TY - JOUR
T1 - A four-dimensional spatial transcriptome atlas of barley caryopsis development and germination
AU - Peirats-Llobet, Marta
AU - Staka, Zorana
AU - Yang, Xiujuan
AU - Zhu, Yanqiao
AU - He, Cunman
AU - Hurgobin, Bhavna
AU - Ayora, Felipe
AU - Yangzon, Maria Sofia L.
AU - Murcha, Monika W.
AU - Marisa, Valencia
AU - Khan, Ghazanfar Abbas
AU - Zhang, Runxuan
AU - Milne, Iain
AU - Shou, Huixia
AU - Tucker, Matthew R.
AU - Lewsey, Mathew G.
AU - Whelan, James
N1 - Publisher Copyright:
© The Author(s) 2026. Published by Oxford University Press on behalf of American Society of Plant Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence (https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial reproduction and distribution of the work, in any medium, provided the original work is not altered or transformed in any way, and that the work is properly cited. For commercial re-use, please contact [email protected] for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact [email protected].
PY - 2026/5
Y1 - 2026/5
N2 - A 4-dimensional spatial gene expression atlas of Hordeum vulgare (barley) grain development and germination was generated using spatial transcriptomic analysis of serial sections to reconstruct transcript abundance in 3 physical dimensions and with temporal kinetics. We investigated the subtissue localizations of specific biological activities, using energy biology as an example, including genes encoding proteins involved in starch synthesis and degradation, sugar transport, and mitochondrial and chloroplast activity. This atlas revealed different patterns in gene expression across tissues and developmental stages. Heterogeneity in gene expression was observed between clusters, within domains of the individual clusters, across 2-dimensional (xy, 55-μm resolution) and 3-dimensional (xyz, 8-μm resolution in z-plane) axes. Yet, other genes, including typical housekeeping genes such as Actin, Tubulin, and others, display homogeneous expression patterns. Expression of several genes matched previous gene-specific studies in different barley varieties verifying the robustness of the approach and indicating that patterns of gene expression are conserved at least for some categories of genes between varieties. Trajectory analysis of aleurone tissue spanning from early development to the completion of germination, provided a comprehensive roadmap of tissue development in terms of processes and identified transcription factors with spatial specificity that play roles in seed development and germination. A public visualization browser is available to view 2- and 3-dimensional transcription abundance profiles at https://barley-4d.latrobe.edu.au/or https://barley-4d-gene-atlas.hutton.ac.uk/.
AB - A 4-dimensional spatial gene expression atlas of Hordeum vulgare (barley) grain development and germination was generated using spatial transcriptomic analysis of serial sections to reconstruct transcript abundance in 3 physical dimensions and with temporal kinetics. We investigated the subtissue localizations of specific biological activities, using energy biology as an example, including genes encoding proteins involved in starch synthesis and degradation, sugar transport, and mitochondrial and chloroplast activity. This atlas revealed different patterns in gene expression across tissues and developmental stages. Heterogeneity in gene expression was observed between clusters, within domains of the individual clusters, across 2-dimensional (xy, 55-μm resolution) and 3-dimensional (xyz, 8-μm resolution in z-plane) axes. Yet, other genes, including typical housekeeping genes such as Actin, Tubulin, and others, display homogeneous expression patterns. Expression of several genes matched previous gene-specific studies in different barley varieties verifying the robustness of the approach and indicating that patterns of gene expression are conserved at least for some categories of genes between varieties. Trajectory analysis of aleurone tissue spanning from early development to the completion of germination, provided a comprehensive roadmap of tissue development in terms of processes and identified transcription factors with spatial specificity that play roles in seed development and germination. A public visualization browser is available to view 2- and 3-dimensional transcription abundance profiles at https://barley-4d.latrobe.edu.au/or https://barley-4d-gene-atlas.hutton.ac.uk/.
UR - https://www.scopus.com/pages/publications/105040510323
U2 - 10.1093/plcell/koag120
DO - 10.1093/plcell/koag120
M3 - Article
C2 - 42015541
AN - SCOPUS:105040510323
SN - 1040-4651
VL - 38
JO - Plant Cell
JF - Plant Cell
IS - 5
M1 - koag120
ER -