Gene Duplication and Hypermutation of the Pathogen Resistance Gene SNC1 in the Arabidopsis bal Variant

Abstract

The bal defect in the Arabidopsis thaliana Columbia strain was spontaneously generated in an inbred ddm1 (decrease in DNA methylation 1) mutant background in which various genetic and epigenetic alterations accumulate. The bal variant displays short stature and curled leaves due to the constitutive activation of defense signaling. These bal phenotypes are metastable and phenotypic suppression is evident in more than one-third of ethyl methanesulfonate (EMS)-treated bal M 1 plants. The semidominant bal allele maps to the RPP5 (recognition of Peronospora parasitica 5) locus, which includes a cluster of disease Resistance (R) genes, many of which show an increase in steady-state expression levels in the bal variant. Here, we report that activation of RPP5 locus R genes and dwarfing in the bal variant are caused by a 55-kb duplication within the RPP5 locus. Although many RPP5 locus R genes are duplicated in the bal variant, the duplication of SNC1 alone is necessary and sufficient for the phenotypic changes in the bal variant. Missense mutations in the SNC1 gene were identified in all three phenotypically suppressed EMS-treated bal lines investigated, indicating that the high-frequency phenotypic instability induced by EMS treatment is caused by a genetic mechanism. We propose that the high degree of variation in SNC1-related sequences among Arabidopsis natural accessions follows the two-step mechanism observed in the bal variant: gene duplication followed by hypermutation.

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

“…Additionally, none of the genetic variants identified by genome resequencing of this population (18) overlapped with any of these C-DMRs. Lastly, restriction enzyme digestion and Southern blot analyses were performed to rule out the possibility that copy number variants were the cause of spontaneous epiallele formation as is the case for the PAI and BAL epialleles (24, 25). In all cases examined, the observed hybridization pattern and gene copy number were identical for each of the MA lines (fig.…”

Genomic Rearrangements inArabidopsisConsidered as Quantitative Traits

“…Variation in the number of unpaired reads at 9.50–9.51 Mb explains 18.3% of the variance in resistance, and is adjacent to a cluster of leucine-rich repeat genes, and the genes RPP4 (Van Der Biezen et al 2002), BAL (Yi and Richards 2009), and RPP5 . This locus is rearranged in some Arabidopsis accessions, and is known to affect disease resistance (Yi and Richards 2009); Figure 6 confirms the founder genomes have complex, polymorphic, SVs in this region. Since the resistance QTL is not completely ablated by the SV traits associated with it, additional nonstructural variants likely contribute to it.…”

Unusual Case of Apparent Hypermutation in Arabidopsis thaliana

“…However, subsequent work demonstrated a genetic mechanism involving duplication of the SNC1 gene followed by an apparent hypermutational process that induced inactivating missense mutations in one copy, thus returning SNC1 expression to a normal level. Mutagenesis appeared to be restricted to the SNC1 duplication because a sequenced control region lacked mutations (Yi and Richards 2009). …”

“…To explain the high incidence of phenotypic suppression in bal1 variants, the authors proposed two hypothetical mechanisms that are not mutually exclusive (Yi and Richards 2009). The stress-induced mutagenesis hypothesis invoked DNA damage induced by EMS acting as the stressful agent.…”