Skip to main content
SpringerLink
Log in

Haplotype analysis of molecular markers linked to stem rust resistance genes in Ethiopian improved durum wheat varieties and tetraploid wheat landraces

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

The recent emergence of wheat stem rust race Ug99 (TTKSK) and related strains threaten Ethiopian as well as world wheat production because they overcome widely used resistance genes that had been effective for many years. The major cause which aggravates the ineffectiveness of Ethiopian wheat varieties against stem rust is the narrow genetic base on which the breeding for resistance has been founded, however, little is known about the resistance genotypes of Ethiopian durum wheat varieties and tetraploid wheat landraces. The objective of the study was to identify stem rust resistance genes that are present in the Ethiopian tetraploid wheat landraces and improved durum wheat varieties using molecular markers and assess which genes are effective for current Ethiopian stem rust races of Puccinia graminis f. sp. tritici including Ug99. The investigated 58 tetraploid wheat accessions consisted of 32 (Triticum durum s.l. incl. Triticum aethiopicum Jakubz., Triticum polonicum) landraces and 22 registered T. durum varieties released in Ethiopia between 1966 and 2009 and four T. durum varieties from ICARDA. A total of 17 molecular markers (SSR, EST and InDel) linked or diagnostic for stem rust resistance genes Sr2, Sr13, Sr22 and Sr35 were used for genotyping. Haplotype analysis indicated that only few of the Ethiopian durum wheat varieties carried Sr13. The resistant variety ‘Sebatel’ showed a haplotype for Sr2 and Sr22 and variety ‘Boohai’ for Sr22, however further evaluation is needed for the diagnostic value of these haplotypes. This study is the first report on the presence of stem rust resistance (Sr) genes in Ethiopian durum wheat varieties and tetraploid wheat landraces based on linked or associated molecular markers. Thus it might help in the identification of varieties carrying resistant alleles that provide valuable genetic material for the development of new improved varieties in further breeding programmes.

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

Abbreviations

BARC:

Beltsville Agriculture Research Center

bp:

Base pair

CI:

Coefficient of infection

CIMMYT:

International Maize and Wheat Improvement Center

cM:

CentiMorgan

DN:

Denbi

DZ:

Debre-Zeit

EST:

Expressed sequence tags

GS:

Growth stage

GWM:

Gatersleben wheat microsatellite

ICARDA:

International Center for Agricultural Research in the Dry Areas

InDel:

Insertion–deletion

IR:

Infection response

IT:

Infection type

LR:

Landrace

MAS:

Marker-assisted selection

MS:

Main season

OS:

Off season

PCR:

Polymerase chain reaction

Pgt :

Puccinia graminis f. sp. tritici

Sev:

Field severity

Sr :

Stem rust resistance

SSR:

Simple sequence repeat

WMC:

Wheat microsatellite consortium

References

  • Admassu B (2010) Genetic and virulence diversity of Puccinia graminis f. sp. tritici populations in Ethiopia and stem rust resistance genes in wheat. Ph.D. thesis, Giessen University, Cuvillier Verlag Göttingen, Germany

  • Admassu B, Embet F, Zerihun K (2004) Physiological races and virulence diversity of Puccinia graminis f. sp. tritici on wheat in Ethiopia. In: 12th regional wheat workshop for Eastern, Central, and Southern Africa, Nakuru, Kenya, 22–26 November 2004, pp 145–150

  • Admassu B, Lind V, Friedt W, Ordon F (2009) Virulence analysis of Puccinia graminis f. sp. tritici populations in Ethiopia with special consideration of Ug99. Plant Pathol 58:362–369

    Google Scholar 

  • Admassu B, Perovic D, Friedt W, Ordon F (2011) Genetic mapping of the stem rust (Puccinia graminis f. sp. tritici Eriks. & E. Henn) resistance gene Sr13 in wheat (Triticum aestivum L.). Theor Appl Genet 122:643–648

    Article  PubMed  CAS  Google Scholar 

  • Babiker E, Ibrahim A, Yen Y, Stein J (2009) Identification of a microsatellite marker associated with stem rust resistance gene Sr35 in wheat. Aust J Crop Sci 3:195–200

    CAS  Google Scholar 

  • Badebo A (2002) Breeding bread wheat with multiple disease resistance and high yield for the Ethiopian highlands: broadening the genetic basis of yellow rust and tan spot resistance. Ph.D. thesis, Georg-August University, Gottingen, Germany

  • Badebo A, Stubbs RW, Van Ginkel M, Getinet G (1990) Identification of resistance genes to Puccinia striiformis in seedlings of Ethiopian and CIMMYT bread wheat varieties and lines. Neth J Plant Pathol 96:199–210

    Article  Google Scholar 

  • Bechere E, Kebede H, Belay G (2000) Durum wheat in Ethiopia: an old crop in an ancient land. Institute of Biodiversity Conservation and Research (IBCR), Addis Ababa, Ethiopia, p 68

  • Beteselassie N, Fininsa C, Badebo A (2007) Sources of resistance to stem rust (Puccinia graminis f. sp. tritici) in Ethiopian tetraploid wheat accessions. Genet Resour Crop Evol 54:337–343

    Article  Google Scholar 

  • CIMMYT (2000)1998/1999 World wheat facts and trends. Global wheat research in a changing world, challenges and achievements. CIMMYT, Mexico

  • CSA (2009) Central Statistical Agency, 2009/2010, agricultural sample survey, report on area and production of crops. Statistical bulletin 446, vol IV. Addis Ababa, Ethiopia, p 14

  • Das BK, Saini A, Bhagwat SG, Jawali N (2006) Development of SCAR markers for identification of stem rust resistance gene Sr31 in the homozygous or heterozygous condition in bread wheat. Plant Breed 125:544–549

    Article  CAS  Google Scholar 

  • Dawit W (2008) Analysis of pathogen virulence and cultivar resistance to yellow rust, Puccinia striiformis f. sp. tritici, in Ethiopia. Ph.D. thesis, Martin-Luther-Universität Halle-Wittenberg, Germany

  • Doyle JJ, Doyle JL (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus 12:13–15

    Google Scholar 

  • FAOSTAT (2003) Crop protection compendium CD. CAB International, UK

    Google Scholar 

  • Forster BP, Ellis RP, Thomas WTB, Newton AC, Tuberosa RTD, El-Enein RA, Bahri MH, Ben Salem M (2000) The development and application of molecular markers for abiotic stress tolerance in barley. J Exp Biol 51:19–27

    CAS  Google Scholar 

  • Gerechter-Amitai ZK, Wahl I, Vardi A, Zohary D (1971) Transfer of stem rust seedling resistance from wild diploid einkorn to tetraploid durum wheat by means of a triploid hybrid bridge. Euphytica 2:281–285

    Article  Google Scholar 

  • Haile JK, Nachit MM, Hammer K, Badebo A, Röder MS (2012a) QTL mapping of resistance to race Ug99 of Puccinia graminis f. sp. tritici in durum wheat (Triticum durum Desf.). Mol Breed. doi:10.1007/s11032-012-9734-7

    Google Scholar 

  • Haile JK, Hammer K, Badebo A, Nachit MM, Röder MS (2012b) Genetic diversity assessment of Ethiopian tetraploid wheat landraces and improved durum wheat varieties using microsatellites and markers linked with stem rust resistance. Genet Resour Crop Evol. doi:10.1007/s10722-012-9855-1

    Google Scholar 

  • Hare RA, McIntosh RA (1979) Genetics and cytogenetics studies of durable adult-plant resistance in ‘Hope’ and related cultivars to wheat rusts. Z Pflanzenzüchtung 83:350–367

    Google Scholar 

  • Hayden MJ, Kuchel H, Chalmers KJ (2004) Sequence tagged microsatellites for the Xgwm533 locus provide new diagnostic markers to select for the presence of stem rust resistance genes Sr2 in bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1641–1647

    Article  PubMed  CAS  Google Scholar 

  • Hiebert CW, Fetch TG Jr, Zegeye T (2010) Genetics and mapping of stem rust resistance to Ug99 in the wheat cultivar Webster. Theor Appl Genet 121:65–69

    Article  PubMed  Google Scholar 

  • Huang XQ, Hsam SLK, Zeller FJ (1997) Chromosomal locations of genes for resistance to powdery mildew in common wheat (Triticum aestivum L. em. Thell.). 4. Gene pm24 in Chinese landrace Chiyacao. Theor Appl Genet 95:950–953

    Article  Google Scholar 

  • Huerta-Espino J (1992) Analysis of wheat leaf and stem rust virulence on a worldwide basis. Ph.D. thesis, University of Minnesota, USA

  • Jin Y, Singh RP, Ward RW, Wanyera R, Kinyua MG, Njau P, Fetch T Jr, Pretorius ZA, Yahyaoui A (2007) Characterization of seedling infection types and adult plant infection responses of monogenic Sr gene lines to race TTKS of Puccinia graminis f. sp. tritici. Plant Dis 91:1096–1099

    Article  Google Scholar 

  • Kerber ER, Dyck PL (1973) Inheritance of stem rust resistance transferred from diploid wheat (Triticum monococcum) to tetraploid and hexaploid wheat and chromosome location of the gene involved. Can J Genet Cytol 15:397–409

    Google Scholar 

  • Khan R, Bariana H, Dholakia B, Naik S, Lagu M, Rathjen A, Bhavani S, Gupta V (2005) Molecular mapping of stem and leaf rust resistance in wheat. Theor Appl Genet 111:846–850

    Article  PubMed  CAS  Google Scholar 

  • Klindworth D, Miller J, Jin Y, Xu SS (2007) Chromosomal locations of genes for stem rust resistance in monogenic lines derived from tetraploid wheat accession STS464. Crop Sci 47:1441–1450

    Google Scholar 

  • Lakew B, Semeane Y, Alemayehu F, Genre H, Grando S, van Leur JAG, Ceccarelli S (1997) Exploiting the diversity of barley landraces in Ethiopia. Genet Resour Crop Evol 44:109–116

    Article  Google Scholar 

  • Leppik EE (1970) Gene centers of plants as a source of disease resistance. Annu Rev Phytopathol 8:323–344

    Article  Google Scholar 

  • Liu S, Yu L-X, Singh RP, Jin Y, Sorrells ME, Anderson JA (2010) Diagnostic and co-dominant PCR markers for wheat stem rust resistance genes Sr25 and Sr26. Theor Appl Genet 120:691–697

    Article  PubMed  CAS  Google Scholar 

  • Mago R, Bariana HS, Dundas IS, Spielmeyer W, Lawrence GJ, Pryor AJ, Ellis JG (2005) Development of broadly useful PCR-markers for the wheat stem rust resistance genes Sr24 and Sr26. Theor Appl Genet 111:496–504

    Article  PubMed  CAS  Google Scholar 

  • Mago R, Brown-Guedira G, Dreisigacker S, Breen J, Jin Y, Singh R, Appels R, Lagudah ES, Ellis J, Spielmeyer W (2011) An accurate DNA marker assay for stem rust resistance gene Sr2 in wheat. Theor Appl Genet 122:735–744

    Article  PubMed  CAS  Google Scholar 

  • Masresha A (1996) Wheat rust races identified in virulence surveys in Ethiopia. In: Tanner DG, Payne TS, Abdalla OS (eds) The ninth wheat regional workshop for Eastern Central and Southern Africa. CIMMYT, Addis Ababa, Ethiopia

  • McIntosh RA (1988) The role of specific genes in breeding for durable stem rust resistance in wheat and triticale. In: Simmonds NW, Rajaram S (eds) Breeding strategies for resistance to the rusts of wheat. CIMMYT, Mexico

    Google Scholar 

  • McIntosh RA, Dyck PL, The TT, Cusick J, Milne DL (1984) Cytogentical studies in wheat XIII: Sr35—a third gene from Triticum monococcum for resistance to Puccinia graminis tritici. Z Pflanzenzüchtung 92:1–14

    Google Scholar 

  • McIntosh RA, Wellings CR, Park RF (1995) Wheat rusts: an atlas of resistance genes. CSIRO, Canberra

    Book  Google Scholar 

  • McIntosh RA, Yamazaki Y, Devos KM, Dubcovsky J, Rogers WJ, Appels R (2003) Catalogue of gene symbols for wheat. In: Pogna NE, Romano M, Pogna A, Galterio G (eds) Proceedings of the 10th International Wheat Genetics Symposium, Paestum, Italy

  • Mujeeb-Kati A, Rajarm S (2000) Transferring alien genes from related species and genera for wheat improvement. In: Citrus BC, Rajarm S, MacPherson Gomez H (eds) Bread wheat improvement and production. FAO, Rome

    Google Scholar 

  • Olivera PD, Rouse M, Badebo A, Abeyo B, Woldeab G, Wanyera W, Jin Y (2011) Races of Puccinia graminis f. sp. tritici in Ethiopia and Kenya. In: McIntosh RA (ed) Proceedings of the Borlaug Global Rust Initiative 2011 technical workshop, June 13–16, St. Paul, MN, USA, p 157

  • Olson EL, Brown-Guedira G, Marshall D, Stack E, Bowden RL, Jin Y, Rouse M, Pumphrey MO (2010) Development of wheat lines having a small introgressed segment carrying stem rust resistance gene Sr22. Crop Sci 50:1823–1830

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  • Pretorius ZA, Singh RP, Wagoire WW, Payne TS (2000) Detection of virulence to wheat stem rust resistance gene Sr31 in Puccinia graminis f. sp. tritici in Uganda. Phytopathology 84:203

    Google Scholar 

  • Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier M-H, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    PubMed  Google Scholar 

  • Roelfs AP, Singh RP, Saari EE (1992) Rust diseases of wheat: concepts and methods of diseases management. CIMMYT, Mexico City

    Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Simons K, Abate Z, Chao S, Zhang W, Rouse M, Jin Y, Elias E, Dubcovsky J (2011) Genetic mapping of stem rust resistance gene Sr13 in tetraploid wheat (Triticum turgidum ssp. durum L.). Theor Appl Genet 122:649–658

    Article  PubMed  Google Scholar 

  • Singh RP, Hodson DP, Jin Y, Huerta-Espino J, Kinyua MG, Wanyera R, Njau P, Ward RW (2006) Current status, likely migration and strategies to mitigate the threat to wheat production from race Ug99 (TTKS) of stem rust pathogen. Perspect Agric Vet Sci Nutr Nat Resour 1:1–13

    CAS  Google Scholar 

  • Singh RP, Hodson DP, Huerta-Espino J, Jin Y, Njau P, Wanyera R, Ward WR (2008) Will stem rust destroy the world’s wheat crop? Adv Agron 98:271–309

    Article  CAS  Google Scholar 

  • Singh RP, Huerta-Espino J, Bhavani S, Singh D, Singh PK, Herrera-Foessel SA, Njau P, Wanyera R, Jin Y (2009) Breeding for minor gene-based resistance to stem rust of wheat. In: Proceedings of the Borlaug Global Rust Initiative, C.D. Obregon, Mexico

  • Spielmeyer W, Sharp PJ, Lagudah ES (2003) Identification and validation of markers linked to broad-spectrum stem rust resistance gene Sr2 in wheat (Triticum aestivum L.). Crop Sci 43:333–336

    Article  CAS  Google Scholar 

  • Sunderlund SD, Roelfs AP (1980) Greenhouse evaluation of the adult plant resistance of Sr2 to wheat stem rust. Phytopathology 70:634–637

    Article  Google Scholar 

  • Teklu Y, Hammer K (2009) Diversity of Ethiopian wheat germplasm: breeding opportunities for improving grain yield potentials and quality traits. Plant Genet Resour 7:1–8

    Article  Google Scholar 

  • Temam H (1984) Distribution and prevalence of physiologic races of Puccinia graminis f. sp. tritici in some parts of Ethiopia and reaction of wheat cultivars to these races. M.Sc. thesis, Addis Ababa University, Ethiopia

  • Tsilo TJ, Jin Y, James A, Anderson JA (2008) Diagnostic microsatellite markers for the detection of stem rust resistance gene Sr36 in diverse genetic backgrounds of wheat. Crop Sci 48:253–261

    Article  CAS  Google Scholar 

  • Vanzetti LS, Campos P, Demichelis M, Lombardo LA, Aurelia PR, Vaschetto LM, Bainotti CT, Helguera M (2011) Identification of leaf rust resistance genes in selected Argentinean bread wheat cultivars by gene postulation and molecular markers. Electron J Biotechnol 14(3). http://dx.doi.org/10.2225/vol14-issue3-fulltext-14

  • Vavilov NI (1929) Wheats of Ethiopia. Bull Appl Bot Genet Plant Breed 20:324–356

    Google Scholar 

  • Wu S, Pumphrey M, Bai G (2009) Molecular mapping of stem rust-resistance gene Sr40 in wheat. Crop Sci 49:1682–1686

    Article  Google Scholar 

  • Yu LX, Liu S, Anderson JA, Singh RP, Jin Y, Dubcovsky J, Guidera GB, Bhavani S, Morgounov A, He Z, Huerta-Espino J, Sorrells ME (2010) Haplotype diversity of stem rust resistance loci in uncharacterized wheat lines. Mol Breed 26:667–680

    Article  Google Scholar 

  • Yu LX, Lorenz A, Rutkoski J, Singh RP, Bhavani S, Huerta-Espino J, Sorrells ME (2011) Association mapping and gene–gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor Appl Genet 123:1257–1268

    Article  PubMed  CAS  Google Scholar 

  • 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

The first author was supported by a scholarship from the Deutscher Akademischer Austauschdienst (DAAD), Germany, to conduct this research. We would like to thank the Ethiopian Institute of Agricultural Research for providing leave of absence for Jemanesh K. Haile to carry out the research and providing experimental plots and funding for the field trials. Authors are thankful to Anette Heber, Rosemarie Czihal, Sonja Allner, Chuchu Kebede and Betelhem Hibdo for excellent technical assistance. Dr. Yue Jin (USDA-ARS Cereal Disease Laboratory) and CIMMYT Bread Wheat Section are acknowledged for providing stem rust differential lines and related information. We also would like to thank Dr. Miloudi Nachit for providing the ICARDA durum wheat varieties and Dr. Zewdie Abate (UCDavis) for his helpful comments.

Author information

Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Germany

    Jemanesh K. Haile & Marion S. Röder

  2. Department of Agrobiodiversity, Institute of Crop Sciences, University of Kassel, 37213, Witzenhausen, Germany

    Karl Hammer

  3. Ethiopian Institute of Agricultural Research, Debre-Zeit Agricultural Research Centre, P.O. Box 32, Debre-Zeit, Ethiopia

    Ayele Badebo

  4. International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico

    Ravi P. Singh

Authors
  1. Jemanesh K. Haile
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Karl Hammer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ayele Badebo
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ravi P. Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Marion S. Röder
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jemanesh K. Haile.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 79 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Haile, J.K., Hammer, K., Badebo, A. et al. Haplotype analysis of molecular markers linked to stem rust resistance genes in Ethiopian improved durum wheat varieties and tetraploid wheat landraces. Genet Resour Crop Evol 60, 853–864 (2013). https://doi.org/10.1007/s10722-012-9880-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-012-9880-0

Keywords

Search

Navigation