Validation of Molecular Markers for Low Kunitz Trypsin Inhibitor Content in European Soybean (Glycine max L. Merr.) Germplasm

Trypsin inhibitors (TI) in raw soybean grain, mainly represented by the Kunitz trypsin inhibitor protein (KTI), prevent the normal activity of the digestive enzymes trypsin and chymotrypsin in humans and monogastric livestock. The inactivation of TI is achieved through costly and time-consuming heat treatment. Thermal processing also impairs the solubility and availability of the soybean grain protein. Therefore, the genetic elimination of KTI has been proposed as a suitable alternative to heat treatment. The aim of this study was to screen the collection of European soybean cultivars with six genetic markers (one SSR marker and five SNP markers) previously proposed as tightly linked to the <i>KTI3</i> gene encoding the major Kunitz trypsin inhibitor seed protein of soybean and validate their usability for marker-assisted selection (MAS). The six markers were validated on a subset of 38 cultivars with wide variability in KTI content and in the F₂ and F_3:5 progenies of two crosses between the known high- and low-KTI cultivars. Three genetic markers (SSR Satt228 and two SNP markers, Gm08_45317135_T/G and Gm08_45541906_A/C) were significantly associated with KTI content in a subset of 38 cultivars. Low-KTI alleles were detected in both low- and high-KTI genotypes and vice versa, high-KTI alleles were found in both high- and low-KTI genotypes, indicating a tight but not perfect association of these markers with the <i>KTI3</i> gene. The genetic marker SSR Satt228 showed a significant association with KTI content in the F₂ progeny, while the SNP markers Gm08_45317135_T/G and Gm08_45541906_A/C allowed significant discrimination between progeny with high- vs. low-KTI progenies in the F_3:5 generation. These three markers could be applied in MAS for low-KTI content but not without the additional phenotyping step to extract the desired low-KTI genotypes.