Recombination between paralogues at the rp1 rust resistance locus in maize

Rp1 is a complex rust resistance locus of maize. The HRp1-D haplotype is co mposed of Rp1-D and eight paralogues, seven of which also code fur predicte d nucleotide binding site-leucine rich repeat (NBS-LRR) proteins similar to the Rp1-D gene. The paralogues are polymorphic (DNA identities 91-97%), es pecially in the C-terminal LRR domain. The remaining family member encodes a truncated protein that has no LRR domain. Seven of the nine family member s, including the truncated gene, are transcribed. Sequence comparisons betw een paralogues provide evidence for past recombination events between paral ogues and diversifying selection, particularly in the C-terminal half of ti le LRR domain. Variants selected for complete or partial loss of Rp1-D resi stance can he explained by unequal crossing over that occurred mostly withi n coding regions. The Rp1-D gene is altered or lost in all variants, the re combination breakpoints occur throughout the genes, and most recombinant ev ents (9/14 examined) involved the same untranscribed paralogue with the Rp1 -D gene. One recombinant with a complete LRR from Rp1-D, hut the aminotermi nal portion from another homologue, conferred the Rp1-D specificity but wit h a reduced level of resistance.