Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis

In Arabidopsis ecotype Landsberg erecta (Ler), RPP5 confers resistance to t he pathogen Peronospora parasitica. RPP5 is part of a clustered multigene f amily encoding nucleotide binding-leucine-rich repeat (LRR) proteins. We co mpared 95 kb of DNA sequence carrying the Ler RPP5 haplotype with the corre sponding 90 kb of Arabidopsis ecotype Columbia (Col-0). Relative to the rem ainder of the genome, the Ler and Col-0 RPP5 haplotypes exhibit remarkable intraspecific polymorphism. The RPP5 gene family probably evolved by extens ive recombination between LRRs from an RPP5-like progenitor that carried on ly eight LRRs. Most members have variable LRR configurations and encode dif ferent numbers of LRRs. Although many members carry retroelement insertions or frameshift mutations, codon usage analysis suggests that regions of the genes have been subject to purifying or diversifying selection, indicating that these genes were, or are, functional. The RPP5 haplotypes thus carry dynamic gene clusters with the potential to adapt rapidly to novel pathogen variants by gene duplication and modification of recognition capacity. We propose that the extremely high level of polymorphism at this complex resis tance locus is maintained by frequency-dependent selection.