Molecular Breeding

, Volume 14, Issue 4, pp 349–361 | Cite as

Discovery, localization, and sequence characterization of molecular markers for the crown rust resistance genes Pc38, Pc39, and Pc48 in cultivated oat (Avena sativa L.)

  • Charlene P. Wight
  • Louise S. O’Donoughue
  • James Chong
  • Nicholas A. Tinker
  • Stephen J. Molnar


Molecular markers for the crown rust resistance genes Pc38, Pc39, and Pc48 in cultivated oat (Avena sativa L.) were identified using near-isogenic lines and bulked segregant analysis. Six markers for Pc48, the closest being 6 cM away, were found in a ‘Pendek-39’ × ‘Pendek-48’ (Pendek3948) population, but none was found in a ‘Pendek-48’ × ‘Pendek-38’ (Pendek4838) population. Three markers for Pc39 were found in the Pendek3948 population, one of which cosegregated with the gene. This same marker was found to be 6 cM away from the gene in an ‘OT328’ × ‘Dumont’ (OT328Du) population. Nine markers for Pc38 were found in the Pendek4838 population, eight of which are within 2 cM of the gene. One other marker for Pc38 was found in the OT328Du population; however, comparative mapping suggests that the Pc38 region in OT328Du is in a different location than that in Pendek4838. A number of markers unlinked to the genes under study formed linkage groups in both the Pendek3948 and Pendek4838 populations. Four of these show homology or homoeology to each other and to the Pc39 region in Pendek3948. Two RFLP clones closely linked to Pc38 code for a putative leucine-rich repeat transmembrane protein kinase and a cre3 resistance gene analogue. This study provides information to support molecular breeding in oat, and contributes to ongoing research into genomic regions associated with fungal pathogen resistance.

Key words

Avena Crown rust resistance Molecular marker Oat Puccinia coronata 


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  1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W. and Lipman D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25: 3389–3402.Google Scholar
  2. Boyko E., Kalendar R., Korzun V., Fellers J., Korol A., Schulman A.H. and Gill B.S. 2002. A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function. Plant Molec. Biol. 48: 767–790.Google Scholar
  3. Brown C.M. and Jedlinski H. 1983. Ogle Spring oat. Crop Sci. 23: 1012.Google Scholar
  4. Bush A.L. and Wise R.P. 1998. High-resolution mapping adjacent to the Pc71 crown-rust resistance locus in hexaploid oat. Mol. Breed. 4: 13–21.Google Scholar
  5. Chong J. 2000. Incidence and virulence of Puccinia coronata f. sp. avenae in Canada from 1996 to 1998. Can. J. Plant Pathol. 22: 99–109.Google Scholar
  6. Chong J. and Aung T. 1998. Interaction of the crown rust resistance gene Pc94 with several Pc genes. Proc. 9th European and Mediterranean Cereal Rusts and Powdery Mildews Conference, 2–6 September 1996, Lunteren, The Netherlands. European and Mediterranean Cereal Rust Foundation, Wageningen, pp. 172–175.Google Scholar
  7. Chong J. and Brown P.D. 1996. Genetics of resistance to Puccinia coronata f. sp. avenae in two Avena sativa accessions. Can. J. Plant Path. 18: 286–292.Google Scholar
  8. Chong J., Howes N.K., Brown P.D., and Harder D.E. 1994. Identification of the stem rust resistance gene Pg9 and its association with crown rust resistance and endosperm proteins in ‘Dumont’ oat. Genome 37: 440–447.Google Scholar
  9. Chong J., Leonard K.J. and Salmeron J.J. 2000. A North American system of nomenclature for Puccinia coronata f. sp. avenae. Plant Disease 84: 580–585.Google Scholar
  10. Chong J., Reimer E., Somers D., Aung T. and Penner G.A. 2004. Development of a sequence characterized amplified region marker for the crown rust resistance gene Pc94 in oat. Can. J. Plant Pathol. 26: 89–96Google Scholar
  11. Chong J. and Zegeye T. 2004. Physiologic specialization of Puccinia coronata f. sp. avenae in Canada from 1999 to 2001. Can. J. Plant Pathol. 26: 97–108Google Scholar
  12. Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J., Hofmann K., and Bairoch A. 2002. The PROSITE database, its status in 2002. Nucl. Acids Res. 30: 235–238.Google Scholar
  13. Fleischmann G. and McKenzie R.I.H. 1968. Inheritance of crown rust resistance in Avena sterilis. Crop Sci. 8: 710–713.Google Scholar
  14. Fleischmann G., McKenzie R.I.H. and Shipton W.A. 1971. Inheritance of crown rust resistance genes in Avena sterilis collections from Israel, Portugal and Tunisia. Can. J. Genet. Cytol. 13: 251–255.Google Scholar
  15. Harder D.E., McKenzie R.I.H. and Martens J.W. 1980. Inheritance of crown rust resistance in three accessions of Avena sterilis. Can. J. Genet. Cytol. 22: 27–33.Google Scholar
  16. Heun M., Kennedy A.E., Anderson J.A., Lapitan N.L.V., Sorrells M.E. and Tanksley S.D. 1991. Construction of a restriction fragment length polymorphism map for barley (Hordeum vulgare). Genome 34: 437–447.Google Scholar
  17. Holloway J.L. and Knapp S.J. 1993. G-MENDEL 3.0: Software for the analysis of genetic markers and maps, pp. 1–130. Oregon State University, Corvallis, USA.Google Scholar
  18. Howes N.K., Chong J. and Brown P.D. 1992. Oat endosperm proteins associated with resistance to stem rust of oats. Genome 35: 120–125.Google Scholar
  19. Kiehn F.A., McKenzie R.I.H. and Harder D.E. 1976. Inheritance of resistance to Puccinia coronata avenae and its association with seed characteristics in four accessions of Avena sterilis. Can. J. Genet. Cytol. 18: 717–726.Google Scholar
  20. Ladizinsky G. 1970. Chromosome rearrangements in the hexaploid oats. Heredity 25: 457–461.Google Scholar
  21. Lander E., Green P., Abrahamson J., Barlow A., Daly M., Lincoln S. and Newburg L. 1987. MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1: 174–181.PubMedGoogle Scholar
  22. Larson S.R., Kadyrzhanova D., McDonald C., Sorrells M.E. and Blake T.K. 1996. Evaluation of barley chromosome-3 yield QTLs in a backcross F2 population using STS-PCR. Theor. Appl. Genet. 93: 618–625.Google Scholar
  23. Leach G.D. and McMullen M.S. 1989. Genetics of a reciprocal interchange producing unexpected segregation for crown rust conditioned by Pc-38 in crosses of Steele/Dumont oat (Avena sativa L.). In: Agronomy Abstracts, ASA, Madison, WI, USA, pp. 90.Google Scholar
  24. Marchler-Bauer A., Anderson J.B., DeWeese-Scott C., Fedorova N.D., Geer L.Y., He S., Hurwitz D.I., Jackson J.D., Jacobs A.R., Lanczycki C.J., Liebert C.A., Liu C., Madej T., Marchler G.H., Mazumder R., Nikolskaya A.N., Panchenko A.R., Rao B.S., Shoemaker B.A., Simonyan V., Song J.S., Thiessen P.A., Vasudevan S., Wang Y., Yamashita R.A., Yin J.J. and Bryant S.H. 2003. CDD: a curated Entrez database of conserved domain alignments. Nucl. Acids Res. 31: 383–387.Google Scholar
  25. Martens J.W. and Dyck P.L. 1989. Genetics of resistance to rust in cereals from a Canadian perspective. Can. J. Plant Path. 11: 78–85.Google Scholar
  26. Martens J.W., McKenzie R.I.H. and Harder D.E. 1980. Resistance to Puccinia graminis avenae and P. coronata avenae in the wild and cultivated Avena populations of Iran, Iraq, and Turkey. Can. J. Genet. Cytol. 22: 641–649.Google Scholar
  27. McKenzie R.I.H., Brown P.D., Martens J.W., Harder D.E., Nielsen J., Gill C.C. and Boughton G.R. 1984. Registration of Dumont oats. Crop Sci. 24: 207.Google Scholar
  28. McKenzie R.I.H., Martens J.W. and Rajhathy T. 1970. Inheritance of oat stem rust resistance in a Tunisian strain of Avena sterilis. Can. J. Genet. Cytol. 12: 501–505.Google Scholar
  29. McMullen M.S. and Patterson F.L. 1992. Oat cultivar development in the USA and Canada.. In: Marshall H.G. and Sorrells M.E. (eds), Oat Science and Technology, American Society of Agronomy and Crop Science Society of America, Madison, USA, pp. 573–612.Google Scholar
  30. McMullen M.S., Phillips R.L. and Stuthman D.D. 1982. Meiotic irregularities in Avena sativa L. / A. sterilis L. hybrids and breeding implications. Crop Sci. 22: 890–897.Google Scholar
  31. Michelmore R.W. and Meyers B.C. 1998. Clusters of resistance genes in plants evolve by divergent selection and a birth-anddeath process. Genome Res. 8: 1113–1130.Google Scholar
  32. Michelmore R.W., Paran I. and Kesseli R.V. 1991. Identification of markers linked to disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl. Acad. Sci. USA 88: 9828–9832.Google Scholar
  33. Murphy H.C. 1935. Physiologic specialization in Puccinia coronata avenae. U.S. Dep. Agric. Tech. Bull. 433.Google Scholar
  34. O’Donoughue L.S., Chong J., Wight C.P., Fedak G. and Molnar S.J. 1996. Localization of stem rust resistance genes and associated molecular markers in cultivated oat. Phytopath. 86: 719–727.Google Scholar
  35. O’Donoughue L.S., Kianian S.F., Rayapati P.J., Penner G.A., Sorrells M.E., Tanksley S.D., Phillips R.L., Rines H.W., Lee M., Fedak G., Molnar S.J., Hoffman D., Salas C.A., Wu B., Autrique E., and Van Deynze A. 1995. A molecular linkage map of cultivated oat. Genome 38: 368–380.Google Scholar
  36. O’Donoughue L.S., Wang Z., Röder M., Kneen B., Leggett M., Sorrells M.E., and Tanksley S.D. 1992. An RFLP-based linkage map of oats based on a cross between two diploid taxa (Avena atlantica × A. hirtula). Genome 35: 765–771.Google Scholar
  37. Pedersen W.L. and Leath S. 1988. Pyramiding major genes for resistance to maintain residual effects. Ann. Rev. Phytopath. 26: 496–500.Google Scholar
  38. Penner G., Chong J., Levesque M., Molnar S.J. and Fedak G. 1993a. Identification of a RAPD marker linked to the oat stemrust gene Pg3. Theor. Appl. Genet. 85: 702–705.Google Scholar
  39. Penner G.A., Chong J., Wight C.P., Molnar S.J. and Fedak G. 1993b. Identification of an RAPD marker for the crown rust resistance gene Pc68 in oats. Genome 36: 818–820.Google Scholar
  40. Portyanko V.A., Hoffman D.L., Lee M. and Holland J.B. 2001. A linkage map of hexaploid oat based on grass anchor DNA clones and its relationship to other oat maps. Genome 44: 249–265.CrossRefPubMedGoogle Scholar
  41. Rayapati P.J., Gregory J.W., Lee M. and Wise R.P. 1994. A linkage map of diploid Avena based on RFLP loci and a locus conferring resistance to nine isolates of Puccinia coronata var. avenae. Theor. Appl. Genet. 89: 831–837.Google Scholar
  42. Rooney W.L., Rines H.W. and Phillips R.L. 1994. Identification of RFLP markers linked to crown rust resistance genes Pc91 and Pc92 in oat. Crop Sci. 34: 940–944.Google Scholar
  43. Salmon S.C. and Parker J.H. 1921. Kanota: An early oat for Kansas. SC091.PDF.Google Scholar
  44. Simons M.D. 1954. A North American race of crown rust attacking the oat varieties Landhafer and Santa Fe. Plant Dis. Repr. 39: 505–506.Google Scholar
  45. Takahashi A., Casais C., Ichimura K. and Shirasu K. 2003. HSP90 interacts with RAR1 and SGT1 and is essential for RPS2-mediated disease resistance in Arabidopsis. Proc. Natl. Acad. Sci. 100: 11777–11782.Google Scholar
  46. Tatusova T.A. and Madden T.L. 1999. Blast2 sequences - a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174: 247–250.Google Scholar
  47. Tinker N.A. 1999. Management of multiple molecular marker maps with multiple molecular marker map manager ‘Mmmmm’. J. Ag. Genomics 4. Published with permission from CAB International. Full text available from Scholar
  48. Tragoonrung S., Kanazin V., Hayes P.M. and Blake T.K. 1992. Sequence-tagged-site-facilitated PCR for barley genome mapping. Theor. Appl. Genet. 84: 1002–1008.Google Scholar
  49. van der Biezen E.A. and Jones J.D.G. 1998. The NB-ARC domain: a novel signaling motif shared by plant resistance gene products and regulators of cell death in animals. Curr. Biol. 8: R226-R227.Google Scholar
  50. Wight C.P., Penner G.A., O’Donoughue L.S., Burrows V.D., Molnar S.J. and Fedak G. 1994. The identification of random amplified polymorphic DNA (RAPD) markers for daylength sensitivity in oat. Genome 37: 910–914.Google Scholar
  51. Wight C.P., Tinker N.A., Kianian S.F., Sorrells M.E., O’Donoughue L.S., Hoffman D.L., Groh S., Scoles G.J., Li C.D., Webster F.H., Phillips R.L., Rines H.W., Livingston S.M., Armstrong K.C., Fedak G. and Molnar S.J. 2003. A molecular marker map in Kanota × Ogle hexaploid oat (Avena spp.) enhanced by additional markers and a robust framework. Genome 46: 28–47.CrossRefPubMedGoogle Scholar
  52. Wilson W.F. and McMullen M.S. 1997a. Recombination between a crown rust resistance locus and an interchange breakpoint in hexaploid oat. Crop Sci. 37: 1694–1698.Google Scholar
  53. Wilson W.F. and McMullen M.S. 1997b. Dosage dependent genetic suppression of oat crown rust resistance gene Pc62. Crop Sci. 37: 1699–1705.Google Scholar
  54. Zhu S. and Kaeppler H.F. 2003a. A genetic linkage map for hexaploid, cultivated oat (Avena sativa L.) based on an intraspecific cross ‘Ogle/MAM17-5’. Theor. Appl. Genet. 107: 26–35.Google Scholar
  55. Zhu S. and Kaeppler H.F. 2003b. Identification of quantitative trait loci for resistance to crown rust in oat line MAM17-5. Crop Sci. 43: 358–366.Google Scholar

Copyright information

© Minister of Public Works and Government Services Canada 2004

Authors and Affiliations

  • Charlene P. Wight
    • 1
  • Louise S. O’Donoughue
    • 1
  • James Chong
    • 2
  • Nicholas A. Tinker
    • 1
  • Stephen J. Molnar
    • 1
  1. 1.Eastern Cereal and Oilseed Research CentreAgriculture and Agri-Food Canada, Central Experimental FarmOttawaCanada
  2. 2.Cereal Research CentreAgriculture and Agri-Food CanadaWinnipegCanada

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