Initiation of endosperm proliferation and phase transition from endosperm proliferation to embryo development in Arabidopsis

In Arabidopsis and some dicots, seed development starts with an early endosperm proliferation from 1 to 4 Days After Pollination (DAP). In the second phase, the embryo grows after 4 to 5 DAP to replace the endosperm at maturity. The initial endosperm proliferation in many dicots is closely correlated with the mature seed size. SHORT HYPOCOTYL UNDER BLUE1 (SHB1) activates an array of endosperm proliferation genes such as IKU2 and MINI3 after pollination. To explore the molecular action of SHB1, we identified a few critical transcription factors that recognize an array of target loci for endosperm proliferation and recruits SHB1. Some of the transcription factors were only detected at 2 to 3 DAP but not at 4 to 5 DAP. We also isolated suppressor mutants of shb1-D larger seed phenotype. The mutations are allelic and found in proteins such as chromatin modification enzyme. At 4 to 5 DAP, the key endosperm proliferation genes are repressed. Two MADS-box AGL proteins associate with the key endosperm proliferation loci and recruit the FIS-PRC2 repressive complex. AGL9 and AGL15 only accumulate toward the end of endosperm proliferation at 4 to 5 DAP and promote the deposition of H3K27me3 marks at the key genomic loci. Knockouts of AGL9 and AGL15 or overexpression of AGL9 or AGL15 significantly influence endosperm proliferation and cellularization. Other key endosperm proliferation loci repressed by the FIS-PRC2 complex are also revealed through RNA-seq and CUT&Tag analysis. In contrast, seeds of some angiosperms such as cereals have persistent endosperm development. A directional increase in relative embryo to endosperm ratio is an evolutionary trend within the angiosperms. The cereal seeds are filled almost entirely by endosperm. IKU2, the key Arabidopsis regulator of early endosperm proliferation, is also conserved in monocots such as Brachypodium and rice. In contrast to Arabidopsis IKU2, the Brachypodium and rice IKU2 loci sustain a continuous expression and are devoid of H3K27me3 marks. A conserved IKU2 function but a divergent epigenetic regulation of IKU2 expression may contribute to the development of two vastly different seed ontogenies.