Cultivated soybeans have undergone many transformations during domestication. In this study, we report a comprehensive assessment of the evolution of gene co-expression networks based on the analysis of 40 transcriptomes from developing soybean seeds in cultivated and wild soybean accessions. We identified 2,680 differentially expressed genes during seed maturation and established two cultivar-specific gene co-expression networks. Through analysis of the two networks and integration with quantitative trait locus data, we identified two potential key drivers GA20OX and NFYA for seed trait formation. GA20OX encodes an enzyme in a rate-limiting step of GA biosynthesis, and NFYAencodes a transcription factor. Overexpression of the GA20OX and NFYA enhanced seed size/weight and oil contents respectively in seeds of transgenic plants. The two genes showed significantly higher expressions in cultivated soybeans than those in wild soybeans, and the increases in expression were associated with the genetic variations in the promoter region of the two genes. Moreover, the expressions of the GA20OX and NFYAin seeds of soybean accessions correlated with seed weight and oil contents respectively. Our study reveals transcriptional adaptation during soybean domestication and may identify a mechanism of selection by expression for seed trait formation, providing strategies for future breeding practice. 

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