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Soybean is the most economically important oilseed in the world, being one of the main sources of oil and protein in human and animal food. The objective of this work was to select F3 segregating populations for agronomic and physiological traits and vegetation indices (VIs). The experiment was carried out in the 2018/2019 crop seasons in a randomized block design with three replicates and 10 F3 populations (P1, P2, P3, P4, P5, P6, P7, P8, P9, and P10). The evaluated traits were as fallows: number of days to maturity (NDM); number of pods per plant (NPP); number of nodes per plant (NNP); number of lateral stems per plant (NSP); grain yield (GY); photosynthesis (A); stomatal conductance (gs); internal CO2 concentration (Ci); transpiration (E); NIR, Red-edge, Red and Green wavelengths; and NDVI and NDRE vegetation indices. Regarding the physiological traits evaluated in soybean F3 populations, the P8 and P6 populations presented the highest averages for photosynthesis, while the P3, P10, and P9 populations presented the highest Ci, E, and gs. For VIs evaluated in soybean F3 populations, the populations P7, P2, and P1 presented higher averages for NIR and Red-edge wavelengths. P5 and P4 showed a higher NDRE, and P8 showed a higher red wavelength. For agronomic traits, population P2 showed better results for the traits NNP and NSP. Populations P1 and P3 had a higher NDM. The P7 population presented the highest NPP, and the P6 population presented the highest GY. [ABSTRACT FROM AUTHOR]