Paternally-acting canonical RNA-directed DNA methylation pathway genes sensitize Arabidopsis endosperm to paternal genome dosage

Abstract Seed development is sensitive to parental dosage, with excess maternal or paternal genomes creating reciprocal phenotypes. Paternal genomic excess frequently results in extensive endosperm proliferation without cellularization and seed abortion. We previously showed that loss of the RNA Pol IV gene nrpd1 in tetraploid fathers represses seed abortion in paternal excess crosses. Here we show genetically that RNA-directed DNA methylation (RdDM) pathway activity in the paternal parent is sufficient to determine the viability of paternal excess seeds. We compared transcriptomes, DNA methylation, and small RNAs from endosperm of balanced crosses (diploid × diploid) and lethal (diploid × tetraploid) and viable paternal excess (diploid × tetraploid nrpd1 ). Endosperm from both lethal and viable paternal excess seeds share widespread transcriptional and DNA methylation changes at genes and TEs. Interploidy seed abortion is thus unlikely to be caused by either transposable element or imprinted gene mis-regulation, and its repression by loss of paternal RdDM is associated with only modest gene expression changes. Finally, using allele-specific transcription data, we present evidence for a transcriptional buffering system that increases expression of maternal alleles and represses paternal alleles in response to excess paternal genomic dosage. These findings prompt reconsideration of models for dosage sensitivity in endosperm.