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Background  Barley is an important cereal crop cultivated for malt and ruminant feed and in certain regions it is used for human consumption. It is vulnerable to numerous foliar diseases including barley leaf rust caused by the pathogen  Puccinia hordei .    Results  A temporarily designated resistance locus  RphCantala  ( RphC ) identified in the Australian  Hordeum vulgare  L. cultivar ‘Cantala’ displayed an intermediate to low infection type (“;12 = N”) against the  P. hordei  pathotype 253P- (virulent on  Rph1, Rph2, Rph4, Rph6, Rph8  and  RphQ) . Phenotypic assessment of a ‘CI 9214’ (susceptible) x ‘Stirling’ ( RphC ) (CI 9214/Stirling) doubled haploid (DH) population at the seedling stage using  P. hordei  pathotype 253P-, confirmed that  RphC  was monogenically inherited. Marker-trait association analysis of  RphC  in the CI 9214/Stirling DH population using 4,500 DArT-seq markers identified a highly significant (−log 10 Pvalue > 17) single peak on the long arm of chromosome 5H (5HL). Further tests of allelism determined that  RphC  was genetically independent of  Rph3, Rph7 ,  Rph11, Rph13  and  Rph14,  and was an allele of  Rph12  ( Rph9.z ), which also maps to 5HL.    Conclusion  Multipathotype tests and subsequent pedigree analysis determined that 14 related Australian barley varieties (including ‘Stirling’ and ‘Cantala’) carry  RphC  and that the likely source of this resistance is via a Czechoslovakian landrace LV-Kvasice-NA-Morave transferred through common ancestral cultivars ‘Hanna’ and ‘Abed Binder’.  RphC  is an allele of  Rph12  ( Rph9.z ) and is therefore designated  Rph9.am . Bioinformatic analysis using sequence arrays from DArT-seq markers in linkage disequilibrium with  Rph9.am  identified possible candidates for further gene cloning efforts and marker development at the  Rph9 / Rph12 / Rph9.am  locus.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-014-0382-4) contains supplementary material, which is available to authorized users.

Genetic mapping of a new race specific resistance allele effective to Puccinia hordei at the Rph9/Rph12locus on chromosome 5HL in barley