High-resolution HPLC-MS/MS profiling of group A and group B seed saponins in 711 diverse soybean germplasms

Soybean seeds are rich in saponins, yet their variation across germplasm and environments is poorly explored. We developed an HPLC-MS/MS method to extract and quantify Group A and B saponins and profiled 711 soybean accessions across four environments. Genotype, accession type, ecoregion, seed coat colour, and seed tissue all significantly affected saponin content, with five-fold variation (1376.19-6764.67 μg/g). Group A saponins were dominant (77.5%), led by Ab (46.0%) and Aa (23.0%). Black-seeded accessions showed the highest total saponin content. Moreover, the hypocotyl exhibited high total saponin content (45,230.40 μg/g; 93.5% Group A). Total saponins positively correlated with all constituents (except Af) and with oil, but negatively with protein. Geographical distribution revealed that Northern and Huang Huai-Hai Region accessions had high levels of Group A and total saponins. This study provides comprehensive and novel insights into seed saponin profiles and identifies elite accessions to support breeding and industrial applications.