Genetic variation of single nucleotide polymorphisms identified at the mating type locus correlates with form-specific disease phenotype in the barley net blotch fungus Pyrenophora teres

Mating-type (MAT) locus-specific single nucleotide polymorphisms (SNPs) have been shown to be sufficient for conventional PCR-based differentiation of Pyrenophora teres f. teres (Ptt) and P. teres f. maculata (Ptm), the cause of the net and spot form, respectively, of barley net blotch. Here, we report the cloning and characterization of the MAT locus from 10 California isolates that cause atypical blotch symptoms on barley. Analysis of the full-length nucleotide sequences of one MAT1-1 (1,993 bp) and nine MAT1-2 (2,149 or 2,161 bp) idiomorphs revealed high (98–99 %) similarity to those of Ptt isolates. However, distinct SNP patterns were identified in the newly cloned MAT idiomorphs. Two new MAT1-2-specific SNPs were found to be conserved in one Australia and eight California isolates that all cause similar atypical blotch symptoms. Phylogenetic analysis indicated that all 10 California isolates form a separate branch (or clade) within the Ptt group, except for one that appears to be ancestral to both Ptt and Ptm. PCR primers designed based on the identified SNP patterns were used successfully to differentiate each atypical isolate from highly virulent forms. This study extends our previous work and, taken together, the results demonstrate that the genetic variation at the MAT locus correlates with variation in the form-specific disease phenotype, and that MAT-specific SNPs can serve as reliable and convenient markers for subspecies level differentiation in P. teres, an economically important plant-pathogenic ascomycete (http://en.wikipedia.org/wiki/Single_nucleotide_polymorphism).