Using pathogen genomics to decipher the plant-fungal interaction of Pyrenophora teres f. teres and barley

Jonathan K. Richards 1 Nathan A. Wyatt 1,2 Robert S. Brueggeman 1,2 Timothy L. Friesen 1,2,3
1Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
2Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
3Cereal Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Fargo, ND, USA

Pyrenophora teres f. teres, a fungal pathogen of barley and causal agent of net form net blotch, interacts with the host in a complex manner, exhibiting hallmarks of gene-for-gene and inverse gene-for-gene interactions, indicated by dominant resistance and susceptibility, respectively. Previously, using the 15A × 6A population, four loci (VR1, VR2, VK1, VK2) were identified corresponding to virulence (dominant susceptibility) on barley lines Rika and Kombar. Using the FGOH04Ptt-21 × BB25 population, a major locus (Tif1) was identified corresponding to avirulence (dominant resistance) on Tifang barley and a gene-for-gene interaction was identified in barley line CI5791 effective against a broad range of P. teres f. teres isolates. However, the CI5791 dominant resistance was recently defeated by a population of Moroccan isolates. The specific pathogen molecules eliciting most of these responses have yet to be identified. To mediate effector identification, reference quality genomes of isolates 15A, 6A, FGOH04Ptt-21, and BB25 were developed via PacBio sequencing and RNAseq was conducted to facilitate gene annotation. A VR2 candidate encoding a 422 aa secreted protein was disrupted in a 15A × 6A progeny isolate, resulting in a loss of virulence, functionally validating the VR2 gene. Underlying the Tif1 avirulence locus in isolate BB25, an ~100 kb expansion containing 23 genes was found lacking homology to P. teres f. teres genome sequences, but conserved in P. tritici-repentis, providing several candidate genes for validation. Additionally, a natural population of 146 P. teres f. teres isolates were sequenced at ~25× coverage, resulting in the identification of 83,043 SNPs/INDELs used for association mapping. A highly significant association was detected corresponding to avirulence on CI5791, underlying which are two candidate genes in close proximity. The validation of VR2 and the continued investigation of other effector loci will allow us to understand the intricate host-pathogen molecular interactions governing this pathosystem.