Genotypic influence on soybean protein quality: Linking molecular structure, functional properties, and nutritional quality through principal component and correlation analyses

Soybean is one of the most dominant sources of plant-based protein due to its high nutritional value and versatility in food applications. However, variety-dependent differences in the structural, functional, and nutritional attributes of soy protein isolates (SPIs) remain insufficiently explored for targeted product design and breeding. Eight soybean varieties (SPI 1-8) were characterized from seed composition to detailed structural, functional, and nutritional analyses. Significant varietal differences were observed in solubility, emulsifying activity (EA) (1.21-1.88), water-holding capacity (WHC) (2.82-5.64 g water/g), particle size (35.88-125.58 nm), and zeta potential (-20.12 to -26.51 mV). Varieties with higher β-turn content (74.48%), such as SP6, exhibited greater solubility (61.84%) and enhanced emulsifying performance. SP1 showed the highest essential amino acid content (32.88%), high solubility (53.13%), superior WHC, and improved protein digestibility-corrected amino acid score (PDCAAS). Variation was also evident in antinutritional factors, including trypsin inhibitor (3.33 to 3.36 TIU/mg) and phytic acid (0.52 to 0.62 g/kg). Principal component analysis revealed that SP2 and SP4 clustered with PDCAAS, WHC, and amino acid profiles, whereas SP8 clustered near antinutritional factors and away from solubility. Correlation analysis showed that solubility was negatively correlated with β-sheet content but positively correlated with turbidity; EAA was positively associated with PDCAAS. These distinct functional and nutritional profiles support the rational selection of soybean varieties for products requiring high protein digestibility (e.g., nutritional beverages), strong emulsification (e.g., dressings, plant-based meats), high solubility, and higher EAA. Overall, these findings provide insight into protein quality prediction and future breeding strategies.