Thirteen alleles ( L , L1 to L11 , and LH ) from the flax L locus, which encode Toll/interleukin-1 receptor homology–nucleotide binding site–leucine-rich repeat (TIR-NBS-LRR) rust resistance proteins, were sequenced and compared to provide insight into their evolution and into the determinants of gene-for-gene resistance specificity. The predicted L6 and L11 proteins differ solely in the LRR region, whereas L6 and L7 differ solely in the TIR region. Thus, specificity differences between alleles can be determined by both the LRR and TIR regions. Functional analysis in transgenic plants of recombinant alleles constructed in vitro provided further information: L10–L2 and L6–L2 recombinants, encoding the LRR of L2 , conferred L2 resistance specificity, and an L2–L10 recombinant, encoding the LRR of L10 , conferred a novel specificity. The sequence comparisons also indicate that the evolution of L alleles has probably involved reassortment of variation, resulting from accumulated point mutations, by intragenic recombination. In addition, large deletion events have occurred in the LRR-encoding regions of L1 and L8, and duplication events have occurred in the LRR-encoding region of L2 .
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