Comparative temporal gene regulatory networks reveal conserved and species-specific regulatory programs driving storage organ development in kohlrabi stems and sugar beet roots

Storage organs have evolved independently across diverse plant lineages. Nevertheless, how morphologically and anatomically distinct organs converge on similar storage functions via divergent developmental programs remains incompletely understood. In this study, we performed a comparative investigation on the developmental processes of stem‑derived storage organ in kohlrabi and root‑derived storage organ in sugar beet, integrating anatomical characterization and time‑series transcriptomics. Anatomical analyses uncovered divergent developmental trajectories: swelling of the kohlrabi stem is predominantly driven by pith expansion, whereas sugar beet root development is characterized by persistent cambial activity and successive rounds of tertiary growth. To dissect the regulatory mechanisms underlying these distinct developmental strategies, we constructed time‑series gene co‑expression networks for each species. Comparative network analyses revealed a conserved hormone‑centered regulatory framework. The biosynthesis and signaling of auxin, cytokinin, gibberellin, and brassinosteroid reside at the upstream of this framework, and likely exert cascading effects to directly or indirectly modulate downstream key developmental events, including meristematic activity, cell proliferation and expansion, cell‑wall remodeling, and vascular tissue development. Despite sharing this conserved regulatory backbone, cross‑species network comparison further uncovered organ‑specific regulatory processes. In kohlrabi, light‑responsive signaling is coupled with pith expansion and vacuolation; by contrast, sugar beet relies more heavily on sustained meristem activity, vascular remodeling, as well as sucrose‑associated metabolism and signal transduction. Hierarchical analysis of the brassinosteroid‑associated subnetwork further identified multi‑layered regulatory cascades that link upstream transcription factors and hormone biosynthetic processes to downstream regulators governing meristem activity, vascular development, and tissue differentiation. Moreover, predicted transcription factor‑target gene interactions further support the inferred architecture of this regulatory network. This comparative framework provides new insights into the developmental and regulatory basis of storage organ formation and identifies regulatory modules with potential relevance to the genetic improvement of storage crops.