SeedMatExplorer: The transcriptome atlas of Arabidopsis seed maturation

Seed maturation is a critical developmental phase during which seeds acquire essential traits for nutritional value and desiccation survival. Abscisic acid (ABA) signalling has long been recognized as a key positive regulator of this process, coordinating the expression of genes that drive the acquisition of vital seed quality traits (SQTs) crucial for survival, resilience, and storage. However, the precise molecular regulation of many SQTs remains elusive. To address this gap, we conducted an extensive transcriptome analysis of seed maturation in Arabidopsis thaliana , focusing on Col-0 wild-type and ten mutant lines affecting ABA biosynthesis, signaling, and catabolism from 12 days after pollination up to the dry seed stage. Our study employed Weighted Gene Co-Expression Network Analysis (WGCNA) and module-trait correlation to uncover specific gene groups linked to the regulation of multiple SQTs. We identified Late Embryogenesis Abundant ( LEA ) genes uniquely associated with desiccation tolerance and three DREB AND EAR MOTIF PROTEIN ( DEAR ) transcription factors involved in seed longevity regulation. The value of our dataset lies not only in its depth and detail, but also in its integration into SeedMatExplorer, a web tool specifically designed to advance seed maturation research. SeedMatExplorer serves as a unique resource, enabling researchers to explore, visualize, and generate new hypotheses about gene expression regulation during seed maturation and the intricate control of SQTs. This physiological and transcriptomic atlas offers unprecedented insights into the complex, coordinated gene expression that drives SQT acquisition in Arabidopsis seeds, making it an invaluable asset for the scientific community.