Clusters of resistance genes in plants evolve by divergent selection and abirth-and-death process

Classical genetic and molecular data show that genes determining disease re sistance in plants are frequently clustered in the genome. Genes for resist ance (R genes) to diverse pathogens cloned from several species encode prot eins that have motifs in common. These motifs indicate that R genes are par t of signal-transduction systems. Most of these R genes encode a leucine-ri ch repeat (LRR) region. Sequences encoding putative solvent-exposed residue s in this region are hypervariable and have elevated ratios of nonsynonymou s to synonymous substitutions; this suggests that they have evolved to dete ct variation in pathogen-derived ligands. Generation of new resistance spec ificities previously had been thought to involve frequent unequal crossing- over and gene conversions. However, comparisons between resistance haplotyp es reveal that orthologs are more similar than paralogs implying a low rate of sequence homogenization from unequal crossing-over and gene conversion. We propose a new model adapted and expanded from one proposed for the evol ution of vertebrate major histocompatibility complex and immunoglobulin gen e families. Our model emphasizes divergent selection acting on arrays of so lvent-exposed residues in the LRR resulting in evolution of individual R ge nes within a haplotype. Intergenic unequal crossing-over and gene conversio ns are important but are not the primary mechanisms generating variation.