The development of seeds in flowering plants is placed under complex interactions between maternal tissues, the embryo, and the endosperm. The endosperm plays a major role in the regulation of seed size. In Arabidopsis thaliana, endosperm size depends on the coordination of the genetic pathway HAIKU (IKU) with epigenetic controls comprising genome dosage, DNA methylation, and trimethylated lysine 27 on histone H3 (H3K27me3) deposition. However, the effectors that integrate these pathways have remained unknown. Here, we identify a target of the IKU pathway, the cytokinin oxidase CKX2, that affects cytokinin signaling. CKX2 expression is activated by the IKU transcription factor WRKY10 directly and promotes endosperm growth. CKX2 expression also depends on H3K27me3 deposition, which fluctuates in response to maternal genome dosage imbalance and DNA demethylation of male gametes. Hence, the control of endosperm growth by CKX2 integrates genetic and epigenetic regulations. In angiosperms, cytokinins are highly active in endosperm, and we propose that IKU effectors coordinate environmental and physiological factors, resulting in modulation of seed size.
