Plant defense variation studies typically focus on single large effect genes within a host or specialist pathogen that interact only with each other. However, resistance to most generalist pathogens is quantitative and cannot be investigated using few genotypically distinct individuals. Generalist pathogens place evolutionary pressure across plant lineages, yet this cross-lineage pressure is rarely systematically addressed. This project is one of the first direct surveys of how genomic diversity within and across core plant lineages may be shaped by genomic diversity in a broad spectrum generalist fungus that can infect most if not all plants.

We are using Botrytis cinerea, a necrotrophic pathogen that attacks numerous crops and causes significant economic loss. Botrytis is a highly variable pathogen and we are using the model plant Arabidopsis and crop species to identify resistance mechanisms that can inhibit large diverse Botrytis genotypes.

This project aims to:

1) Measure lesion development with a high-throughput platform across sixteen plant species that have independently undergone domestication (lettuce, tomato, grape, soy and Brassicas) with 100 genome sequenced isolates of the pathogen, Botrytis cinerea

2) Use the genome wide association mapping dataset to identify pathogenicity networks within the pathogen that allow it to infect these diverse hosts

3) Identify and validate plant gene targets of these networks using a new co-species co-expression network approach to test if the pathogen targets defense mechanisms that are conserved or variant across plants and if these defense mechanisms have been affected by human driven domestication

4) Conduct transcriptome profiling across these plant/pathogen combinations to identify conserved or variant transcriptional responses across the eudicot lineages.

Fig. 1 from Caseys et al. 2021 https://doi.org/10.1093/g3journal/jkab175

Disease symptoms caused by B. cinerea observed on plants from the core Eudicots. The tree represents major orders from the basal Eudicots (in green), Asterids (in orange), and Rosids (in pink). The size of the circle at the end of the branches is proportional to the species diversity of the order.  For each order, the number of species with known disease symptom is indicated.