Primary metabolite contents are correlated with seed protein and oil traits in near-isogenic lines of soybean

Soybean (Glycine max [L.] Merr.) is an important source of human dietary protein and vegetable oil. A strong negative correlation between protein and oil contents has hindered efforts to improve soybean seed quality. The metabolic and genetic bases of soybean seed composition remain elusive. We evaluated metabolic diversity in a soybean near-isogenic line (NIL) population derived from parents (JD12 and CMSD) with contrasting seed oil contents. Using GC-TOF/MS, we compared seed primary metabolites of high protein/low oil lines, low protein/high oil lines, and their parents. Principal-components analysis showed that metabolic profiles of all progeny lines could be discriminated based on protein and oil contents. Univariate analysis revealed wide variation and transgressive segregation of metabolites in the population. Twenty-eight annotated metabolites, in particular free asparagine, free 3-cyanoalanine, and L-malic acid, were correlated with seed protein content or seed oil content or seed protein and oil content. These results shed light on the metabolic and genetic basis of soybean seed composition.