Chromosomal location of the crown rust resistance gene Pc98 in cultivated oat (Avena sativa L.)


Key message

SNP loci linked to the crown rust resistance gene Pc98 were identified by linkage analysis and KASP assays were developed for marker-assisted selection in breeding programs.


Crown rust is among the most damaging diseases of oat and is caused by Puccinia coronata var. avenae f. sp. avenae (Urban and Marková) (Pca). Host resistance is the preferred method to prevent crown rust epidemics. Pc98 is a race-specific, seedling crown rust resistance gene obtained from the wild oat Avena sterilis accession CAV 1979 that is effective at all growth stages of oat. Virulence to Pc98 has been very low in the Pca populations that have been tested. The objectives of this study were to develop SNP markers linked to Pc98 for use in marker-assisted selection and to locate Pc98 on the oat consensus map. The Pc98 gene was mapped using F2:3 populations developed from the crosses Pc98/Bingo and Pc98/Kasztan, where Pc98 is a single-gene line carrying Pc98. Both populations were evaluated in seedling inoculation experiments. Pc98 was mapped relative to Kompetitive Allele-Specific PCR SNP markers in both populations, placing Pc98 on the Mrg20 linkage group of the consensus map. Pc98 was bracketed by two SNP markers GMI_ES22_c3052_382_kom399 and GMI_ES14_lrc18344_662_kom398 in the Pc98/Bingo mapping population with genetic distances of 0.9 cM and 0.3 cM, respectively. Pc98 co-segregated with four SNP markers in the Pc98/Kasztan population, and the closest flanking markers were GMI_DS_LB_6017_kom367 and avgbs2_153634.1.59_kom410 with genetic distances of 0.7 cM and 0.3 cM, respectively. Two SNP loci defined a haplotype that accurately predicted Pc98 status in a diverse group of oat germplasm, which will be valuable for marker-assisted selection of Pc98 in breeding of new oat cultivars.

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Fig. 1

Availability of data and materials

Data supporting the current study can be obtained by contacting the corresponding author (



Collaborative Oat Research Enterprise




Infection type


Kompetitive Allele-Specific PCR


Logarithm of odds


Marker-assisted selection

Pca :

Puccinia coronata var. avenae f. sp. avenae


Restriction fragment length polymorphism


Single nucleotide polymorphism


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The authors thank Leslie Bezte, Suzanne Enns, Alain Ngantcha, and Sharon Deceuninck for technical support. The study was funded by the Prairie Oat Growers Association - Prairie Oat Breeding Consortium Agricultural Innovation Project with matching funding from Agriculture and Agri-Food Canada (AAFC) Growing Forward II.

Author information

JZ, AZK, JGM, EPG, JC, JWMF, ADB, YYP, and CAM planned and organized the study. JZ, AZK, and CAM designed DNA markers and collected marker data. JZ and JGM collected crown rust data. EPG developed mapping populations. JZ and CAM conducted linkage analyses. All authors contributed to and approved the final manuscript.

Correspondence to Curt A. McCartney.

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Zhao, J., Kebede, A.Z., Menzies, J.G. et al. Chromosomal location of the crown rust resistance gene Pc98 in cultivated oat (Avena sativa L.). Theor Appl Genet (2020) doi:10.1007/s00122-020-03535-x

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