A mutation in the gene encoding the raffinose synthase 2 enzyme, RS2, in soybean, Glycine max (L.) Merr., is associated with a reduced raffinose and stachyose seed phenotype. Soybean homozygous for a mutant allele of the RS2 gene which encodes an amino acid change to isoleucine at position 107 of the enzymes amino acid sequence exhibit significantly reduced seed raffinose and stachyose content, and increased seed sucrose content. Nucleic acid samples of soybean may be assayed for the presence of this mutant allele, and soybean containing the allele may be selected for breeding to generate reduced raffinose and stachyose soybean lines. Alternatively, the mutation may be detected by analysis of the RS2 enzyme produced in the soybean to determine the presence of either an isoleucine or a threonine at amino acid 107. Molecular markers have been developed for detecting the presence or absence of the mutant allele.
