Soybean is one of the important economic crops, which supplies a great deal of vegetable oil and proteins for human. The content of nutrients in different soybean seeds is different, which is related to the expression of multiple genes, but the mechanisms are complicated and still largely uncertain. In this study, to reveal the possible causes of the nutrients difference in soybeans A7 (containing low oil and high protein) and A35 (containing high oil and low protein), RNA-seq technology was performed to compare and identify the potential differential expressed genes (DEGs) at different seed developmental stages. The results showed that DEGs mainly presented at the early stages of seeds development and more DEGs were up-regulated at the early stage than the late stages. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEGs have diverged in A7 and A35. In A7, the DEGs were mainly involved in cell cycle and stresses, while in A35 were the fatty acids and sugar metabolism. Specifically, when the DEGs contributing to oil and protein metabolic pathways were analyzed, the differences between A7 and A35 mainly presented in fatty acids metabolism and seeds storage proteins (SSPs) synthesis. Furthermore, the enzymes, fatty acid dehydrogenase 2, 3-ketoacyl-CoA synthase and 9S-lipoxygenase, in the synthesis and elongation pathways of fatty acids, were revealed probably to be involved in the oil content difference between A7 and A35, the SSPs content might be due to the transcription factors: Leafy Cotyledon 2 and Abscisic acid-intensitive 3, while the sugar transporter, SWEET10a, might contribute to both oil and protein content differences. Finally, six DEGs were selected to analyze their expression using qRT-PCR, and the results were consistent with the RNA-seq results. Generally, the study provided a comprehensive and dynamic expression trends for the seed development processes, and uncovered the potential DEGs for the differences of oil in A7 and A35.

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