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

Abstract

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.

Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates

“…This can be explained by the property of Pst and EMS mutagenesis. i) The two nuclei in Pst urediniospores were found to be highly heterozygous in many isolates [37,39,58,59]. ii) Previous studies observed Pst isolates with a low virulence spectrum tended to be highly heterozygous [39,60].…”

“…However, omission of haplotigs in the genome analysis may miss some important information. Due to the lack of phased assembles as reference genomes, previous association studies to identify effector candidates on Pst and Pt focused only on primary contigs [39,40]. In the present study, we detected SNPs and Indels from both primary scaffolds and haplotigs and conducted association analysis using all identified variants.…”

“…It is worth mentioning that motif [Y/F/W]xC was found within 100 bp from the cleavage sites of seven putative effectors with high-degree confidence. Motif [Y/F/W]xC has been detected in SPs in Pgt [46,47] and predicted Pst candidates [39]. Due to the limited number of cloned effectors in the Puccinia species, we could not determine whether [Y/F/W]xC is a conserved motif of effectors in the genus Puccinia.…”

“…Cantu et al [33] identified five Pst candidate effector genes from 2999 predicted secreted protein (SP) genes. Xia et al [39] predicted a set of 25 Pst Avr candidate genes from 2146 predicted SPs by combining comparative genomics with association analyses. Similar approaches were also used in detecting Avr candidate genes in Puccinia triticina (Pt), the wheat leaf rust pathogen [40].…”

Genomic insights into host adaptation between the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei)

“…One additional Psh isolate (04–051) was sequenced using the Ion Proton technology following the previously described method [ 64 ]. This isolate was collected from Oregon, Washington in 2004 and was virulent on barley differentials Topper, Heils Franken, Hiproly, Abed Binder 12, Trumpf, I 5 and Bancroft but avirulent on the remaining barley differentials (Emir, Astrix, Varunda, Mazurka and Bigo) and all wheat differentials for identifying Pst races.…”