Wading Across the Gene Pool: Cross-Species Comparative Analyses of Plant Disease Resistance Genes

Plant response to pathogens entails a two step process of pathogen detection followed by activation of defenses.  Genes encoding nucleotide binding site-leucine rich repeat (NBS-LRR) proteins account for about 75% of all disease resistance (R) genes in plant genomes and a typical plant genome contains several dozen to several hundred NBS-LRR genes. The LRR domain is fast evolving, consistent with its role in pathogen detection.  The NBS domain is slower to evolve since its function is constrained for signal transduction and activation of defenses.  But evolutionary changes in the LRR in response to changes in pathogen populations require coordinate changes in the NBS to maintain protein structure critical for proper function.  The NBS has proven to be a useful region for phylogenetic analyses of R proteins.  In an attempt to leverage knowledge of well characterized crop species for cross-species comparative analyses of R-genes, we have developed conceptual frameworks for organization of NBS-LRR R-genes in the Solanaceae and Rosaceae.  Using a DNA diversity ‘binning’ approach, NBS gene sequences are assigned to lineages that reflect DNA cross hybridization potential and evolutionary relatedness.  Higher order phylogenetic analyses reveal patterns of R-gene representation across the genomes of plant species and patterns of R-gene allelic diversification, providing clues to gene function.  The resulting SolaR80 and RosaR80 frameworks, corresponding to Solanaceous and Rosaceous R-genes, respectively, have multiple applications for the study of R-gene evolution and crop improvement.  Online resources are being developed for each system.  The SolaR80 and RosaR80 systems are amendable and augmentable.