Genomic Architecture Of Rust-Wheat Interaction: Implications For Breeding Disease-Resistant Crops

To predict the outcome of plant-pathogen interaction, the genetic factors of both host and pathogen should be identified. We studied interaction between stem rust and wheat using the next-generation sequencing of rust genomes and transcriptomes of infected wheat tissues. The Sr35 gene was used as entry point to characterize specific interactions between stem rust and wheat. This gene confers resistance to multiple races of stem rust including Ug99 and Ug99-derived races. Positional cloning showed that the Sr35 resistance co-segregates with a gene that belongs to CC-NBS-LRR family. To identify pathogen’s candidate genetic factors controlling virulence, we performed comparative whole genome analysis of 16 races including Sr35 virulent and avirulent genotypes. In a panel of wheat differential lines the virulence profiles of sequenced races showed correlation with levels of genetic differentiation among races. The level of genetic diversity in stem rust genomes was elevated in effector genes that encode small secreted proteins. Clustering of stem rust races based on the patterns effector presence/absence variation showed good consistency with Sr35 virulent and avirulent phenotypes. RNA-seq expression profiling demonstrated race- and host-specific responses in different combinations of stem rust and wheat genotypes. Our data is consistent with the models suggesting that genotype-by-genotype interactions between host and pathogen can define the resistance phenotype. The genetic factors controlling these interactions need to be taken into account in future breeding strategies for developing varieties resistant to race shifts in populations of pathogens.