Over the past decade, candidate gene approaches have become increasing popular as a means to identify and characterize genes associated with the agronomically important traits in crop species. The studies outlined in this dissertation describe an attempt to elucidate the molecular basis of two important traits related to soybean seed quality through the implementation of this approach.

Soybean germplasm possessing a high stearic acid (18:0) content is favorable for meeting the demands for oxidatively stable vegetable oils that don’t require hydrogenation, a process that generates undesirable trans fatty acids. We isolated a novel Δ⁹-stearoyl-ACP-desaturase gene, designated SACPD-C, whose enzymatic function serves to convert stearic acid (18:0) to oleic acid (18:1) specifically during seed development. SACPD-C was found to be mutated in two independent high stearic acid soybean lines, A6 and FAM94-41. A molecular marker was generated that can distinguish the mutant SACPD-C gene in FAM94-41 and can thus serve as a useful tool in introducing the trait into elite germplasm using marker assisted selection.

Lowering the phytic acid levels in soybeans would not only enhance the nutritional value of the seed for its use as livestock feed, but also help reduce problems associated with phosphorus pollution of soils and groundwater. We applied a candidate gene approach to identify genes responsible for one low phytic acid soybean germplasm G03PHY-443. Comparison of myo-inositol and myo-inositol phosphate intermediates between the wildtype and mutant lines suggested that the mutation occurs at an early step of the phytic acid biosynthetic pathway. Biochemical assays of phosphatidylinositol kinase and diacylglycerol kinase activities suggested that the lipid dependent branch of the phytic acid metabolic pathway may actually be upregulated in the mutant G03PHY-443 germplasm. Even more surprising, analysis of what we considered the three best candidate genes failed to reveal any perturbation that could count for the reduced phytic acid phenotype. Cumulatively, the results from this study enhanced our understanding of phytic acid biosynthesis in soybean seed and suggested that nonconvertional gene mutations are responsible for the low accumulations of the compound in line G03PHY-443.