Global gene expression profiles in developing soybean seeds

The gene expression profiles in soybean (Glycine max L.) seeds at 4 stages of development, namely, pod, 2-mm bean, 5-mm bean, and full-size bean, were examined by DNA microarray analysis. The total genes of each sample were classified into 4 clusters based on stage of development. Gene expression was strictly controlled by seed size, which coincides with the development stage. First, stage specific gene expression was examined. Many transcription factors were expressed in pod, 2-mm bean and 5-mm bean. In contrast, storage proteins were mainly expressed in full-size bean. Next, we extracted the genes that are differentially expressed genes (DEGs) that were extracted using the Rank products method of the Bioconductor software package. These DEGs were sorted into 8 groups using the hclust function according to gene expression patterns. Three of the groups across which the expression levels progressively increased included 100 genes, while 3 groups across which the levels decreased contained 47 genes. Storage proteins, seed-maturation proteins, some protease inhibitors, and the allergen Gly m Bd 28K were classified into the former groups. Lipoxygenase (LOX) family members were present in both the groups, indicating the multi-functionality with different expression patterns.

► The gene expression profiles in soybean seeds at 4 stages of development were examined by DNA microarray analysis.
► Gene expression was strictly controlled by seed size, which coincides with the development stage.
► In early developing stage, many ranscription factors were expressed.
►  Genes drastically changing expression were extracted by hierarchical analysis with ‘hclust’ function.
► The expressions of storage proteins, seed maturation proteins and some protease inhibitors increased as seed grew.