Research PGR: Co-transcriptome networks to identify conserved and lineage specific plant resistance against a generalist pathogen

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To live and reproduce, any organism must prevent disease caused by pathogens like viruses, bacteria and fungi. Understanding the mechanisms controlling this battle between host and pathogens is necessary for understanding ecology and evolution and efforts to improve productivity in agricultural systems. These host-pathogens interactions span a wide range of systems from specialized where one host faces off with one pathogen to more general systems where a pathogen may attack a wide range of hosts. Most mechanistic knowledge is limited to the specialized systems and this project will work to deepen our knowledge of generalist host-pathogen systems. By using a fungal pathogen, Botrytis cinerea, that causes disease on nearly any plant, this project will test the diversity of plant defense mechanisms to a common attacker. Do plants defend themselves with a common defense system, novel individualized mechanisms or a blend of common and novel defense mechanisms? This information will improve our understanding of when evolution generates novel solutions versus slight tweaks to existing solutions to improve disease resistance. This knowledge can be used to understand how and when evolution of defense has occurred, improve crops resistance to disease and also help guide our efforts to engineer new biological systems. Theories of plant-pathogen interactions are molded by extensive research on host-specialist pathogen interactions controlled by lineage-specific large-effect genes. Those theories shape how plants are bred for disease resistance. However, large-effect models do not describe host-generalist pathogen interactions, dominated by numerous small to moderate effect genes distributed across diverse mechanisms. The polygenic nature of host-generalist interactions complicates the translation of any mechanistic insights from one host to another as mechanisms can be lineage specific or conserved. Identifying these conserved mechanisms will improve the ability translate mechanisms across species. This work will identify resistance mechanisms that are lineage specific versus conserved using a collection of the generalist pathogen Botrytis cinerea to measure lesion development across 16 dicot plant species representing eight rosid and asterid lineages. Incorporating a co-transcriptome approach, we will measure the host and pathogens transcriptome responses and identify conserved or lineage-specific regulatory networks. By developing rules to predict conserved and lineage-specific resistance mechanisms, this project will increase the ability to predictively translate scientific discoveries from one species to another. The identified conserved and lineage specific resistance mechanisms in Tomato, Lettuce and Arabidopsis will be validated for their influence on disease resistance via genome editing. This project will also provide an integrative introduction to STEM for first generation and transfer college students that are often overlooked in broader outreach efforts. They will be trained in modern quantitative analysis of gene networks to prepare them for future careers in industry or academics. This award was co-funded by the Plant Genome Research Program and the Plant Biotic Interactions Program in the Division of Integrative Organismal Systems.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.