Multi-omics analysis of the effects of hydroponic nutrient flow environment on lignin biosynthesis in lettuce root

•Multi-omics shows hydroponic flow rate effects on lettuce root lignin biosynthesis.•Molecular mechanisms in environment-plant biochemical pathway interaction revealed.•Modulating expression of three gene families affects lignin content in root cell wall. The flow of nutrient solutions in hydroponics markedly affects plant growth and development. Suitable flow rates can improve root morphology, facilitating nutrient absorption. Altered cell wall composition upon sensing external stimuli can promote environmental adaptation. Lignin, an important plant cell wall component, enhances structural strength; however, the effects of nutrient solution flow on lignin synthesis remain unexplored. Here, we applied high-throughput metabolomic, transcriptomic, and proteomic techniques to systematically study hydroponically grown lettuce (Lactuca sativa), revealing significant regulatory effects of nutrient solution flow on lignin metabolism in lettuce roots. Gene and protein expression differed in lettuce roots under different flow rates, consistent with the underlying molecular mechanisms elucidated by metabolomic analyses. Specifically, under no-flow conditions, the contents of p-coumaryl alcohols (H-lignin) and coniferyl alcohols (G-lignin) were elevated, whereas high-flow conditions upregulated sinapyl alcohols synthesizing S-lignin. Moreover, lignin synthesis-related HCT, CAD, and PER gene families were highly expressed under no-flow and high-flow conditions, with coordinate changes in lignin content, indicating that nutrient flow influenced their expression; thereby affecting root cell lignin content. This study enhances our understanding of plant growth and secondary metabolic regulatory mechanisms in hydroponic environments and lays a theoretical foundation for optimizing plant growth conditions in hydroponic systems. [Display omitted]