Establishment of cell transcriptional identity during seed germination

Abstract

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.

A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

“…A deeper investigation of the shared markers of germinating seeds revealed that many of the identified genes with shared expression across cell types encode a diverse range of ribosomal protein subunits. The unified expression of ribosomal proteins across cell types in the germinating seed dataset coincides with global increases in ribosome biogenesis and translation during seed germination in both Arabidopsis 41,42 and Barley grains 43 . While the expression of many ribosomal protein genes is present across several cell types of germinating seeds, this was not observed for all of the other tissues assayed, where subsets of ribosomal proteins were expressed only in specific cell types among all tissue and organs assayed, supporting the hypothesis that the heterogeneous composition of ribosomes is developmentally regulated 44 , and may explain the higher levels of homogeneity within this tissue.…”

“…While the expression of many ribosomal protein genes is present across several cell types of germinating seeds, this was not observed for all of the other tissues assayed, where subsets of ribosomal proteins were expressed only in specific cell types among all tissue and organs assayed, supporting the hypothesis that the heterogeneous composition of ribosomes is developmentally regulated 44 , and may explain the higher levels of homogeneity within this tissue. As seed development progresses from imbibition to germination, embryo cell types progress through reprogramming 42 , suggesting that a snapshot of cellular state was captured in our germinating seedling dataset.…”