Auxin regulates endosperm cellularization in Arabidopsis

Natural Variation in Ovule Morphology Is Influenced by Multiple Tissues and Impacts Downstream Grain Development in Barley (Hordeum vulgare L.)

The ovule plays a critical role in cereal yield as it is the site of fertilization and the progenitor of the grain. The ovule primordium is generally comprised of three domains, the funiculus, chalaza, and nucellus, which give rise to distinct tissues including the integuments, nucellar projection, and embryo sac. The size and arrangement of these domains varies significantly between model eudicots, such as Arabidopsis thaliana, and agriculturally important monocotyledonous cereal species, such as Hordeum vulgare (barley). However, the amount of variation in ovule development among genotypes of a single species, and its functional significance, remains unclear. To address this, wholemount clearing was used to examine the details of ovule development in barley. Nine sporophytic and gametophytic features were examined at ovule maturity in a panel of 150 European two-row spring barley genotypes, and compared with grain traits from the preceding and same generation. Correlations were identified between ovule traits and features of grain they produced, which in general highlighted a negative correlation between nucellus area, ovule area, and grain weight. We speculate that the amount of ovule tissue, particularly the size of the nucellus, may affect the timing of maternal resource allocation to the fertilized embryo sac, thereby influencing subsequent grain development.

Arabidopsis EMSY-like (EML) histone readers are necessary for post-fertilization seed development, but prevent fertilization-independent seed formation

Seed development is a complex regulatory process that includes a transition from gametophytic to sporophytic program. The synchronized development of different seed compartments (seed coat, endosperm and embryo) depends on a balance in parental genome contributions. In the most severe cases, the disruption of the balance leads to seed abortion. This represents one of the main obstacles for the engineering of asexual reproduction through seeds (apomixis), and for generating new interspecies hybrids. The repression of auxin synthesis by the Polycomb Repressive Complex 2 (PRC2) is a major mechanism contributing to sensing genome balance. However, current efforts focusing on decreasing PRC2 or elevating auxin levels have not yet resulted in the production of apomictic seed. Here, we show that EMSY-Like Tudor/Agenet H3K36me3 histone readers EML1 and EML3 are necessary for early stages of seed development to proceed at a normal rate in Arabidopsis. We further demonstrate that both EML1 and EML3 are required to prevent the initiation of seed development in the absence of fertilization. Based on the whole genome expression analysis, we identify auxin transport and signaling genes as the most enriched downstream targets of EML1 and EML3. We hypothesize that EML1 and EML3 function to repress and soften paternal gene expression by fine-tuning auxin responses. Discovery of this pathway may contribute to the engineering of apomixis and interspecies hybrids.

Paternally Acting Canonical RNA-Directed DNA Methylation Pathway Genes Sensitize Arabidopsis Endosperm to Paternal Genome Dosage

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 × diploid) and lethal (diploid × tetraploid) and viable paternal excess crosses (diploid × 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.