Isoflavone contents are one of the most important quality traits in soybean. Although there has been a large amount of research focusing on isoflavone biosynthesis in plants, several questions are still unclear, including 1) What are the accumulation patterns of isoflavones accumulation during seed development; 2) Which genes are the most major genes regulating isoflavone synthesis; 3) What are the dynamic molecular networks modulating isoflavones accumulation in developing seed. Moreover, most of reported genetic factors of isoflavones in soybean are QTL rather than QTG, which could not be utilized to molecular breeding directly. To answer these questions, here we selected 10 representative lines from a RIL population, and combined the developmental dynamic transcriptome analysis and meta-analysis, and integrated mutiple algorithms. Finally, we 1) characterized the dynamic accumulation and regulation pattern of isoflavones in physiological and gene expression level; 2) obtained several major genes affecting the accumulation of isoflavones free from the environments; 3) discussed the dynamic molecular patterns regulating isoflavones accumulation in developing soybean. The results could promote the understandings on the biosynthesis and regulation of isoflavones physiological and molecular level.
