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.