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Background  Pathogen avirulence ( Avr ) genes can evolve rapidly when challenged by the widespread deployment of host genes for resistance. They can be effectively isolated by positional cloning provided a robust and well-populated genetic map is available.    Results  An updated, SSR-based physical map of the rice blast pathogen  Magnaporthe oryzae  ( Mo ) has been constructed based on 116 of the 120 SSRs used to assemble the last map, along with 18 newly developed ones. A comparison between the two versions of the map has revealed an altered marker content and order within most of the  Mo  chromosomes. The avirulence gene  AvrPi12  was mapped in a population of 219 progeny derived from a cross between the two  Mo i solates CHL42 and CHL357. A bulked segregant analysis indicated that the gene was located on chromosome 6, a conclusion borne out by an analysis of the pattern of segregation shown by individual isolates. Six additional PCR-based markers were developed to improve the map resolution in the key region.  AvrPi12  was finally located within the sub-telomeric region of chromosome 6, distal to the SSR locus LSM6–5.    Conclusions  The improved SSR-based linkage map should be useful as a platform for gene mapping and isolation in  Mo . It was used to establish the location of  AvrPi12 , thereby providing a starting point for its positional cloning.    Electronic supplementary material  The online version of this article (10.1186/s12866-018-1192-x) contains supplementary material, which is available to authorized users.

Reconstruction of an SSR-based Magnaporthe oryzae physical map to locate avirulence gene AvrPi12