Table 1.

Summary of the epigenetic mechanism leading to various phenotypes in different plant species.

Species	Target gene or loci	Target phenotype	Epigenetic mechanism	Reference
Arabidopsis thaliana	FWA	Late flowering	Hypomethylation in the promoter region leading to higher expression	Soppe et al., 2000
	DWF4	Lack of elongation in shoots and petioles	Insertion of CACTA family transposon that is activated by hypomethylation	Miura et al., 2001
	BNS	Short, compact inflorescence, reduced plant height	Hypermethylation in the entire gene	Saze and Kakutani, 2007
	FASCIATA1	Abnormal flower development	Insertion of gypsy class retrotransposon that is activated by hypomethylation	Tsukahara et al., 2009
	QTLs	Enhanced growth	De novo epigenetic variation resulting from the use of MSH1 silencing line	Virdi et al., 2015
	QTLs	Flowering time, plant height, fruit number, biomass, root:shoot ratio	Variation of DNA methylation resulting from the use of epigenetic inbred lines	Johannes et al., 2009; Reinders et al., 2009;
Canola	QTLs	Variation of energy use efficiency (EUE)	Epigenetic variation within the population	Hauben et al., 2009
Cotton	COL2D	Photoperiodicity	Hypomethylation on the 5’ region	Song et al., 2017
Linaria vulgaris	Lcyc	Radial symmetry (peloric) flower	DNA methylated and transcriptionally silent	Cubas et al., 1999
Maize	B1, R1, Pl1, P	Anthocyanin pathway pigmentation of various shoot tissues	Paramutation	Hollick, 2017
	low phytic acid 1	Reduced seed phytic acid, elevated seed inorganic P	Paramutation	Pilu et al., 2009
Melon	CmWIP1	Sex deteminaton	Hypermethylation on promotor leading formation of female flower	Martin et al., 2009
Oil palm	Karma	Mantled trait from somaclonal variant	Hypomethylation on karma	Ong-Abdullah et al., 2015
Orange	ripening-related genes	Ripening process	Hypermethylation during fruit-repening	Huang et al., 2019
Persimmon	MeGI	Sex deteminaton	Hypermethylation on the promoter region leading male flower, hypomethylation leads female flower	Akagi et al., 2016
Rice	QTLs	Energy use efficiency (EUE), enhanced seed yield	Epigenetic variation within the population	Schmidt et al., 2018
	RIZBZ1, RPBF	Aleurone layer formation	Demethylation by OsROS1a during grain maturation	Liu et al., 2018
	D1	Dwarfing	Hypermethylation and repressive histone mark on the promoter region	Miura et al., 2009
	OsFIE1	Dwarfing, flower developement	Hypomethylation and H3K9me2 depleation on the 5’ region	Zhang et al., 2012
	RAV6	Leaf angle	Hypomethylation on the promoter region	Zhang et al., 2015
	OsAK1	Chlorophyll formation	Hypermethylation on the promoter region	Wei et al., 2017
	OsSPL14	Grain yield	Hypomethylation on upstream 2.6-kb region	Miura et al., 2010
Sorghum	QTLs	Grain yield, tiller number, plant height, flowering time	De novo epigenetic variation resulting from the use of MSH1 silencing line	Ketumile et al., 2022
Soybean	QTLs	Reduced growth rate, male sterility, enhanced branching and altered leaf and floral morphology	De novo epigenetic variation resulting from the use of MSH1 silencing line	Raju et al., 2018
Strawberry	ripening-related genes	Ripening process	Demethylation during fruit-repening	Cheng et al., 2018
Tomato	SLTAB2	SULFUREA	Paramutation	Gouil et al., 2016
	QTLs	Leaf morphology, variegation, dwarfing, male sterility, flower development, and flower timing	De novo epigenetic variation resulting from the use of MSH1 silencing line	Yang et al., 2015
	LeSPL-CNR	Abnormal ripening, colorless fruit	Silencing of expression by increased DNA methylaiton in the promoter region	Manning et al., 2006
	CNR, VTE3	Ripening process	Demethylation by SlDML2 during fruit-repening	Liu et al., 2018