Rp1 is a complex disease resistance locus in maize that is exceptional in both allelic variability and meiotic instability. Genomic sequence analysis of three maize BACs from the Rp1 region of the B73 inbred line revealed 4 Rp1 homologs and 18 other gene-homologous sequences, of which at least 16 are truncated. Thirteen of the truncated genes are found in three clusters, suggesting that they arose from multiple illegitimate break repairs at the same sites or from complex repairs of each of these sites with multiple unlinked DNA templates. A 43-kb region that contains an Rp1 homolog, six truncated genes, and three Opie retrotransposons was found to be duplicated in this region. This duplication is relatively recent, occurring after the insertion of the three Opie elements. The breakpoints of the duplication are outside of any genes or identified repeat sequence, suggesting a duplication mechanism that did not involve unequal recombination. A physical map and partial sequencing of the Rp1 complex indicate the presence of 15 Rp1 homologs in regions of ‫ف‬ 250 and 300 kb in the B73 inbred line. Comparison of fully sequenced Rp1 -homologous sequences in the region demonstrates a history of unequal recombination and diversifying selection within the Leu-rich repeat 2 region, resulting in chimeric gene structures.

A 268-kb chromosomal segment containing sorghum (Sorghum bicolor) genes that are orthologous to the maize (Zea mays) Rp1 disease resistance (R) gene complex was sequenced. A region of approximately 27 kb in sorghum was found to contain five Rp1 homologs, but most have structures indicating that they are not functional. In contrast, maize inbred B73 has 15 Rp1 homologs in two nearby clusters of 250 and 300 kb. As at maize Rp1, the cluster of R gene homologs is interrupted by the presence of several genes that appear to have no resistance role, but these genes were different from the ones found within the maize Rp1 complex. More than 200 kb of DNA downstream from the sorghum Rp1-orthologous R gene cluster was sequenced and found to contain many duplicated and/or truncated genes. None of the duplications currently exist as simple tandem events, suggesting that numerous rearrangements were required to generate the current genomic structure. Four truncated genes were observed, including one gene that appears to have both 5Ј and 3Ј deletions. The maize Rp1 region is also unusually enriched in truncated genes. Hence, the orthologous maize and sorghum regions share numerous structural features, but all involve events that occurred independently in each species. The data suggest that complex R gene clusters are unusually prone to frequent internal and adjacent chromosomal rearrangements of several types.Disease resistance (R) genes in plants provide a major mode of defense against a wide variety of pathogens and pests. The most abundant class of R genes encodes proteins with a nucleotide-binding site (NBS) and a Leu-rich repeat (LRR) region. The genome of the model plant, Arabidopsis, contains more than 120 NBS-LRR genes (Arabidopsis Genome Initiative, 2000), but the possible R specificities of these candidate R genes are only known for a handful of loci. From the few NBS-LRR genes that have received functional analysis, it appears that the LRR region provides the specificity for recognition of a pathogen gene product (Ellis et al., 2000a), thereby leading to the initiation of a signal transduction cascade that activates several defense pathways.Most of the R gene loci in plants are highly complex, containing numerous nearby R genes (Ellis et al., 2000b). Unequal recombination within an R gene cluster can result in variation in the size and organization of a complex locus. New R genes with novel pathogen-recognition specificities can be generated by this unequal recombination process (Richter et al., 1995). Some R genes appear to be the obvious products of unequal crossing over and/or conversion between R genes in the same tandem array, thereby providing a new "chimeric" locus with a possible new recognition specificity. Hence, complex R gene loci can undergo rapid internal reorganization. In addition, R gene loci often show a lack of synteny in closely related species (Leister et al., 1998), suggesting that they are also unstable in their gross chromosomal locations. For instance, neither the Lr1 R gene of wheat (Triti...

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