| The bal variant in Arabidopsis thaliana was spontaneously generated from a repeatedly self-pollinated ddm1 (decrease in DNA methylation 1) mutant, in which genetic and epigenetic alterations accumulate over generations. The bal allele maps to the RPP5 (Recognition of Peronospora parasitica 5) locus, which contains a cluster of disease Resistance (R) genes. The semidominant phenotypes in the bal variant are associated with the up-regulation of SNC1, one of the R genes in the locus. The following observations suggested that the bal allele was an epigenetic defect. First, no nucleotide sequence changes were identified in a 7 kb region that includes the entire coding sequence and putative promoter of SNC1 in the bal variant, although transgenic over-expression of SNC1 induces bal-like phenotypes. Second, a high frequency (∼10%) phenotypic suppression, which was accompanied by the down-regulation of SNC1, was induced after the bal allele was exposed to mutagens. However, the mechanism by which the expression level of SNC1 is elevated in the bal variant and the molecular change that lowers the SNC1 expression after the bal variant is exposed to DNA-damaging conditions have not been determined.;The results of this dissertation show that many RPP5 locus R genes, including SNC1, are coordinately regulated both positively and negatively, and that the locus-wide regulation involves a positive feedback mechanism as well as RNA silencing of paralogous R genes in the locus. Moreover, the results reveal that the bal allele was generated by a tandem duplication of a 55 kb region in the RPP5 locus that includes SNC1 and five other RPP5 locus R genes, through an apparent unequal crossing-over event. This dissertation also reports that the high frequency phenotypic suppression of the bal variant induced by mutagen treatment is associated with missense mutations in the SNC1 coding sequence that diminish or abolish SNC1 function. The results provide an example supporting the hypothesis that the clustered RPP5 locus R genes evolve by unequal crossing-over. Moreover, the data suggest that the RPP5 locus can adopt a metastable state highly susceptible to mutations that could facilitate the evolution of R genes in the locus. |
