Sequential gene activation and gene imprinting during early embryo development in maize

Abstract

Gene imprinting is a widely observed epigenetic phenomenon in maize endosperm; however, whether it also occurs in the maize embryo remains controversial. Here, we used high-throughput RNA sequencing on laser capture microdissected and manually dissected maize embryos from reciprocal crosses between inbred lines B73 and Mo17 at six time points (3-13 days after pollination, DAP) to analyze allelic gene expression patterns. Co-expression analysis revealed sequential gene activation during maize embryo development. Gene imprinting was observed in maize embryos, and a greater number of imprinted genes were identified at early embryo stages. Sixty-four strongly imprinted genes were identified (at the threshold of 9:1) on manually dissected embryos 5-13 DAP (more imprinted genes at 5 DAP). Forty-one strongly imprinted genes were identified from laser capture microdissected embryos at 3 and 5 DAP (more imprinted genes at 3 DAP). Furthermore, of the 56 genes that were completely imprinted (at the threshold of 99:1), 36 were not previously identified as imprinted genes in endosperm or embryos. In situ hybridization demonstrated that most of the imprinted genes were expressed abundantly in maize embryonic tissue. Our results shed lights on early maize embryo development and provide evidence to support that gene imprinting occurs in maize embryos.

Genomic Imprinting Was Evolutionarily Conserved during Wheat Polyploidization

“…In plants, imprinting primarily occurs in the endosperm; however, recent studies have shown that a portion of genes are also imprinted in the embryo of Arabidopsis thaliana (Raissig et al, 2013), rice (Oryza sativa) (Luo et al, 2011), and maize (Zea mays) (Meng et al, 2017). This uniparental transcription pattern indicates that, to some extent, parental genomes might not contribute equally to the filial genome, at least for some specific loci, if not at the genome-wide level (Vielle-Calzada et al, 2000;Grimanelli et al, 2005;Autran et al, 2011).…”

Construction and applications of a B vitamin genetic resource for investigation of vitamin‐dependent metabolism in maize

“…By contrast, endosperms carrying two doses of pdx2-mu1023708 are consistently above the threshold for functional vitamin deficiency. While preferential expression of the maternally transmitted pdx2 allele in the embryo due to imprinting could also explain these results, Pdx2 is not among the relatively small set of imprinted genes so far detected in the maize embryo (Meng et al, 2018). Conversely, a dependence of the embryo phenotype on dosage of pdx2 alleles in endosperm would suggest that pyridoxine in endosperm is not only required for endosperm formation, but also for embryo development.…”

Transcriptomics at maize embryo/endosperm interfaces identify a novel transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum (EAS)

“…As in other flowering plants, seed development in maize is governed by specific temporal and spatial genetic programs, distinguishing early development, filling and maturation on one hand and embryo, endosperm and pericarp on the other Downs et al, 2013;Li et al, 2014;Lu et al, 2013;Meng et al, 2018;Qu et al, 2016). Recently a transcriptome analysis on nucellus (including the fertilized embryo sac) increased the temporal resolution and allowed unprecedented access to information regarding the genetic control of early seed developmental (Yi et al, 2019).…”

“…Genome-wide gene expression studies at numerous developmental stages of whole kernels and/or hand-dissected endosperm and embryo Downs et al, 2013;Li et al, 2014;Lu et al, 2013;Meng et al, 2018;Qu et al, 2016) have been complemented by a recent transcriptomic analysis of laser-capture micro-dissected cell types and subcompartments of 8 DAP kernels (Zhan et al, 2015). However, even the latter study did not address specifically the transcriptomic profiles of the embryo/endosperm interfaces and did not answer the question of whether the endosperm at the scutellum/endosperm interface is composed of cells with specific transcriptional identities.…”