title: 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 approximately 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.
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.
authors.forename: Wusirika
authors.initials: W
authors.lastname: Ramakrishna
authors.forename: John
authors.initials: J
authors.lastname: Emberton
authors.forename: Matthew
authors.initials: M
authors.lastname: Ogden
authors.forename: Phillip
authors.initials: P
authors.lastname: SanMiguel
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Bennetzen
mesh_terms: D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D020440:Gene Duplication; D017343:Genes, Plant / Q000235:genetics; D007113:Immunity, Innate / Q000235:genetics; D000090263:Leucine-Rich Repeat Proteins; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D011506:Proteins / Q000235:genetics; D011995:Recombination, Genetic; D018626:Retroelements / Q000235:genetics; D017422:Sequence Analysis, DNA; D003313:Zea mays / Q000235:genetics* / Q000502:physiology
chemical_list: D018744:DNA, Plant; D000090263:Leucine-Rich Repeat Proteins; D010940:Plant Proteins; D011506:Proteins; D018626:Retroelements; C113020:ZmCip1 protein, Zea mays