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Background Spot form net blotch (SFNB) caused by the necrotrophic fungal pathogen  Pyrenophora teres  f.  maculata  ( Ptm ) is an economically important disease of barley that also infects wheat. Using genetic analysis to characterize loci in  Ptm  genomes associated with virulence or avirulence is an important step to identify pathogen effectors that determine compatible (virulent) or incompatible (avirulent) interactions with cereal hosts. Association mapping (AM) is a powerful tool for detecting virulence loci utilizing phenotyping and genotyping data generated for natural populations of plant pathogenic fungi. Results Restriction-site associated DNA genotyping-by-sequencing (RAD-GBS) was used to generate 4,836 single nucleotide polymorphism (SNP) markers for a natural population of 103  Ptm  isolates collected from Idaho, Montana and North Dakota. Association mapping analyses were performed utilizing the genotyping and infection type data generated for each isolate when challenged on barley seedlings of thirty SFNB differential barley lines. A total of 39 marker trait associations (MTAs) were detected across the 20 barley lines corresponding to 30 quantitative trait loci (QTL); 26 novel QTL and four that were previously mapped in  Ptm  biparental populations. These results using diverse US isolates and barley lines showed numerous barley- Ptm  genetic interactions with seven of the 30  Ptm  virulence/avirulence loci falling on chromosome 3, suggesting that it is a reservoir of diverse virulence effectors. One of the loci exhibited reciprocal virulence/avirulence with one haplotype predominantly present in isolates collected from Idaho increasing virulence on barley line MXB468 and the alternative haplotype predominantly present in isolates collected from North Dakota and Montana increasing virulence on barley line CI9819. Conclusions Association mapping provided novel insight into the host pathogen genetic interactions occurring in the barley- Ptm  pathosystem. The analysis suggests that chromosome 3 of  Ptm  serves as an effector reservoir in concordance with previous reports for  Pyrenophora teres  f.  teres , the causal agent of the closely related disease net form net blotch .  Additionally, these analyses identified the first reported case of a reciprocal pathogen virulence locus. However, further investigation of the pathosystem is required to determine if multiple genes or alleles of the same gene are responsible for this genetic phenomenon.

Association mapping reveals a reciprocal virulence/avirulence locus within diverse US Pyrenophora teres f. maculata isolates