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 polymerase IV gene NUCLEAR RNA POLYMERASE D1 (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 Arabidopsis (Arabidopsis thaliana) seeds. We compared transcriptomes, DNA methylation, and small RNAs from the endosperm of seeds from balanced crosses (diploid 3 diploid) and lethal (diploid 3 tetraploid) and viable paternal excess crosses (diploid 3 tetraploid nrpd1). Endosperms from both lethal and viable paternal excess seeds share widespread transcriptional and DNA methylation changes at genes and transposable elements. Interploidy seed abortion is thus unlikely to be caused by transposable elements or imprinted gene misregulation, and its repression by the 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 the 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.

Epigenetics Regulates Reproductive Development in Plants

“…Inheritance of a paternal Pol IV mutation can rescue the seed abortion phenotype caused by excess paternal genome dosage [154]. In a following up study, RdDM activity from the paternal parent was shown to be sufficient to determine seed viability in the cross with paternal excess in Arabidopsis [155]. Misregulation in TEs and imprinted genes was found to be unlikely to cause seed abortion in the cross with paternal excess, and a model of a transcriptional buffering system of balanced gene expression between parental alleles was proposed [155].…”

“…In a following up study, RdDM activity from the paternal parent was shown to be sufficient to determine seed viability in the cross with paternal excess in Arabidopsis [155]. Misregulation in TEs and imprinted genes was found to be unlikely to cause seed abortion in the cross with paternal excess, and a model of a transcriptional buffering system of balanced gene expression between parental alleles was proposed [155]. The above results were not consistent with the role of easiRNAs in dosage effects on seed development discussed in the previous paragraph.…”

“…One big difference was that they showed that these 21-22 nt easiRNAs depend on Pol IV-DCL2/4-RDR6 non-canonical RdDM pathway, whereas the paternal mutations in DCL3, RDR2, and Pol V cannot rescue the seed abortion caused by paternal excess [74,75]. However, Satyaki and Gehring showed that mutations in canonical RdDM pathway genes (Pol V and DRM2) are sufficient for suppressing seed abortion with paternal excess [155]. One of the reasons to explain this discrepancy is that Martinez et al used the omission of second division (osd1) mutant to generate conditions of paternal excess [75], whereas the other study used the true tetraploid wild type and mutants generated by treatment with colchicine [155].…”

Abundant expression of maternal siRNAs is a conserved feature of seed development

“…Genomic coverage was determined using mosdepth (Pedersen and Quinlan, 2018) with options -x and -Q 10, and a custom Python script (bed_coverage_to_x_coverage.py). Per-cytosine methylation was extracted with MethylDackel (Ryan, 2015) in two passes, first to determine the inclusion bounds based on methylation bias per read position using MethylDackel mbias, and then with MethylDackel extract. MethylDackel options were --CHG, --CHH, and --methylKit.…”

Resetting of the 24-nt siRNA landscape in rice zygotes

“…Multiple studies reported that disruption of RdDM leads to a variety of reproductive phenotypes, including aborted embryos (Autran et al 2011;Grover et al 2018), arrested pollen (Wang et al 2020), defective triploid block when the seeds were produced from a 2n maternal × 4n paternal cross (Erdmann et al 2017;Borges et al 2018;Martinez et al 2018;Satyaki and Gehring 2019) and defective floral development (Dorweiler et al 2000;Moritoh et al 2012). These observations suggest siRNAs and RdDM are essential for normal plant reproduction.…”