A proteome-centered atlas links tissue specialization and phytohormone variation in rapeseed

Rapeseed is a globally important oil crop cultivated worldwide, but its proteome remains uncharacterized. Here, we established a quantitative atlas of the proteome and phosphoproteome spanning 24 major tissues. Using Orbitrap Astral MS instrument, we quantified 28,217 proteins and 13,455 phosphoproteins (covering over 60,000 phosphorylation sites) during rapeseed vegetative and reproductive stages, representing the most extensive proteomic and phosphoproteomic dataset for rapeseed to date. Tissue-specific protein expression highlights functional specificity with significant variations between transcript and protein levels across tissues. We also present a phytohormone atlas resource, identifying their key role in tissue specificity. We further integrated phytohormone abundance with transcriptomic, proteomic, and phosphorylation-site profiles using weighted gene co-expression network analysis (WGCNA), revealing partially distinct hormone-associated modules across molecular layers. Functional analysis of BnaTT3, a proteome-prioritized seed hormone-associated candidate, supports its role in coordinating seed development and phytohormone homeostasis. These comprehensive multi-omics resources advance our understanding of rapeseed biology and provide a valuable resource for crop improvement.