FTIR spectroscopy and Chemometrics for distinguishing soil-based and hydroponic red Amaranth (Amaranthus tricolor L.)

Environmental conditions have the major effect the metabolic composition of staple crops, influencing their nutritional quality and functional properties. Red amaranth (Amaranthus tricolor L.) is nutrient-dense, phytochemical-rich, and ideal for studying environmental metabolic effects. This study aimed to characterize and compare the biochemical profiles of red amaranth leaves, stem, and roots cultivated in conventional soil versus hydroponic system using Fourier-transform infrared (FTIR) spectroscopy integrated with principal component analysis (PCA) and partial/orthogonal least squares discriminant analysis (PLS/OPLS-DA). The first principal component (65.9 % variance) of PCA distinguished plant organs and the second component (17.8 % variance) separated the two growing environments. The PLS-DA and OPLS-DA models demonstrated strong classification performance, with R²Y value exceeding 0.85 and Q² values above 0.79, reflecting excellent model fit and predictive reliability during cross-validation. Further analysis using volcano plots and variable importance in projection (VIP) scores highlighted key spectral bands. These bands corresponded to variations in functional groups such as N-H/O-H stretch, CH stretch, CO carbonyl, NH bend/C=C stretch, aromatic CH bend, and CC skeletal vibration groups that are associated with phenolics, proteins, lipids, and carbohydrates. Leaves and roots grown in soil exhibited higher level pf stress-related phenolics and glycosides, while stems and roots cultivated in hydroponic systems showed greater accumulation of lipid and carbohydrates. The finding demonstrates that FTIR-based chemometric profiling efficiently detect environment-induces metabolomic shifts in red amaranth, making it an important instrument for precision agriculture, crop quality monitoring, and the optimization of cultivation practices to enhance desired phytochemical traits.