Genome-wide identification of novel candidate genes with resistance to biotrophic and necrotrophic pathogens in plants

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Of all microbial pathogens causing plant diseases, some (known as biotrophs) thrive on nutrients from living host cells while others (known as necrotrophs) kill host cells prior to or during colonization and absorb nutrients from dead host tissues. When disease resistance is controlled by genes of major effects in host plants, the classic `gene-for-gene' relationship governs host interactions with biotrophic pathogens whereas the inverse of gene-for-gene relationship governs host interactions with necrotrophic pathogens. At molecular level, biotrophic diseases occur when plant resistance (R) proteins recognize specific pathogen proteins (effectors) and elicit an effector-triggered immunity (ETI); the necrotrophic diseases arise from the recognition of necrotrophic effectors (NEs) [also known as host-specific toxins (HSTs)] by non-R proteins mediating the host sensitivity to the toxins. However, a huge challenge in direct molecular and functional characterizations of disease-resistance genes in wheat and barley is the lack of deep and complete sequencing of their large and complex genomes, thereby motivating me to exploit the use of rich, underutilized genomic resources available in model plants, Arabidopsis and Brachypodium, for inferring homologous resistance genes in cereal crop plants. This proposal will examine responses to a pair of biotrophic (rusts) and nectrotrophic (tan spot) pathogens in cereal plants to test the hypothesis that there is partial sharing of genes over the host genomes with resistance to both biotrophs and necrotrophs. This pair of pathogens are chosen because they often co-occur and are a major threat to cereal production in western Canada and elsewhere. I will develop a powerful combination of comparative genomics and bioinformatics approaches for genome-wide mining and discovery of candidate genes with resistance to rust and tan spot pathogens in cereal crop species. The mining capability will be greatly enhanced through detecting and utilizing high levels of inter-species homology between Arabidopsis and cereal species. The proposed genome-wide identification will uncover the patterns and distributions of genomic regions at two sets of novel candidate genes with resistance to biotrophic (rusts) and necrotrophic (tan spot) pathogens. My proposed comparative assessment of the two sets of genes in terms of their genomic locations, structural diversity (e.g., regulatory vs. protein-coding genes), functional diversity (e.g., distributions of the resistance genes over different gene families) and possible `hot spot' genomic regions where the resistance genes are concentrated over the host genomes will shed light on the fundamental question surrounding the shared genes with resistance to both biotrophs and nectrotrophs. The results from this proposed project will have important implications for accelerated genetic improvement of simultaneous resistance to cereal rusts and tan spot in western Canada.