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Research article - Peer-reviewed, 2023

SeedTransNet: a directional translational network revealing regulatory patterns during seed maturation and germination

Bai, Bing; Schiffthaler, Bastian; van der Horst, Sjors; Willems, Leo; Vergara, Alexander; Karstrom, Jacob; Mahler, Niklas; Delhomme, Nicolas; Bentsink, Leonie; Hanson, Johannes


We describe the dramatic shifts in translation that occur during seed maturation, germination, and seedling establishment. Using network analysis, we identify putative regulatory relationships and subsequently confirm some of them in vivo.Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.


Arabidopsis thaliana; mRNA regulation; ribosome; seed germination; seed maturation; translatome profiling

Published in

Journal of Experimental Botany
2023, volume: 74, number: 7, pages: 2416-2432

Authors' information

Bai, Bing
Umea University
Bai, Bing
Wageningen University and Research
Schiffthaler, Bastian
Umea University
van der Horst, Sjors
Utrecht University
Willems, Leo
Wageningen University and Research
Vergara, Alexander
Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology
Karstrom, Jacob
Umea University
Mahler, Niklas
Umea University
Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology
Bentsink, Leonie
Wageningen University and Research
Hanson, Johannes
Umea University

UKÄ Subject classification

Plant Biotechnology

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