There has been significant interest in soybean oil, fatty acid, and sugar composition to develop new value-added soybean products. Thus, compositional analysis is critical for developing value-added soybeans. In the present study, we showed simple screening tools (near infrared spectroscopy (NIR) and high-performance thin layer chromatography (HPTLC)) coupled with multivariate analysis for the sample classification of 14 soybeans as a proof-of-concept. We further determined major non-polar and polar metabolites responsible for differences between different soybeans using gas and ion chromatography. These differences in soybean profiles were attributed to lower levels of total oil content in wild soybeans (~9%) versus cultivated soybeans (16%–22%). In addition, higher levels of linolenic acid (~17%) and stachyose (~53%) were determined in wild type, whereas higher levels of oleic acid (~19%) and sucrose (~59%) were detected in cultivated soybeans. Interestingly, one cultivated soybean had a desirable sugar profile with a high amount of sucrose (86%) and a low abundance of stachyose (9%). The correlation studies showed a positive correlation between oil and soluble sugars (R2
= 0.80) and negative correlations between methyl linolenate and soluble sugars (R2
= −0.79), oil (R2
= −0.94), and methyl oleate (R2
= −0.94) content. Both polar and non-polar metabolites showed significant differences in wild and cultivated soybeans.
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