Induced instability of two Arabidopsis constitutive pathogen-response alleles

Paramutation is an example of a non-Mendelian-directed allelic interaction that results in the epigenetic alteration of one allele. We describe a paramutation-like interaction between two alleles, bal and cpr1–1 (constitutive expressor of PR genes 1), which map to a complex R-like gene cluster on Arabidopsis chromosome 4. Both alleles cause dwarfing and constitutive defense responses, similar to another dwarf variant, ssi1 (suppressor of SA-insensitivity 1). Previous work has demonstrated that the bal and ssi1 phenotypes are caused by overexpression of an R-like gene from the cluster, which activates an salicylic acid-dependent defense pathway. Here, we show that the cpr1–1 variant does not alter gene expression from the R-like gene cluster. The bal and cpr1–1 alleles did not complement each other in F(1) hybrids, but F(2) populations that segregated bal and cpr1–1 alleles contained plants with normal morphology at a frequency of 20%. By using molecularly marked bal and cpr1–1 lines, we found that the majority of the normal phenotypes were correlated with inheritance of an altered cpr1–1 allele. Our observation that cpr1–1 is a metastable allele suggests that cpr1–1 is an epigenetic allele. The cpr1–1 allele is the third candidate epigenetic allele originating from this R-like gene cluster, making the region a possible hotspot of epigenetic variation.