Epigenetic inheritance is more widespread in plants than in mammals, in part because mammals erase epigenetic information by germline reprogramming. We sequenced the methylome of three haploid cell types from developing pollen: the sperm cell, the vegetative cell, and their precursor, the postmeiotic microspore, and found that unlike in mammals the plant germline retains CG and CHG DNA methylation. However, CHH methylation is lost from retrotransposons in microspores and sperm cells and restored by de novo DNA methyltransferase guided by 24 nt small interfering RNA, both in the vegetative nucleus and in the embryo after fertilization. In the vegetative nucleus, CG methylation is lost from targets of DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1), and their homologs, which include imprinted loci and recurrent epialleles that accumulate corresponding small RNA and are premethylated in sperm. Thus genome reprogramming in pollen contributes to epigenetic inheritance, transposon silencing, and imprinting, guided by small RNA.NIH grant: (R01 GM067014); Temasek Lifescience Laboratory; NSERC graduate student fellowship; Fred C. Gloeckner Foundation; Belgian American Educational Foundation postdoctoral fellowship: (Herbert Hoover)

We have identified mutant alleles of two sporophytically acting genes, HAIKU2 (IKU2) and MINISEED3 (MINI3). Homozygotes of these alleles produce a small seed phenotype associated with reduced growth and early cellularization of the endosperm. This phenotype is similar to that described for another seed size gene, IKU1. MINI3 encodes WRKY10, a WRKY class transcription factor. MINI3 promoter::GUS fusions show the gene is expressed in pollen and in the developing endosperm from the two nuclei stage at Ϸ12 hr postfertilization to endosperm cellularization at Ϸ96 hr. MINI3 is also expressed in the globular embryo but not in the late heart stage of embryo development. The early endosperm expression of MINI3 is independent of its parent of origin. IKU2 encodes a leucine-rich repeat (LRR) KINASE (At3g19700). IKU2::GUS has a similar expression pattern to that of MINI3. The patterns of expression of the two genes and their similar phenotypes indicate they may operate in the same genetic pathway. Additionally, we found that both MINI3 and IKU2 showed decreased expression in the iku1-1 mutant. IKU2 expression was reduced in a mini3-1 background, whereas MINI3 expression was unaltered in the iku2-3 mutant. These data suggest the successive action of the three genes IKU1, IKU2, and MINI3 in the same pathway of seed development.autoregulation ͉ endosperm development S eed development involves a complex of processes, including the expansion and growth of the maternal integuments of the ovule and the development of the diploid zygote after the union of the maternal egg cell with one of the two sperm cells delivered to the embryo sac by the pollen tube. It also involves the development of a triploid endosperm after the union of the two nuclei of the homodiploid central cell of the embryo sac with the second sperm cell (1). In eudicots such as Arabidopsis, endosperm development progresses through phases of syncytial growth, cellularization, and cell death. The syncytial phase is characterized by successive divisions of the triploid nuclei without cytokinesis (2). The endosperm cytoplasm is initially compartmentalized into nuclear cytoplasmic domains (3), and subsequently cellularization occurs after the eighth round of syncytial mitoses, initially in the region surrounding the embryo, and proceeding toward the chalazal region (4). Viable seed formation results from the integrated growth and development of the genetically diverse integument, embryo, and endosperm tissues.Major seed controls are provided by genes that define the development of the maternal integument and the new-generation embryo and endosperm. A number of mutations have been described that impair integument development (5, 6), and genes disrupting embryo pattern formation have also been described (7-9). Endosperm development controls are represented by the FIS loci, MEA, FIS2, and FIE, as well as MSI1 (10-12). These genes code for proteins that are components of a chromatin-associated polycomb complex that prevents endosperm development before double fertilization....