GENOMIC SEQUENCING OF SELECTED RACES AND A SEXUAL POPULATION FOR IDENTIFICATION AND MOLECULAR MAPPING OF AVIRULENCE GENES AND UNDERSTANDING THE EVOLUTION OF PUCCINIA STRIIFORMIS
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Stripe rust fungus Puccinia striiformis (Ps) is a great threat to agriculture in the world. However, the molecular mechanisms underlying the Ps pathogenicity to different cereals and virulence to different cultivars have not been well understood. Taking the advancement of whole-genome sequencing technologies, the objectives of this project were to i) identify and characterize avirulence genes (Avr) in Ps, and ii) decipher the genomic basis of host adaptation of Ps at the forma specialis level. Firstly, we revealed putative pathogenicity mechanisms in P. striiformis f. sp. tritici (Pst, the causal agent of wheat stripe rust) by characterization of secretome and comparison with other rust fungi. We detected a large portion of species-specific secreted proteins that may have specific roles when the fungus interacts with the wheat host. Candidate avirulence genes were identified by incorporating virulence phenotypes into a correlation analysis by whole-genome sequencing of fourteen Pst isolates with balanced virulence profiles. Secondly, we generated genomes with high continuity for Pst and P. striiformis f. sp. hordei (Psh, the causual agent of barley stripe rust). These genomes provide high-quality resources for deciphering the genomic basis of rapid evolution and host adaptation. Thirdly, we compared the genomes of Pst and Psh to study the genomic basis of host adaptation. We found that host adaptation of Ps at the forma specialis level is a complex pathogenic trait, involving not only virulence-related genes but also other genes. Gene loss, which might be adaptive and driven by transposable element activities, provides genomic basis for host adaptation of different Ps formae speciales. Fourthly, we generated a segregating population by self-fertilizing Pst isolate 12-368 to genetically map Avr genes. A genetic map was constructed through whole-genome sequencing of the parental isolate and 117 progeny isolates. Quantitative trait loci analysis mapped six Avr genes to the genetic map. Through referring the molecular markers to the high quality Pst genome, we identified secreted protein genes that could be candidates for further cloning the avirulence genes. Our studies significantly advanced the understanding of the genomic basis of rapid evolution of virulence in the Pst-wheat pathosystem.