Identification of Subtle Differences in the Physiological Quality of Commercial Soybean Seed Lots Using Shotgun Proteomics During Germination

Soybean seeds with similar germination rates may exhibit subtle differences in physiological quality, influencing field performance and storage longevity. This study used a shotgun proteomics approach to characterize the proteomic profile of two commercial soybean seed lots (higher- and lower-quality) during germination, aiming to identify biomarkers associated with vigor and deterioration. Proteins were analyzed across three germination phases: imbibition (Phase I, 0.5 h), metabolic activation (Phase II, 20 h), and radicle protrusion (Phase III, 51 h). A total of 777 proteins were identified, and of these differentially abundant proteins (DAPs), the following totals were detected: 12 in Phase I, 17 in Phase II, and 28 in Phase III. In Phase I, ribosomal proteins were more abundant in high-quality seeds, indicating efficient translation and preparation for germination. Conversely, in Phase III, low-quality seeds showed increased levels of storage proteins and stress-response proteins, including alcohol dehydrogenase (ADH), heat shock proteins, and annexins, reflecting delayed germination and more deterioration. These findings highlight the dynamic nature of protein expression during germination and demonstrate the potential of proteomics to detect subtle differences in physiological quality. The identified biomarkers provide insights for seed quality assessment and offer practical applications for improving classification and management of commercial soybean seed lots.