Even though pathogens enjoy the advantage of rapid generation times and enormous population sizes, hosts don’t typically die of infection in nature. Why not? We have discovered the prevalence of ancient balanced polymorphisms segregating at plant R-genes in Arabidopsis, indicating the preservation of particular resistance alleles. Our efforts to understand how selection maintains such a balanced polymorphism revealed an important role of community context, including microbes sharing a focal host as well as alternative hosts for a focal pathogen. We are thus exploring this complexity to understand how plants and pathogens interact in realistic community contexts. Our current focus is on how the interactions and coevolution of microbes influences microbiome development, plant health/fitness, and the evolution of resistance among shared hosts.
Microbial networks and communities
Plants harbor diverse arrays of microbes that can impact host phenotypes and fitness. Greater insights into the ecological forces that structure these microbial communities are needed to develop effective strategies to promote host health and resist pathogen invasion. We use GWAS mapping to determine the host factors that shape microbial communities growing within Arabidopsis thaliana and use controlled experiments to test the importance of candidate host factors in shaping microbial communities. In a recent collaboration with the laboratories of Detlef Weigel and Fabrice Roux, we are exploring species interactions with the aim of understanding community assembly across host genotypes, and are embarking on efforts to understand the factors that make microbial communities robust. Ultimately, our goal is to enhance plant resistance by identifying conditions that favor protective microbes.
Genomics of adaptation
A long-term focus of our laboratory has been to build genetic resources and tools in Arabidopsis thaliana and its associated microbes. In collaboration with the Magnus Nordborg lab, we have established that A. thaliana has patterns of linkage disequilibrium well suited for GWAS mapping and have genotyped sets of accessions to allow mapping by members of the community. We have made extensive collections of A. thaliana accessions and made these publically available and have collected tens of thousands of isolates from within plant leaves. We are currently making use of these resources for genome-wide studies of local adaptation in Arabidopsis thaliana, as well as targeted studies of the molecular evolution of focal plant and microbial traits such as resistance to suites of natural enemies, virulence across hosts, chemical defense and tolerance to abiotic stress. A recent collaboration with the Manyuan Long laboratory begins to explore the functional role played by new genes in Arabidopsis and rice, again with an eye towards the genetic basis of adaptation.