Non-equivalent contributions of maternal and paternal genomes to early plant embryogenesis

Abstract

Zygotic genome activation in metazoans typically occurs several hours to a day after fertilization, and thus maternal RNAs and proteins drive early animal embryo development. In plants, despite several molecular studies of post-fertilization transcriptional activation, the timing of zygotic genome activation remains a matter of debate. For example, two recent reports that used different hybrid ecotype combinations for RNA sequence profiling of early Arabidopsis embryo transcriptomes came to divergent conclusions. One identified paternal contributions that varied by gene, but with overall maternal dominance, while the other found that the maternal and paternal genomes are transcriptionally equivalent. Here we assess paternal gene activation functionally in an isogenic background, by performing a large-scale genetic analysis of 49 EMBRYO DEFECTIVE genes and testing the ability of wild-type paternal alleles to complement phenotypes conditioned by mutant maternal alleles. Our results demonstrate that wild-type paternal alleles for nine of these genes are completely functional 2 days after pollination, with the remaining 40 genes showing partial activity beginning at 2, 3 or 5 days after pollination. Using our functional assay, we also demonstrate that different hybrid combinations exhibit significant variation in paternal allele activation, reconciling the apparently contradictory results of previous transcriptional studies. The variation in timing of gene function that we observe confirms that paternal genome activation does not occur in one early discrete step, provides large-scale functional evidence that maternal and paternal genomes make non-equivalent contributions to early plant embryogenesis, and uncovers an unexpectedly profound effect of hybrid genetic backgrounds on paternal gene activity.

Arabidopsis LORELEI, a Maternally Expressed Imprinted Gene, Promotes Early Seed Development

“…Additionally, monoallelic expression of LRE expression after fertilization in the developing seed is earlier than reported for other MEGs (Jahnke and Scholten, 2009;Ngo et al, 2012;Nodine and Bartel, 2012;Raissig et al, 2013). Because the patrigenic allele of LRE remains silent in various stages of seed development after 24 HAP Gehring et al, 2011;Hsieh et al, 2011;Nodine and Bartel, 2012;Raissig et al, 2013), our observations also cannot be explained by delayed paternal genome activation (Autran et al, 2011;Del Toro-De León et al, 2014;García-Aguilar and Gillmor, 2015). Based on these observations, we conclude that LRE expression is imprinted in both zygote and endosperm.…”

“…LRE expression after fertilization can arise from expression in either one or both tissues. Additionally, parent-of-origin-dependent gene expression has been reported in both endosperm (Gehring, 2013;Bai and Settles, 2015) and embryo (Jahnke and Scholten, 2009;Nodine and Bartel, 2012;Raissig et al, 2013;Del Toro-De León et al, 2014), two distinct cell types within an embryo sac. The RT-PCR and AS-PCR assays in Figure 1 could not distinguish LRE expression in maternal sporophytic tissues of ovules from expression in the developing embryo sac, nor can it rule out contamination of seeds with RNA from maternal tissues, as was reported for endosperm and early embryo transcriptomes in Arabidopsis (Schon and Nodine, 2017).…”

The Molecular Dialog between Flowering Plant Reproductive Partners Defined by SNP-Informed RNA-Sequencing

“…Accession-specific transcriptional responses have been previously observed (Autran et al, 2011;Nodine and Bartel, 2012;Del Toro-De León et al, 2014), so it is not surprising that Col and Cvi accessions display variation in transcriptional profiles of reproductive cells and tissues. Interestingly, we identified members of gene families that were enriched in the Col pollination transcriptome that were absent from Cvi pollinations such as small secreted defensin-like proteins ( Figure 5D), low molecular weight cysteine-rich proteins ( Figure 5E), and NBS-LRR genes (TIR-NBS-LRR; Figure 5F).…”

“…Using this approach, we have analyzed pollen tube and pistil gene expression in crosses between Cape Verde Island-0 (Cvi) pistils and Columbia-0 (Col) pollen. Interestingly, analysis of gene expression in hybrid embryos revealed that the onset of paternal allele expression varied depending upon the combination of parental accessions (Autran et al, 2011;Nodine and Bartel, 2012;Del Toro-De León et al, 2014). Our application of this approach analyzes gene expression in reproductive tissues before formation of any hybrid cells (embryo and endosperm).…”

Widespread Contamination of Arabidopsis Embryo and Endosperm Transcriptome Data Sets

“…Advances in transcriptomics made it feasible to study global gene expression of these two fertilization products and more than 100 transcriptomes from Arabidopsis thaliana embryos and endosperm have been generated to date Bartel, 2010, 2012;Belmonte et al, 2013;Autran et al, 2011;Slane et al, 2014;Xiang et al, 2011;Hsieh et al, 2011;Gehring et al, 2011;Pignatta et al, 2014). However, data from independent studies investigating parental contributions to early embryo and endosperm transcriptomes has been inconsistent, and the parental genomic contributions to early zygotic transcriptomes has remained controversial (Nodine and Bartel, 2012;Autran et al, 2011;Weijers et al, 2001;Meyer and Scholten, 2007;Del Toro-De Leó n et al, 2014). We hypothesized that inconsistencies between the studies mentioned above are due to varying amounts of RNA contaminants from cells surrounding the tissues of interest.…”