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The objective of this study is to validate the effectiveness of hyperspectral data and select hyperspectral variables to indicate differences between the non-transgenic parent and the progenies of transgenic rice regardless of gene expression. Statistically significant differences were observed in the range 510-735 nm. More differences could be observed from first-order derivative than from the original reflectance spectra. Spectral position- and index-based variables were calculated to find out the potential indicators. Both the maximum value of first-order derivative and the sum of first-order derivative in the ranges 490-530 and 560-650 nm, photochemical reflectance index (PRI) and modified chlorophyll absorption ratio index (MCARI) were different between parent group and progeny groups of transgenic rice.