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Stripe (yellow) rust, caused by  Puccinia striiformis  f. sp.  tritici  ( Pst ), is one of the most destructive diseases of wheat worldwide. Planting resistant cultivars is an effective way to control this disease, but race-specific resistance can be overcome quickly due to the rapid evolving  Pst  population. Studying the pathogenicity mechanisms is critical for understanding how  Pst  virulence changes and how to develop wheat cultivars with durable resistance to stripe rust. We re-sequenced 7  Pst  isolates and included additional 7 previously sequenced isolates to represent balanced virulence/avirulence profiles for several avirulence loci in seretome analyses. We observed an uneven distribution of heterozygosity among the isolates. Secretome comparison of  Pst  with other rust fungi identified a large portion of species-specific secreted proteins, suggesting that they may have specific roles when interacting with the wheat host. Thirty-two effectors of  Pst  were identified from its secretome. We identified candidates for  Avr  genes corresponding to six  Yr  genes by correlating polymorphisms for effector genes to the virulence/avirulence profiles of the 14  Pst  isolates. The putative  AvYr76  was present in the avirulent isolates, but absent in the virulent isolates, suggesting that deleting the coding region of the candidate avirulence gene has produced races virulent to resistance gene  Yr76 . We conclude that incorporating avirulence/virulence phenotypes into correlation analysis with variations in genomic structure and secretome, particularly presence/absence polymorphisms of effectors, is an efficient way to identify candidate  Avr  genes in  Pst . The candidate effector genes provide a rich resource for further studies to determine the evolutionary history of  Pst  populations and the co-evolutionary arms race between  Pst  and wheat. The  Avr  candidates identified in this study will lead to cloning avirulence genes in  Pst , which will enable us to understand molecular mechanisms underlying  Pst -wheat interactions, to determine the effectiveness of resistance genes and further to develop durable resistance to stripe rust.

frontiers in microbiology

Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici