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Spatially resolved transcriptomic analysis of the germinating barley grain

Version 2 2023-09-12, 06:36
Version 1 2023-09-12, 06:23
journal contribution
posted on 2023-09-12, 06:36 authored by Marta Peirats-LlobetMarta Peirats-Llobet, Changyu YiChangyu Yi, Lim LiewLim Liew, Oliver BerkowitzOliver Berkowitz, Reena NarsaiReena Narsai, Mathew LewseyMathew Lewsey, James WhelanJames Whelan
Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at


The work in M.G.L.’s lab was supported by an Australian Research Council (ARC) Discovery Program grant [DP220102840]; J.W. and L.C.L. were funded by an ARC Discovery Program grant [DP210103258]; J.W. is supported by a Kun Peng Fellowship from the Zhejiang Provincial government. Funding for open access charge: Zhejiang Provincial Government - Kun Peng Fellowship; Australian Research Council [DP210103258, DP220102840]. Conflict of interest statement. None declared.


Publication Date



Nucleic Acids Research






22p. (p. 7798-7819)


Oxford University Press



Rights Statement

© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact

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