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Peer-reviewedCC BY-NC-NDBMC Plant Biology

SeedMatExplorer: the transcriptome atlas of Arabidopsis seed maturation

  • Mariana A S Artur1
  • Robert A. Koetsier2
  • Leo A. J. Willems1
  • Lars L. Bakermans1
  • Annabel D. van Driel1
  • Joram A. Dongus1
  • Bas J. W. Dekkers1
  • Alexandre C. S. S. Marques1
  • Asif Ahmed Sami1
  • Harm Nijveen2
  • Leónie Bentsink1
  • Henk W. M. Hilhorst3,1
1 more authors
  • Renake Nogueira Teixeira4,1
4 affiliations
  1. 1Laboratory of Plant Physiology, Wageningen Seed Science Centre, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
  2. 2Bioinformatics Group, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
  3. 3Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
  4. 4Hazera Seeds B.V., Schanseind 27, 4921 PM Made
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Abstract

BACKGROUND: Seed maturation is a critical developmental phase during which seeds acquire traits essential for nutritional value, desiccation tolerance, and long-term survival. Abscisic acid (ABA) signalling is a key regulator of this process, coordinating gene expression programs underlying the acquisition of seed quality traits. However, the molecular regulation of many of these traits remains poorly understood. To address this, we performed a comprehensive analysis of seed maturation in Arabidopsis thaliana, combining physiological and transcriptomic approaches across wild-type plants and mutants affected in ABA biosynthesis, signalling, and catabolism. RESULTS: We generated a high-resolution transcriptome dataset covering seed development from 12 days after pollination to the dry seed stage in wild-type and ten mutant lines. In parallel, we characterized the temporal acquisition of multiple seed traits, including germination capacity, dormancy, chlorophyll fluorescence, longevity and desiccation tolerance. Integration of these datasets using weighted gene co-expression network analysis (WGCNA) identified gene modules associated with specific trait acquisition patterns. This approach enabled the identification of coordinated transcriptional programs linked to distinct seed quality traits, extending beyond individual gene-level analyses. Notably, modules associated with desiccation tolerance and longevity were enriched for genes involved in stress responses and ABA-regulated pathways, highlighting the complex and multifactorial regulation of these traits. CONCLUSIONS: This study provides a comprehensive physiological and transcriptomic framework for understanding seed maturation and the acquisition of key seed quality traits in Arabidopsis thaliana. By linking gene expression dynamics to trait development, our work offers new insights into the regulatory networks underlying seed resilience and storage capacity. The dataset is made accessible through SeedMatExplorer ( https://www.bioinformatics.nl/SeedMatExplorer ), an open-access web platform that enables interactive exploration and supports hypothesis generation. Together, this resource represents a valuable tool for advancing research on seed biology and improving seed performance in agricultural contexts.

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Cite

BibTeXRIS
BibTeX
@article{artur2026seedmatexplorer,
  title = {{SeedMatExplorer: the transcriptome atlas of Arabidopsis seed maturation}},
  author = {Mariana A S Artur and Robert A. Koetsier and Leo A. J. Willems and Lars L. Bakermans and Annabel D. van Driel and Joram A. Dongus and Bas J. W. Dekkers and Alexandre C. S. S. Marques and Asif Ahmed Sami and Harm Nijveen and Leónie Bentsink and Henk W. M. Hilhorst and Renake Nogueira Teixeira},
  journal = {BMC Plant Biology},
  year = {2026},
  month = jun,
  doi = {10.1186/s12870-026-09313-z},
  url = {https://doi.org/10.1186/s12870-026-09313-z},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - SeedMatExplorer: the transcriptome atlas of Arabidopsis seed maturation
AU  - Mariana A S Artur
AU  - Robert A. Koetsier
AU  - Leo A. J. Willems
AU  - Lars L. Bakermans
AU  - Annabel D. van Driel
AU  - Joram A. Dongus
AU  - Bas J. W. Dekkers
AU  - Alexandre C. S. S. Marques
AU  - Asif Ahmed Sami
AU  - Harm Nijveen
AU  - Leónie Bentsink
AU  - Henk W. M. Hilhorst
AU  - Renake Nogueira Teixeira
PY  - 2026
DA  - 2026/06/25
JO  - BMC Plant Biology
DO  - 10.1186/s12870-026-09313-z
UR  - https://doi.org/10.1186/s12870-026-09313-z
AB  - BACKGROUND: Seed maturation is a critical developmental phase during which seeds acquire traits essential for nutritional value, desiccation tolerance, and long-term survival. Abscisic acid (ABA) signalling is a key regulator of this process, coordinating gene expression programs underlying the acquisition of seed quality traits. However, the molecular regulation of many of these traits remains poorly understood. To address this, we performed a comprehensive analysis of seed maturation in Arabidopsis thaliana, combining physiological and transcriptomic approaches across wild-type plants and mutants affected in ABA biosynthesis, signalling, and catabolism. RESULTS: We generated a high-resolution transcriptome dataset covering seed development from 12 days after pollination to the dry seed stage in wild-type and ten mutant lines. In parallel, we characterized the temporal acquisition of multiple seed traits, including germination capacity, dormancy, chlorophyll fluorescence, longevity and desiccation tolerance. Integration of these datasets using weighted gene co-expression network analysis (WGCNA) identified gene modules associated with specific trait acquisition patterns. This approach enabled the identification of coordinated transcriptional programs linked to distinct seed quality traits, extending beyond individual gene-level analyses. Notably, modules associated with desiccation tolerance and longevity were enriched for genes involved in stress responses and ABA-regulated pathways, highlighting the complex and multifactorial regulation of these traits. CONCLUSIONS: This study provides a comprehensive physiological and transcriptomic framework for understanding seed maturation and the acquisition of key seed quality traits in Arabidopsis thaliana. By linking gene expression dynamics to trait development, our work offers new insights into the regulatory networks underlying seed resilience and storage capacity. The dataset is made accessible through SeedMatExplorer ( https://www.bioinformatics.nl/SeedMatExplorer ), an open-access web platform that enables interactive exploration and supports hypothesis generation. Together, this resource represents a valuable tool for advancing research on seed biology and improving seed performance in agricultural contexts.
SN  - 1471-2229
ER  -