Contrasting modes of evolution acting on the complex N locus for rust resistance in flax

Three rust resistance specificities, N, N1 and N2, map to the complex N loc us of flax. We used a degenerate PCR approach, with primers directed to the nucleotide binding site (NIBS) domain characteristic of many plant resista nce genes, to isolate resistance gene analogs (RGAs) from flax. One RGA clo ne detected RFLPs co-segregating with alleles of the N locus. With this pro be we isolated four related genes that occur within a 30kbp region and enco de proteins with NBS and leucine-rich repeat (LRR) domains and N-terminal T oll/Interleukin-1 Receptor homology (TIR) domains. One of these four genes was identified as the N resistance gene by sequence analysis of three mutan t alleles and by transgenic expression. We isolated homologous genes from t wo flax lines containing the N1 or N2 specificities and from flax lines car rying no N locus resistance specificities. Analysis of shared polymorphisms among this set of 18 N locus sequences revealed three groups of genes with independent lineages. Sequence exchanges have only occurred between genes within each group, but not between groups. Two of the groups contain only o ne sequence from each haplotype and probably represent orthologous genes. H owever, the third group contains two genes from each haplotype. We suggest that the re-assortment of variation by recombination/gene conversion at thi s locus is limited by the degree of sequence identity between genes.