Final Report Summary - IMMUNEMESIS (The Plant Immune System: Epistasis and Fitness-Tradeoffs) A fundamental question in biology is how multicellular organisms distinguish self and non-self. If they were not able to make this distinction, animals and plants could not detect and respond to pathogens without triggering immune reactions directed against their own cells. This requirement places constraints on the diversification of pathogen recognition systems, resulting in conflicts between effective detection of enemies, adaptive changes in the cellular machinery and mating with divergent genotypes from the same species. In plants, there is generally a trade-off between immunity and growth, and priming of the immune system to respond to pathogens is often associated with impaired development. IMMUNEMESIS was designed to reveal the genetic basis for this widely observed phenomenon. In plants, there are many examples of spontaneous activation of the immune system in F1 hybrids, due to epistatic, non-additive interactions between (mostly unknown) genes contributed by the different parents. An overt sign of such autoimmunity is often leaf necrosis, and hybrid necrosis has been described in both wild species and crops. Another common phenomenon in F1 progeny from two inbred parents is hybrid vigor, or heterosis. In the model plant Arabidopsis thaliana, we had previously discovered random crosses between natural strains (accessions) that result in F1 hybrid necrosis. In IMMUNEMESIS, we produced a systematic map of dominant hybrid necrosis loci in A. thaliana, cloned many of the responsible genes, showed that most encode immune receptors, and that the underlying mechanism is usually aberrant protein-protein interaction. To compare opportunities for within-species immune system conflict, we have been comparing inbreeding and outcrossing species of a genus closely related to Arabidopsis, Capsella. We found that even when there are very strong genetic bottlenecks, diversity at immune loci is maintained, indicating that selfing species will not necessarily suffer from fewer immune system conflicts. Because the hybrid necrosis syndrome spans a range of severity, we had been hypothesizing that previously described cases represent only the tip of the iceberg, and that there are many more subtle epistatic interactions that affect both the state of the plant immune system and growth. We developed a platform for systematic analysis of growth phenotypes, and showed that it can be used to compare large numbers of both inbreds and hybrid genotypes. In combination with molecular analyses, we learned that subthreshold activation of the immune system is not likely to be a major impediment to F1 hybrid performance. However, many F2 populations show transmission ratio distortion, where certain regions of the genome are underrepresented, often caused by a single genomic region.Finally, we developed methods for monitoring microbial diversity on wild A. thaliana populations, and for reconstructing the immune receptor repertoire of such populations.