A single-nucleus transcriptomic atlas reveals distinct cell identities and key regulators of cellular differentiation during early rice seed development.
Aug 2026· Journal of Integrative Plant Biology· 0 citations· 56 references
Medicine
TL;DR
This study provides a single-cell resolution framework for understanding early rice seed development, identifies the embryo-endosperm interface as an important cellular domain associated with embryogenesis, and offers a valuable resource for dissecting the molecular basis of seed formation in rice and related cereals.
Abstract
The early morphogenesis of the embryo and endosperm sets the upper limit of rice grain yield; yet, the cellular dynamics and regulatory mechanisms underlying this critical stage remain largely elusive. Here, we present a single-cell atlas of developing rice seeds based on single-nucleus RNA sequencing of 67,922 high-quality nuclei from rice caryopses. Integration with bulk RNA-seq, in situ hybridization, and promoter-GUS staining enabled systematic cell-type annotation and revealed a distinct population of embryo-endosperm interface (EEI) cells occupying the boundary between the developing embryo and endosperm. Comparative analyses with maize data sets, together with trajectory inference, suggested that a subset of EEI cells shares molecular features with maize embryo-adjacent scutellum cells and shows transcriptional continuity with starchy endosperm cells. Embryo-endosperm interface cells were enriched in transport-related and developmental regulatory genes with known functions in seed development and embryogenesis. Focusing on the EEI-enriched regulator OsBZR4, we found that loss of OsBZR4 altered cellular composition and transcriptional programs during early seed development, disrupted embryonic developmental progression, and reduced the expression of embryonic genes, including OsCDP3.10 and RINO1. Together, our study provides a single-cell resolution framework for understanding early rice seed development, identifies the embryo-endosperm interface as an important cellular domain associated with embryogenesis, and offers a valuable resource for dissecting the molecular basis of seed formation in rice and related cereals.
The findings establish seeds as a transcriptionally complex organ with high cell type heterogeneity and provide a basis for investigating the differentiation of diverse cell layers and spatial transcript profiles.
Khadija L. B. Rombi, Thomas Hartwig, Nora R. Zöllner et al.· bioRxiv· 0 citations
Anthocyanins are important plant pigments that contribute to leaf coloration and stress adaptation, but how their biosynthesis is regulated across different leaf cell types remains unclear, especially in woody plants. Here, we combined single-nucleus RNA sequencing (snRNA-seq) and bulk RNA-seq to investigate anthocyanin-associated regulatory programs in Pistacia chinensis leaves. We found that epidermal cells followed a largely unidirectional transition toward high-anthocyanin states, whereas mesophyll cells differentiated into multiple functional subtypes, revealing substantial cellular heterogeneity. Although epidermal and mesophyll cells shared the core anthocyanin biosynthetic pathway, their upstream regulatory programs differed. Integrative analysis identified multiple transcription factors associated with anthocyanin accumulation, several of which showed distinct expression patterns between high-anthocyanin epidermal cells and anthocyanin-enriched mesophyll cells. Functional assays showed that PcMYB113a and PcMYB113b promote anthocyanin accumulation and interact with conserved MBW-complex components. Overall, this study provides cell-resolved insight into anthocyanin-associated regulatory programs in woody plant leaves.
ERECTA signaling is identified as a local brake on embryonic stomatal cell maturation, discovering another way to push precocious stomatal cell maturation that results in a complex, partially mature cell state that provide insights into the limitations on cell embryonic cell maturation.
Yadhusankar Sasidharan, Vijay Suryavanshi, Pablo González-Suárez et al.· bioRxiv· 0 citations
Early embryogenesis is governed by tightly regulated transcriptional programs, including the maternal-to-zygotic transition (MZT), zygotic genome activation (ZGA), and maintenance of pluripotency. While these processes are well studied in model vertebrates, they remain poorly understood in salmonid fishes, whose genomes are shaped by a relatively recent whole genome duplication (WGD) event. Here, we present a temporally resolved transcriptomic analysis of Atlantic salmon (Salmo salar) embryogenesis using bulk RNA-seq across key stages spanning early embryogenesis. Dimensionality reduction and unsupervised clustering of gene expression revealed stage-specific transitions encompassing maternal RNA clearance, cell cycle regulation, and the onset of metabolic activity. We demonstrate that ZGA occurs early and in multiple phases, beginning soon after fertilization, accompanied by chromatin remodelling and the activation of epigenetic regulators. Duplicated gene pairs retained from the salmonid WGD frequently displayed asynchronous expression, indicative of functional divergence and the evolution of additional regulatory complexity of embryonic development. To gain insights into pluripotency, we integrated analyses of gene expression, transcription factor motifs, and chromatin accessibility, to reveal conserved regulators including genes encoding Pou5f3, Nanog, and Sox19b, alongside divergent functions of Klf family members. Our cross-stage profiling allowed us to define a novel panel of stably-expressed reference genes for normalization during quantitative PCR analyses, which were used to validate pluripotency- and differentiation-associated dynamics inferred by RNA-seq. Together, our findings delineate the transcriptional architecture of early embryogenesis in Atlantic salmon, revealing both conserved and lineage-specific features of pluripotency regulation, and providing a foundational resource for future functional genomics and stem cell applications in salmonids.
Prabin Sharma Humagain, Diego Perojil Morata, M. Wessel et al.· bioRxiv· 0 citations
It is reported that NtProRP1, an extracellular protein, localizes to the cell wall immediately after fertilization in Nicotiana tabacum, uncovering a new mechanism for NtProRP1 in regulating early embryogenesis and delivering a unique transcriptomic resource that advances understanding of extracellular signaling in plant embryogenesis.
An Luo, Ying Qiao, Siyuan Li et al.· Plant and Cell Physiology· 0 citations
This study provides the first comprehensive panorama of epigenetic regulators in the soybean pan-genome, highlighting wild germplasm as a valuable reservoir for recovering lost alleles (Group2 homologs) and identifying Wm82-HAC1 (Group 1) as a prime target for precision breeding of seed traits.
Chaojun Wang, Dan Huang, Zhicheng Dong et al.· BMC Plant Biology· 0 citations