This study investigates the effect of different pre-treatments, viz., soaked and germinated millet flour of barnyard and browntop on the anti-nutritional, nutritional, functional, rheological, and digestion characteristics of barnyard millet (BM) and browntop millet (BTM). The soaking treatments were conducted for 12, 16, and 20 h at temperatures of 25 °C, 30 °C, and 35 °C using seed-to-water ratios of 1:2, 1:3, and 1:4. Germination followed soaking (20 h) and was carried out over 24, 36, and 48 h at temperatures of 25 °C, 30 °C, and 35 °C. The findings indicated a significant reduction in anti-nutritional factors (p < 0.05) during soaking and germination. In BM, these values decreased from 5.53 to 3.41 TIU/mg, 1.49 to 0.65 mg/g, 68.76 to 42.39 mg/g, and 6.25 to 2.85 mg/g, for BTM decreased from 6.17 to 4.69 TIU/mg, 2.68 to 1.43 mg/g, 72.39 to 38.27 mg/g, and 5.63 to 1.65 mg/g, for trypsin inhibitor activity, tannin level, oxalic content and phytic acid content respectively. Following soaking and germination, both BM and BTM exhibited reduced bulk density and porosity. In contrast, their water absorption capacity increased to a range of 0.82–0.90 g/g, while oil absorption capacity rose to 1.87–2.73 g/g. Structural and functional alterations were evident in the SEM and FT-IR analyses, indicating notable modifications in the millet samples. In contrast, XRD patterns and crystallinity levels exhibited only minor changes, suggesting a limited impact on the crystalline structure. The pasting behaviour analysis revealed distinct changes in viscosity, indicating structural modifications during processing. In vitro digestibility showed marked improvement, with barnyard millet’s starch digestibility increasing from 5.81 to 15.84 mg maltose per 100 mg, and protein digestibility rising from 72.13 to 76.61 g per 100 g. Similarly, BTM’s starch digestibility increased from 66.44 to 76.98 mg maltose/100 mg, and protein digestibility from 80.68 to 87.17 g/100 g.
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