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Background  Crown rust, caused by  Puccinia coronata  f. sp.  avenae , is the most important disease of oat worldwide. Adult plant resistance (APR), based upon partial resistance, has proven to be a durable rust management strategy in other cereal rust pathosystems. The crown rust APR in the oat line MN841801 has been effective for more than 30 years. The genetic basis of this APR was studied under field conditions in three recombinant inbred line (RIL) populations: 1) AC Assiniboia/MN841801, 2) AC Medallion/MN841801, and 3) Makuru/MN841801. The populations were evaluated for crown rust resistance with the crown rust isolate CR251 (race BRBB) in multiple environments. The 6 K oat and 90 K wheat Illumina Infinium single nucleotide polymorphism (SNP) arrays were used for genotyping the AC Assiniboia/MN841801 population. KASP assays were designed for selected SNPs and genotyped on the other two populations.    Results  This study reports a high density genetic linkage map constructed with oat and wheat SNP markers in the AC Assiniboia/MN841801 RIL population. Most wheat SNPs were monomorphic in the oat population. However the polymorphic wheat SNPs could be scored accurately and integrated well into the linkage map. A major quantitative trait locus (QTL) on oat chromosome 14D, designated  QPc.crc-14D , explained up to 76% of the APR phenotypic variance. This QTL is flanked by two SNP markers, GMI_GBS_90753 and GMI_ES14_c1439_83.  QPc.crc-14D  was validated in the populations AC Medallion/MN841801 and Makuru/MN841801.    Conclusions  We report the first APR QTL in oat with a large and consistent effect.  QPc.crc-14D  was statistically significant in all environments tested in each of the three oat populations.  QPc.crc-14D  is a suitable candidate for use in marker-assisted breeding and also an excellent target for map-based cloning. This is also the first study to use the 90 K wheat Infinium SNP array on oat for marker development and comparative mapping. The Infinium SNP array is a useful tool for saturating oat maps with markers. Synteny with wheat suggests that  QPc.crc-14D  is orthologous with the stripe rust APR gene  Yr16  in wheat.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-014-0250-2) contains supplementary material, which is available to authorized users.

A major quantitative trait locus conferring adult plant partial resistance to crown rust in oat