Theoretical and Applied Genetics

, Volume 131, Issue 3, pp 721–733 | Cite as

Identification, introgression, and molecular marker genetic analysis and selection of a highly effective novel oat crown rust resistance from diploid oat, Avena strigosa

  • Howard W. Rines
  • Marisa E. Miller
  • Martin Carson
  • Shiaoman Chao
  • Tyler Tiede
  • Jochum Wiersma
  • Shahryar F. Kianian
Original Article


Key message

Oat crown rust is one of the most damaging diseases of oat. We identified a new source of resistance and developed KASP and TaqMan markers for selection in breeding programs.


A new highly effective resistance to oat crown rust (Puccinia coronata f. sp. avenae) was identified in the diploid oat Avena strigosa PI 258731 and introgressed into hexaploid cultivated oat. Young plants with this resistance show moderate susceptibility, whereas older plant tissues and adult plants are resistant with no virulent isolates encountered in over 8 years of testing. Resistance was incorporated into hexaploid oat by embryo rescue, colchicine chromosome doubling followed by backcrosses with a hexaploid parent, and selection for stable transmission of resistance. To mitigate flag leaf and panicle chlorosis/necrosis associated with the resistance, crosses were made with derived resistant lines to breeding lines of divergent parentage followed by selection. Subsequently, two F2 sister lines, termed MNBT1020-1 and MNBT1021-1, were identified in which the chlorosis/necrosis was reduced. These two lines performed well in replicated multi-location state trials in 2015 and 2016 out-yielding all cultivar entries. Segregating F2:3 plants resulting from crosses of MNBT lines to susceptible parents were genotyped with the oat 6K SNP array, and SNP loci with close linkage to the resistance were identified. KASP assays generated from linked SNPs showed accurate discrimination of the resistance in derivatives of the resistant MNBT lines crossed to susceptible breeding lines. A TaqMan marker was developed and correctly identified homozygous resistance in over 95% of 379 F4 plants when rust was scored in F4:5 plants in the field. Thus, a novel highly effective resistance and associated molecular markers are available for use in breeding, genetic analysis, and functional studies.



Funding for the project was provided by the US Department of Agriculture—Agricultural Research Service and the Minnesota State Agricultural Experiment Station. At the USDA-ARS Cereal Disease Laboratory, we thank Roger Caspers and the late Gerald Ochocki for valued technical assistance in conducting greenhouse and field oat crown rust tests. We thank Dr. Farhad Ghavami and Eurofins BioDiagnostics Inc. in River Falls, Wisconsin, for KASP assay design and execution. We also thank Shalane Porter, Dinesha Walek, and staff at UMGC for assistance with TaqMan assay design and execution, as well as Dr. Kevin Smith and Karen Beaubien for assistance and input with TaqMan marker-assisted selection. M.E.M was partially supported by a USDA-NIFA Postdoctoral Fellowship Award (2017-67012-26117). Mention of trade names or commercial products in this publication is solely for purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. USDA is an equal opportunity provider and employer.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

122_2017_3031_MOESM1_ESM.pdf (86 kb)
Online Resource 1. List of lines used for molecular marker development (PDF 85 kb)
122_2017_3031_MOESM2_ESM.xlsx (659 kb)
Online Resource 2. Analysis of 6K SNP genotyping data (XLSX 658 kb)
122_2017_3031_MOESM3_ESM.xlsx (14 kb)
Online Resource 3. KASP primer sequences (XLSX 14 kb)
122_2017_3031_MOESM4_ESM.xlsx (20 kb)
Online Resource 4. KASP assay genotyping results (XLSX 19 kb)
122_2017_3031_MOESM5_ESM.xlsx (428 kb)
Online Resource 5. MAS results using a TaqMan marker of the GMI_ES13_c626_111 SNP (XLSX 428 kb)


  1. Aung T, Chong J, Leggett M (1996) The transfer of crown rust resistance gene Pc94 from a wild diploid to cultivated hexaploid oat. In: Kema GHJ, Niks RE, Daamen RA (eds) Proceedings of the 9th European and Mediterranean Cereal Rusts and Powdery Mildews Conference. 2–6 Sept. 1996, Lunteren, Netherlands. European and Mediterranean Cereal Rust Foundation, Wageningen, Netherlands, pp 167–171Google Scholar
  2. Brown CM, Jedlinski H (1983) Ogle spring oat. Crop Sci 23:1012–1013Google Scholar
  3. Cabral AL, Singh D, Park RF (2011) Identification and genetic characterisation of adult plant resistance to crown rust in diploid and tetraploid accessions of Avena. Annals Appl Biol 159:220–228CrossRefGoogle Scholar
  4. Cabral AL, Ganesh BN, Mitchell Fetch JW, McCartney C, Fetch T, Park RF, Menzies JG, McCallum B, Nanaiah GK, Goyal A (2014) Oat fungal diseases and the application of molecular marker technology for their control. In: Goyal A, Manoharachary C (eds) Future challenges in crop protection against fungal pathogens. Springer, New York, pp 343–358Google Scholar
  5. Caffe-Treml M, Hall L, Bauer R, Kleinjan J, Hall N, Ingemansen JA (2017) Registration of oat cultivar ‘Hayden’. J Plant Regist 11:95–99CrossRefGoogle Scholar
  6. Carson ML (2009) Broad-spectrum resistance to crown rust, Puccinia coronata f. sp. avenae, in accessions of the tetraploid slender oat. Avena barbata. Plant Dis 93:363–366CrossRefGoogle Scholar
  7. Carson ML (2011) Virulence in oat crown rust (Puccinia coronata f. sp. avenae) in the United States from 2006 through 2009. Plant Dis 95:1528–1534CrossRefGoogle Scholar
  8. Chaffin AS, Huang Y-F, Smith S, Bekele WA, Babiker E et al (2016) A consensus map in cultivated hexaploid oat reveals conserved grass synteny with substantial subgenome rearrangement. Plant Genome 9.
  9. Dyck PL, Zillinsky FL (1963) Inheritance of crown rust resistance transferred from diploid to hexaploid oats. Can J Genet Cytol 5:398–407CrossRefGoogle Scholar
  10. Gnanesh BN, Mitchell Fetch J, Zegeye T, McCartney CA, Fetch T (2014) Oat. In: Pratap A, Kumar J (eds) Alien gene transfer in plants, vol 2. Achievements and impacts. Springer, New York, pp 51–73CrossRefGoogle Scholar
  11. Jorgensen JH (1992) Discovery, characterization and exploitation of Mlo powdery mildew resistance in barley. Euphytica 63:141–152CrossRefGoogle Scholar
  12. Klos KE, Huang YF, Bekele WA, Obert DE, Babiker E, Beattie AD, Bjørnstad Å, Bonman JM, Carson ML, Chao S, Gnanesh BN et al (2016) Population genomics related to adaptation in elite oat germplasm. Plant Genome. PubMedGoogle Scholar
  13. Kolb FL, Smith NJ, Brucker EA (2012) Registration of ‘Saber’ oat. J Plant Regist 6:277–280CrossRefGoogle Scholar
  14. Lagudah ES (2011) Molecular genetics of race non-specific rust resistance in wheat. Euphytica 179:81–91CrossRefGoogle Scholar
  15. Loarce Y, Navas E, Paniagua C, Fominaya A, Manjón JL, Ferrer E (2016) Identification of genes in a partially resistant genotype of Avena sativa expressed in response to Puccinia coronata infection. Front Plant Sci 7:731CrossRefPubMedPubMedCentralGoogle Scholar
  16. Loskutov IG, Rines HW (2011) Avena. In: Kole C (ed) Wild crop relatives: genomic and breeding resources cereals. Springer, Berlin, pp 109–183CrossRefGoogle Scholar
  17. Marshall HG, Myers WM (1961) A cytogenetic study of certain interspecific Avena hybrids and the inheritance of resistance to diploid and tetraploid varieties to races of crown rust. Crop Sci 1:29–34CrossRefGoogle Scholar
  18. McMullen MS, Doehlert DC, Miller JD (2005) Registration of ‘HiFi’ oat. Crop Sci 45:1664CrossRefGoogle Scholar
  19. Nazareno E, Li F, Smith M, Park RF, Kianian SF, Figueroa M (2017) Puccinia coronata f. sp. avenae: a threat to global oat production. Mol Plant. Google Scholar
  20. Rines HW, Porter HL, Carson ML, Ochocki GE (2007) Introgression of crown rust resistance from diploid oat Avena strigosa into hexaploid cultivated oat A. sativa by two methods: direct crosses and through an initial 2x + 4x synthetic hybrid. Euphytica 158:67–79CrossRefGoogle Scholar
  21. Roelfs AP, Martens JW (1988) An international system of nomenclature for Puccinia graminis f. sp. tritici. Phytopathology 78:526–533CrossRefGoogle Scholar
  22. Tinker NA, Chao S, Lazo GR, Oliver RE, Huang Y-F, Poland JA, Jellen EN, Maughan PJ, Kilian A, Jackson EW (2014) A SNP genotyping array for hexaploid oat. Plant Genome 7.
  23. USDA-ARS CDL (2014) Oat loss to rust. USDA-ARS Cereal Disease Laboratory Accessed 1 Apr 2017

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.USDA-ARS Plant Sciences Research UnitSt. PaulUSA
  2. 2.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulUSA
  3. 3.Department of Plant PathologyUniversity of MinnesotaSt. PaulUSA
  4. 4.USDA-ARS Cereal Disease LaboratorySt. PaulUSA
  5. 5.USDA-ARS, Cereal Crops Research UnitFargoUSA
  6. 6.Department of Agronomy and Plant GeneticsUniversity of MinnesotaCrookstonUSA

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