Google Scholar 

  • Spielmeyer W, Singh RP, McFadden H, Wellings CR, Huerta-Espino J, Kong X, Appels R, Lagudah ES (2008) Fine scale genetic and physical mapping using interstitial deletion mutants of Lr34/Yr18: a disease resistance locus effective against multiple pathogens in wheat. Theor Appl Genet 116:481–490

    Article  PubMed  CAS  Google Scholar 

  • Stojic J, Stöhr H, Weber BHF (2007) Three novel ABCC5 splice variants in human retina and their role as regulators of ABCC5 gene expression. BMC Mol Biol 8:42 (9 pages)

    Article  PubMed  Google Scholar 

  • Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452

    Article  PubMed  CAS  Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases fro the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    PubMed  CAS  Google Scholar 

  • Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ (2009) Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics. doi:10.1093/bioinformatics/btp033

  • Wicker T, Krattinger SG, Lagudah ES, Komatsuda T, Pourkheirandish M, Matsumoto T, Cloutier S, Reiser L, Kanamori H, Sato K, Perovic D, Stein N, Keller B (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

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We are thankful for the technical help provided by Elsa Reimer and Natasa Radovanovic as well as numerous summer students who provided help with field work. We would like to acknowledge Mike Shillinglaw and Joanne Schiavoni for their help with preparing the figures and manuscript. This work was supported by an Agriculture and Agri-Food Canada A-Base Grant.

Author information

Authors and Affiliations

  1. Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB, R3T 2M9, Canada

    Abdulsalam Dakouri, Brent D. McCallum, Andrzej Z. Walichnowski & Sylvie Cloutier

  2. Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada

    Abdulsalam Dakouri

Authors
  1. Abdulsalam Dakouri
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Brent D. McCallum
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Andrzej Z. Walichnowski
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sylvie Cloutier
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sylvie Cloutier.

Additional information

Communicated by B. Keller.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 22 kb)

Supplementary material 2 (PPT 18 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Dakouri, A., McCallum, B.D., Walichnowski, A.Z. et al. Fine-mapping of the leaf rust Lr34 locus in Triticum aestivum (L.) and characterization of large germplasm collections support the ABC transporter as essential for gene function. Theor Appl Genet 121, 373–384 (2010). https://doi.org/10.1007/s00122-010-1316-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-010-1316-7

Keywords

Search

Navigation