UNLABELLED: Seed germination represents the crucial transition from dormancy to active growth, orchestrated by environmental signals and endogenous regulatory networks. This study investigates translational regulation during germination in two Arabidopsis thaliana accessions with contrasting dormancy phenotypes: Columbia (Col-0), which germinates readily, and Cape Verde Islands (Cvi-0), which exhibits deep dormancy. Hormonal profiling revealed dynamic changes in abscisic acid and gibberellins, central regulators of seed dormancy. We isolated monosomal and polysomal RNA from seeds at three stages: freshly harvested (FH), after-ripened (AR), and imbibed (IM), followed by RNA sequencing. Transcriptome analysis identified ~ 14,000 mRNAs in FH seeds, increasing to 19,000 in Col and 17,000 in Cvi after imbibition. Approximately 9,000 transcripts were shared, while ~ 3,000 were genotype-specific in the monosomal fraction. Enrichment analyses indicated differential activation of translation and dormancy-related pathways. RNA modification profiling revealed N1-methyladenosine (m1A) as the most abundant mark, with higher levels in Col peaking three months post-harvest. m⁶A sequencing uncovered distinct modification landscapes, with IM seeds showing the greatest abundance and genotypic divergence in m⁶A-enriched transcripts. m⁶A peak localization correlated with genes showing differential expression between Col and Cvi. Proteomic analysis identified ~ 15,000 proteins, with components of the translational machinery enriched in IM seeds. Genotype-specific differences emerged in both monosomal and polysomal fractions. RNA-binding proteins were similar in FH and AR stages but diverged significantly upon imbibition, with Col showing enrichment in 40S ribosomal subunits, processing bodies, and RNA-associated complexes. These results reveal key translational and post-transcriptional mechanisms underpinning dormancy release and germination. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11103-025-01659-6.

UNLABELLED: The study reveals translational regulation in Arabidopsis germination, demonstrating genotype-specific RNA modifications, gene expression, and protein enrichment, highlighting the role of m6A modification in dormancy release and germination. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11103-025-01659-6.

Centre of Plant Structural and Functional Genomics Institute of Experimental Botany Czech Academy of Sciences Šlechtitelů 31 779 00 Olomouc Czech Republic

Department of Analytical Chemistry Faculty of Science Palacký University Olomouc 17 Listopadu 12 779 00 Olomouc Czech Republic

Department of Botany Faculty of Science Palacký University Olomouc Šlechtitelů 27 779 00 Olomouc Czech Republic

Department of Plant Developmental Genetics Institute of Biophysics Czech Academy of Sciences Královopolská 135 612 00 Brno Czech Republic

Laboratory of Growth Regulators Faculty of Science Palacký University Olomouc and Institute of Experimental Botany Czech Academy of Sciences Šlechtitelů 27 779 00 Olomouc Czech Republic

Laboratory of Pollen Biology Institute of Experimental Botany Czech Academy of Sciences Rozvojová 263 165 00 Prague 6 Czech Republic

Mendel Centre for Plant Genomics and Proteomics Central European Institute of Technology Masaryk University Kamenice 753 5 625 00 Brno Czech Republic

National Centre for Biomolecular Research Faculty of Science Masaryk University Kamenice 753 5 625 00 Brno Czech Republic

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