Assessing and Implementing Value-Added Soybean Innovations in the Soybean Meal and Food Industry

Abstract

Soybean (Glycine max [L.] Merr.) is a vital global crop for food and feed, but its value is constrained by consumer-driven quality traits and the presence of trypsin inhibitors (TIs) - antinutritional proteins that impair protein digestion in monogastric animals. This study employed a multifaceted approach combining phenotyping, genome editing, and association mapping to enhance soybean quality. First, we developed near-infrared reflectance spectroscopy (NIR) calibration models for the rapid estimation of total TI and Kunitz TI content in seeds and meals. Validated against HPLC data, these models demonstrated high predictive accuracy and offer a scalable tool for breeding and industry applications. Second, the CRISPR/Cas9-mediated knockout of KTI1 and KTI3 in the cultivar Williams 82 produced the low-TI line VTI5-26. Across multi-location field trials, VTI5-26 maintained reduced TI levels without compromising yield, maturity, or pest and disease resistance, and displayed significantly improved resistance to soybean cyst nematode. Third, a genome-wide association study (GWAS) of 146 natto soybean accessions identified novel SNPs associated with the key quality traits—water absorption, seed coat deficiency, cooked color, protein, and oil content—many of which were linked to stress-responsive gene networks. Collectively, these efforts illustrate how precision breeding and phenotyping tools can accelerate the development of soybean cultivars with enhanced nutritional and functional qualities.