Skip to main content
Log in

Identification of a robust molecular marker for the detection of the stem rust resistance gene Sr45 in common wheat

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

Abstract

Key message

Fine mapping of the Ug99 effective stem rust resistance gene Sr45 introgressed into common wheat from the D -genome goatgrass Aegilops tauschii.

Abstract

Stem rust resistance gene Sr45, discovered in Aegilops tauschii, the progenitor of the D -genome of wheat, is effective against commercially important Puccinia graminis f. sp. tritici races prevalent in Australia, South Africa and the Ug99 race group. A synthetic hexaploid wheat (RL5406) generated by crossing Ae. tauschii accession RL5289 (carrying Sr45 and the leaf rust resistance gene Lr21) with a tetraploid experimental line ‘TetraCanthatch’ was previously used as the source in the transfer of these rust resistance genes to other hexaploid cultivars. Previous genetic studies on hexaploid wheats mapped Sr45 on the short arm of chromosome 1D with the following gene order: centromere–Sr45Sr33Lr21–telomere. To identify closely linked markers, we fine mapped the Sr45 region in a large mapping population generated by crossing CS1D5406 (disomic substitution line with chromosome 1D of RL5406 substituted for Chinese Spring 1D) with Chinese Spring. Closely linked markers based on 1DS-specific microsatellites, expressed sequence tags and AFLP were useful in the delineation of the Sr45 region. Sequences from an AFLP marker amplified a fragment that was linked with Sr45 at a distance of 0.39 cM. The fragment was located in a bacterial artificial chromosome clone of contig (ctg)2981 of the Ae. tauschii accession AL8/78 physical map. A PCR marker derived from clone MI221O11 of ctg2981 amplified 1DS-specific sequence that harboured an 18-bp indel polymorphism that specifically tagged the Sr45 carrying haplotype. This new Sr45 marker can be combined with a previously reported marker for Lr21, which will facilitate selecting Sr45 and Lr21 in breeding populations.

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

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Akhunov ED, Akhunova AR, Anderson OD, Anderson JA, Blake N et al (2010) Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes. BMC Genomics 11:702

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Anugrahwati DR, Shepherd KW, Verlin DC, Zhang P, Mirzaghaderi G, Walker E, Francki MG, Dundas IS (2008) Isolation of wheat-rye 1RS recombinants that break the linkage between stem rust resistance gene SrR and secalin. Genome 51:341–349

    Article  PubMed  CAS  Google Scholar 

  • Bariana HS, McIntosh RA (1993) Cytogenetic studies in wheat. XV. Location of rust resistance genes in VPM1 and its genetic linkage with other disease resistance genes in chromosome 2A. Genome 36:476–482

    Article  PubMed  CAS  Google Scholar 

  • Bossolini E, Wicker T, Knobel PA, Keller B (2007) Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation. Plant J 49:704–717

    Article  PubMed  CAS  Google Scholar 

  • Feuillet C, Keller B (1999) High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci 96:8265–8270

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Feuillet C, Travella S, Stein N, Albar L, Nublat A, Keller B (2003) Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. Proc Natl Acad Sci 100:15253–15258

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  • Friesen TL, Xu SS, Harris MO (2008) Stem rust, tan spot, Stagonospora nodorum blotch, and hessian fly resistance in Langdon durum-Aegilops tauschii synthetic hexaploid wheat lines. Crop Sci 48:1062–1070

    Article  Google Scholar 

  • Fu YB, Peterson GW, McCallum BD, Huang L (2010) Population based resequencing analysis of improved wheat germplasm at wheat leaf rust resistance locus Lr21. Theor Appl Genet 121:271–281

    Article  PubMed  CAS  Google Scholar 

  • Gill BS, Raupp WJ (1987) Direct genetic transfers from Aegilops squarrosa L. to hexaploid wheat. Crop Sci 27:445–450

    Article  Google Scholar 

  • Gill BS, Raupp WJ, Sharma HC, Browder LE, Hatchett JH, Harvey TL, Moseman JG, Waines JG (1986) Resistance in Aegilops squarrosa to wheat leaf rust, wheat powdery mildew, greenbug and Hessian fly. Plant Dis 70:553–556

    Article  Google Scholar 

  • Guyot R, Yahiaoui N, Feuillet C, Keller B (2004) In silico comparative analysis reveals a mosaic conservation of genes within a novel collinear region in wheat chromosome 1AS and rice chromosome 5S. Funct Integr Genomics 4:47–58

    Article  PubMed  CAS  Google Scholar 

  • Halloran GM, Ogbonnaya FC, Lagudah ES (2008) Triticum (Aegilops) tauschii in the natural and artificial synthesis of hexaploid wheat. Aus J Agric Res 59:475–490

    Article  Google Scholar 

  • Hayden MJ, Nguyen TM, Waterman A, McMichael GL, Chalmers KJ (2008) Application of multiplex-ready PCR for fluorescence-based SSR genotyping in barley and wheat. Mol Breed 21:271–281

    Article  CAS  Google Scholar 

  • Huang L, Brooks SA, Li W, Fellers JP, Trick HN, Gill BS (2003) Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploidy genome of bread wheat. Genetics 164:655–664

    PubMed Central  PubMed  CAS  Google Scholar 

  • Jones SS, Dvorak J, Qualset CO (1990) Linkage relations of Gli-D1, Rg2, and Lr21 on the short arm of chromosome 1D in wheat. Genome 33:937–940

    Article  CAS  Google Scholar 

  • Keller B, Feuillet C, Yahiaoui N (2005) Map-based isolation of disease resistance genes from bread wheat: cloning in a supersize genome. Genet Res 85:93–100

    Article  PubMed  CAS  Google Scholar 

  • Kerber ER (1964) Wheat: reconstitution of the tetraploid component (AABB) of hexaploids. Science 143:253–255

    Article  PubMed  CAS  Google Scholar 

  • Kerber ER (1987) Resistance to leaf rust in hexaploid wheat: Lr32 a third gene derived from Triticum tauschii. Crop Sci 27:204–206

    Article  Google Scholar 

  • Kerber ER, Dyck PL (1969) Inheritance in hexaploid wheat of leaf rust resistance and other characters derived from Aegilops squarrosa. Can J Genet Cytol 11:639–647

    Google Scholar 

  • Kolmer JA, Anderson JA (2011) First detection on North America of virulence in wheat leaf rust (Puccinia triticina) to seedling plants of wheat with Lr21. Plant Dis 95:1032

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Kota R, Spielmeyer W, McIntosh RA, Lagudah ES (2006) Fine genetic mapping fails to dissociate durable stem rust resistance gene Sr2 from pseudo-black chaff in common wheat (Triticum aestivam L.). Theor Appl Genet 112:492–499

    Article  PubMed  CAS  Google Scholar 

  • 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 323:37–395

    Article  CAS  Google Scholar 

  • Lagudah ES, McFadden H, Singh RP, Huerta-Espino J, Bariana HS, Spielmeyer W (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 

  • Ling HQ, Zhu Y, Keller B (2003) High-resolution mapping of the leaf rust disease resistance gene Lr1 in wheat and characterization of BAC clones from the Lr1 locus. Theor Appl Genet 106:875–882

    PubMed  CAS  Google Scholar 

  • Luo MC, Thomas C, You FM, Hsiao J, Ouyang S, Buell CR, Malandro M, McGuire PE, Anderson OD, Dvorak J (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 

  • Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N et al (2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D -genome progenitor. Proc Natl Acad Sci USA 110:7940–7945

    Article  PubMed Central  PubMed  Google Scholar 

  • Mago R, Spielmeyer W, Lawrence GJ, Lagudah ES, Ellis JG, Pryor AJ (2002) Identification and mapping of molecular markers linked to rust resistance genes located on chromosome 1RS of rye using wheat–rye translocation lines. Theor Appl Genet 104:1317–1324

    Article  PubMed  CAS  Google Scholar 

  • Manly KF, Cudmore RH, Meer JM (2001) Map Manager QTX, cross-platform software for genetic mapping. Mamm Genome 12:930–9321

    Article  PubMed  CAS  Google Scholar 

  • Marais GF, Potgieter GF, Roux HS, Roux J (1994) An assessment of the variation for stem rust resistance in the progeny of a cross involving the Triticum species aestivum, turgidum and tauschii. S Afr J Plant Soil 11:15–19

    Article  Google Scholar 

  • Marais GF, Wessels WG, Horn M, Toit F (1998) Association of a stem rust resistance gene (Sr45) and two Russian wheat aphid resistance genes (Dn5 and Dn7) with mapped structural loci in common wheat. S Afr J Plant Soil 15:67–71

    Article  Google Scholar 

  • McIntosh R (2009) History and status of the wheat rusts. In: McIntosh R (ed) Proceedings of Borlaug global rust initiative. Technical workshop, Cd. Obregon, pp 1–16

    Google Scholar 

  • Ogbonnaya FC, Halloran GM, Lagudah ES (2005) D genome of wheat-60 years on from Kihara, Sears and McFadden. In: Tsunewaki K (ed) Frontiers of wheat bioscience. Wheat Information Service No. 100, p 205–220

  • Olson EL, Rouse MN, Pumphrey MO, Bowden RL, Gill BS, Poland JA (2013) Simultaneous transfer, introgression, and genomic localization of genes for resistance to stem rust race TTKSK (Ug99) from Aegilops tauschii to wheat. Theor Appl Genet 126:1179–1188

    Article  PubMed  CAS  Google Scholar 

  • Periyannan S, Moore J, Ayliffe M, Bansal U, Wang X, Huang L, Deal K, Luo M, Kong X, Bariana H, Mago R, McIntosh R, Dodds P, Dvorak J, Lagudah E (2013) The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99. Science 341:786–788

    Article  PubMed  CAS  Google Scholar 

  • Reddy L, Friesen TL, Meinhardt SW, Chao S, Faris JD (2008) Genomic analysis of the Snn1 locus on wheat chromosome arm 1BS and the identification of candidate genes. Plant Genome 1:55–66

    Article  CAS  Google Scholar 

  • Saintenac C, Zhang W, Salcedo A, Rouse MN, Trick HN, Akhunov E, Dubcovsky J (2013) Identification of wheat gene Sr35 that confers resistance to Ug99 stem rust race group. Science 341:783–786

    Article  PubMed  CAS  Google Scholar 

  • Singh RP, Hodson DP, Huerta-Espino J, Jin Y, Bhavani S, Njau P, Herrera-Foessel S, Singh PK, Singh S, Govindan V (2011) The emergence of Ug99 races of the stem rust fungus is a threat to world wheat production. Annu Rev Phytopathol 49(1):465–481

    Article  PubMed  CAS  Google Scholar 

  • Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L). Theor Appl Genet 109:1105–1114

    Article  PubMed  CAS  Google Scholar 

  • Stakman E, Steward D, Loegering W (1962) Identification of physiologic races of Puccinia graminis var. tritici. US Department of Agriculture, ARS (E-617)

  • Zhang W, Olson E, Saintenac C, Rouse M, Abate Z, Jin Y, Akhunov E, Pumphrey M, Dubcovsky J (2010) Genetic maps of stem rust resistance gene Sr35 in diploid and hexaploid wheat. Crop Sci 50:2464–2474

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was funded in part by Borlaug Global Rust Initiative (BGRI) Durable Rust Resistance in Wheat (DRRW) Project (administered by Cornell University with a grant from the Bill & Melinda Gates Foundation and the UK Department for International Development); Australian Centre for International Agricultural Research (ACIAR), Grain Research and Development Corporation (GRDC), National Science Foundation Plant Genome Research DBI-0701916 (Principal Investigator, J. Dvorak). The first author acknowledges the University of Sydney for providing Endeavour International Postgraduate Research Scholarship. We are grateful to Sutha Chandramohan, Libby Viccars, Xiaodi Xia and Hanif Miah for excellent technical support.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The experiments comply with the current laws of Australia.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sambasivam Periyannan.

Additional information

Communicated by F. Ordon.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Periyannan, S., Bansal, U., Bariana, H. et al. Identification of a robust molecular marker for the detection of the stem rust resistance gene Sr45 in common wheat. Theor Appl Genet 127, 947–955 (2014). https://doi.org/10.1007/s00122-014-2270-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-014-2270-6

Keywords

Navigation