ARS | Publication request: 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

Submitted to: European Journal of Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 31, 2012
Publication Date: January 1, 2013
Citation: Lu, S., Edwards, M.C., Friesen, T.L. 2013. 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. European Journal of Plant Pathology. 135(1):49-65.

Interpretive Summary: It can be difficult to distinguish closely-related, but different, fungi, yet correct identification of such fungi can be very important for pathogens like the ones that cause net blotch of barley. There are two recognized forms of this disease: net form net blotch and spot form net blotch. These fungi typically cause yield losses ranging from 10 to 40%, but without correct identification of the net and spot forms of isolates, effective disease management can be difficult because the host resistance to these two different forms is known to be conditioned by independent host genes. We previously developed genetic markers (known as polymerase chain reaction or PCR markers) based on the variation at specific points (single nucleotide polymorphisms or SNPs) in a genetic element known as the mating type (MAT) locus that could be used to differentiate the fungi that cause the net and spot forms of net blotch. The objective of the current study was to develop additional PCR markers to differentiate the fungi that induce typical net blotch symptoms from other isolates that induce atypical net blotch symptoms on barley. By cloning and analyzing the full-length MAT sequences, we identified genetic differences (SNPs) among 10 California field isolates that were originally collected from wild barley and found to cause atypical “spot-like” disease symptoms on barley cultivars. PCR markers developed based on the newly identified SNP sites were used successfully to distinguish these atypical isolates from more highly virulent net and spot form pathogens. The results presented in this study demonstrated that MAT-specific SNPs can serve as reliable markers for subspecies level differentiation of the net blotch fungus, an economically important plant pathogen. This study provides a simple, convenient, and cost-effective diagnostic tool for both laboratory research and disease management. The SNP sites identified here can also be used for large-scale genotyping that utilizes sophisticated systems, thus greatly facilitating population genetics and epidemiological studies on barley net blotch diseases.

Technical Abstract: 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 (Lu et al. 2010, Phytopathology, 100:1298-1306). 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.