Structural Analysis of the Maize Rp1 Complex Reveals Numerous Sites and Unexpected Mechanisms of Local Rearrangement

Abstract

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.

Comparative Sequence Analysis of the Sorghum RphRegion and the Maize Rp1 Resistance Gene Complex

“…The number of Rp1 homologs in the contig was determined by hybridization of NcoI-digested BAC DNAs with the Rp1 5Ј probe. Sun et al (2001) previously suggested that the number of NcoI-hybridizing fragments should correspond to the number of Rp1 homologs in maize, but we found that some Rp1 homologs within a cluster are so similar in sequence that they give identical fragment sizes with most restriction enzymes (Ramakrishna et al, 2002b). In addition, more than one hybridizing band per gene would be observed if there were an NcoI restriction site in the region of Rp1 covered by the probe.…”

“…Transposable elements are often inserted within complex R loci, sometimes causing insertional inactivation of an R gene (Song et al, 1997;Multani et al, 1998;Noel et al, 1999;Dodds et al, 2001;Ramakrishna et al, 2002b). In addition, inserted transposons can provide new regulatory sequences for any adjacent gene (Wessler et al, 1995).…”

“…Small DNA segments containing most of the Rp1 homologs from the maize Rp1-D haplotype have been cloned and sequenced, providing evidence for chimeric gene generation and diversifying selection (Collins et al, 1999;Sun et al, 2001). We have recently sequenced 95-and 99-kb segments of the maize Rp1 cluster from the rust-susceptible inbred B73 (Ramakrishna et al, 2002b), uncovering a complex mixture of duplicated R genes and transposable elements. Most interesting, we found that the Rp1 complex in B73 contains at least one large (43 kb) non-tandem duplication and also several clusters of truncated genes with no homology to any known R gene (Ramakrishna et al, 2002b).…”

“…We have recently sequenced 95-and 99-kb segments of the maize Rp1 cluster from the rust-susceptible inbred B73 (Ramakrishna et al, 2002b), uncovering a complex mixture of duplicated R genes and transposable elements. Most interesting, we found that the Rp1 complex in B73 contains at least one large (43 kb) non-tandem duplication and also several clusters of truncated genes with no homology to any known R gene (Ramakrishna et al, 2002b). Rp1 gene homologs have also been cloned and sequenced from the barley genome, although their function is not known (Ayliffe et al, 2000).…”

The effects of trans modifiers and tandem duplications on meiotic recombination in maize

“…NA, not applicable. CHIN et al 2001;KUANG et al 2004) and in maize including the rpl (RAMAKRISHNA et al 2002;RICHTER et al 1995;SMITH and HULBERT 2005;SUDUPAK et al 1993;SUN et al 2001) and rp3 (WEBB et al 2002) gene clusters. Unequal recombination between tandemly duplicated genes can generate novel alleles as has been observed in rpl (SUN et al 2001), rp3 (WEBB et al 2002), R-r (DOONER and KERMICLE 1971DOONER 1974;ROBBINS et al 1991;STADLER and NUFFER 1953;, bzl , knl (LOWE et al 1992), the 27-kD zein (DAS et al 1991) and pi (ZHANG and PETERSON 2005).…”