Natural variation is a well-recognized concept in several species. Variation in the genomic sequence allows for phenotypic differences among individuals. For Arabidopsis thaliana and other plants, variations are found among accessions with several individuals having the same genomic sequence. The variation in Arabidopsis enables different regulatory networks and mechanisms to shape the phenotypic characteristics. The thesis describes the identification of regulatory RNA encoded by an enzyme encoding gene. The RNA regulates by inducing transgenerationally inherited phenotypes. The function of the RNA is dependent on the genetic background illustrating that polymorphisms are found in either interactors or target genes of the RNA. Furthermore, the RNA provides a mechanistic link between accumulation of glucosinolate and onset of flowering.