SeedMatExplorer: the transcriptome atlas of Arabidopsis seed maturation

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.