Peirats-Llobet, M. | Search bioRxiv

bioRxiv2026

Temporal genomic imprinting regulates grain filling in barley

In cereals, the persistent endosperm accumulates starch and storage proteins, making their grains a major source of food and feed. Early grain development is epigenetically controlled through the parent-of-origin-specific expression of imprinted genes in the endosperm that regulate endosperm proliferation, nutrient accumulation and embryo nourishment. Imprinted genes have been identified in several major cereals, and a few have been functionally characterized. However, it is unclear how imprinted genes regulate the accumulation of storage compounds in cereal grains. Through spatiotemporal transcriptome analysis of 255 imprinted genes in barley (Hordeum vulgare), we identify endosperm transfer cells in grains as a hotspot of expression of imprinted genes. Furthermore, we show that transcription factor LYS3 dynamically regulates grain filling in barley through early expression of the maternal allele, followed by partial activation of the paternal allele.

plant biology↗

bioRxiv2023

Establishment of cell transcriptional identity during seed germination

Germination involves highly dynamic transcriptional programs as the cells of seeds reactivate and express the functions necessary to establish in the environment. Individual cell types have distinct roles within the embryo, so must therefore have cell-type specific gene expression and gene regulatory networks. We can better understand how the functions of different cell types are established and contribute to the embryo by determining how cell-type specific transcription begins and changes through germination. Here we describe a temporal analysis of the germinating Arabidopsis embryo at single-cell resolution. We define the highly dynamic cell-type specific patterns of gene expression and how these relate to changing cellular function as germination progresses. Underlying these are unique gene regulatory networks and transcription factor activity. We unexpectedly discover that most embryo cells transition through the same initial transcriptional state early in germination, after which cell-type specific gene expression is established. Furthermore, our analyses support previous findings that the earliest events leading to the induction of embryo growth take place in the vasculature. Overall, our study constitutes a general framework to characterise Arabidopsis cell states through embryo growth, allowing investigation of different genotypes and other plant species whose seed strategies may differ.

plant biology↗