Table 3. PHE1 target genes previously implicated in endosperm development.

Gene ID	Imprinting status	Description of function
AGL62	Non-imprinted	Type I MADS-box TF involved in endosperm proliferation and seed coat development (Figueiredo et al., 2016; Figueiredo et al., 2015; Kang et al., 2008; Roszak and Köhler, 2011)
YUC10	PEG	Flavin monooxygenase that catalyzes the last step of the Trp-dependent auxin biosynthetic pathway (Zhao, 2012). Involved in endosperm proliferation and cellularization (Batista et al., 2019; Figueiredo et al., 2015)
IKU2	Non-imprinted	Encodes a leucine-rich repeat receptor kinase protein that, together with MINI3, is part of the IKU pathway controlling seed size. iku2 mutants show reduced endosperm growth and early endosperm cellularization (Garcia et al., 2003; Luo et al., 2005).
MINI3	Non-imprinted	WRKY TF that, together with IKU2, is part of the IKU pathway controlling seed size. mini3 mutants show reduced endosperm growth and early endosperm cellularization (Luo et al., 2005).
ZHOUPI	Non-imprinted	Encodes a bHLH TF expressed in the embryo-surrounding region of the endosperm. It is essential for embryo cuticle formation and endosperm breakdown after its cellularization (Xing et al., 2013; Yang et al., 2008).
MEA	MEG	Subunit of the FIS–PRC2 complex, responsible for depositing H3K27me3 at target loci including PEGs (Moreno-Romero et al., 2016; Moreno-Romero et al., 2019). Loss of MEA and, consequently, paternally biased expression of PEGs lead to a 3x-seed-like phenotype (Grossniklaus et al., 1998; Kiyosue et al., 1999).
ADM	PEG	Interacts with SUVH9 and AHL10 to promote H3K9me2 deposition in TEs, influencing the expression of neighboring genes. Mutations in ADM lead to rescue of the 3x seed abortion phenotype (Jiang et al., 2017; Kradolfer et al., 2013; Wolff et al., 2015).
SUVH7	PEG	Encodes a putative histone-lysine N-methyltransferase. Mutations in SUVH7 lead to rescue of the 3x seed abortion phenotype (Wolff et al., 2015).
PEG2	PEG	Encodes an unknown protein, which is not translated in the endosperm. PEG2 transcripts act as a sponge for siRNA854, thus regulating UBP1 abundance (Wang et al., 2018). Mutations in PEG2 lead to rescue of the 3x seed abortion phenotype (Wang et al., 2018; Wolff et al., 2015).
NRPD1a	PEG	Encodes the largest subunit of RNA POLYMERASE IV, which is involved in the RNA-directed DNA methylation pathway. Mutations in NRPD1a lead to rescue of the 3x seed abortion phenotype (Erdmann et al., 2017; Martinez et al., 2018).