Phosphoproteomic insights into the regulation of root length in rice (Oryza sativa L. cv. KDML 105): uncovering key events and pathways involving phosphorylated proteins

Root is a crucial organ in terrestrial plants, with the maximum root length (MRL) trait of the root system positively correlated with both plant growth and adaptation. However, the mechanisms regulating root length remain inadequately understood due to the dynamics of root growth. Protein phosphorylation precisely regulates various biological processes, providing a pathway to investigate the complex regulatory mechanisms of roots. This study aims to identify key events and pathways that are positively involved in regulating MRL in rice. Using liquid chromatography tandem mass spectrometry (LC-MS/MS), the phosphoprotein profiles of roots exhibiting different MRL phenotypes across three cultivating systems: deep water cultivation (DWC), water agar (WA), and vermiculite-based hydroponics (VBH) were examined. The results showed that the MRL trait of rice is strongly influenced by protein phosphorylation events. Further analysis indicated a clear convergence between phosphorylation signaling and phytohormone signaling in the regulation of MRL. The identified potential phosphoprotein promoters may enhance MRL by promoting root adaptation, optimizing hormonal crosstalk, and facilitating the synthesis of beneficial components. However, given the complexity and dose-dependent nature of hormonal networks, additional quantitative studies were necessary to fully elucidate the mechanisms underlying MRL regulation in rice.