Parent-Of-Origin Effects Of Euchromatic PoIIV-Associated siRNAs On Parental Genome Imbalance and Endosperm Development In Arabidopsis Interploidy Crosses

Seed size is important to crop domestication and natural selection and is affected by the balance of maternal and paternal genomes in endosperm. Endosperm, like placenta in mammals, provides reserves to the developing embryo. In angiosperms the endosperm is formed after pollination of the egg by a male gamete (pollen) that contains two sperm nuclei. One sperm fertilizes the egg to form a zygote with a 1:1 maternal to paternal genome ratio (1m: 1p), whereas the other fertilizes two central cell nuclei to form an endosperm cell with a 2:1 maternal to paternal genome ratio (2m:1p). Interploidy crosses disrupt the genome balance in endosperm and alter seed size, depending on the parent-of-origin. In Arabidopsis thaliana, increasing the paternal genome ratio (2m:2p) in endosperm by pollinating a diploid “mother” with a tetraploid “father” (2X4) delays endosperm cellularization (EC) and produces larger seeds. In contrast, increasing the maternal genome ratio (4m: 1p) in endosperm by pollinating a tetraploid mother with a diploid father (4X2) leads to precocious EC and smaller seeds. In plants, RNA polymerase IV (PolIV or p4) encoded by NRPD1a is required for biogenesis of a major class of 24-nt small interfering RNAs (also known as p4-siRNAs), which are predominately expressed in developing endosperm. Here we show that p4-siRNA accumulation depends on the maternal genome dosage, and maternal p4-siRNAs target transposable elements (TEs) and TE-associated genes (TAGs) in seeds. The levels p4-siRNAs negatively affect the expression levels of TAGs in endosperm of interploidy crosses. The parent-of-origin effect is limited to p4-siRNAs that are generated from euchromatic regions but not in heterochromatic regions. While endosperm undergoes global active DNA demethylation, these maternally-derived siRNAs lead to RNA-directed DNA methylation (RdDM) in corresponding loci in the endosperm. Disruption of maternal NRPD1a expression is associated with p4-siRNA reduction, TAG up-regulation and seed size increase in endosperm of reciprocal crosses.