We demonstrate patterns in the penetrance of the mutant gene and the suppressor gene which control suppressed temperature-dependent chlorophyll defects in F1 hybrid progenies of F. pratensis L. obtained through reciprocal crossings of mother plants of different phenotypes, and the contributions of these genes to the epigenetic variation of plant organisms. In F1 hybrid progenies from reciprocal crossings the mutant gene may demonstrate either the same or differential genomic imprinting. Variations of the effect depended on the degree of the chlorophyll defect in the seedlings at desuppression and the modifying action of the suppressor gene at resuppression. Furthermore, the suppressor gene had a multiplier effect, as it not only suppressed the penetrance of the mutant gene that controlled temperature-dependent chlorophyll defects but also masked the different genomic imprinting in individual F1 hybrid phenotypes.