Dynamics of the gene regulatory networks of the inner and rosette leaves in Brassica rapa

Abstract

Chinese cabbage (Brassica rapa ssp. pekinensis) is one of the most important crops in Asian countries. In the heading formation of Chinese cabbage, differential regulation of production and growth between the inner and rosette leaves is the most important developmental process. In general, it is well known that the developmental process is determined by complex interactions among genes. Therefore, it is important to understand the developmental process of Chinese cabbage by studying the crucial genes involved in the cells constituting the inner and rosette leaves and to clarify their dynamic characteristics. A recent study showed that the gene expression patterns of inner and rosette leaves are quite different but the tissue-specific gene regulatory networks of the two types of leaves are still largely unknown. Based on the RNA sequencing profiles of inner, rosette, and young leaves from Chinese cabbage and the gene regulatory network of Arabidopsis thaliana, we reconstructed tissue-specific active subnetworks of inner and rosette leaves of Chinese cabbage. Then, we analyzed the structural and functional characteristics of the two tissue-specific active subnetworks. Notably, we found that coherent feedforward loops were prominent in the inner leaf, whereas incoherent feedforward loops were abundant in the rosette leaf. By exploring the dynamic and functional characteristics of the feedforward loops, we found that the coherent feedforward loops are necessary for maintaining the molecular states, whereas the incoherent feedforward loops are crucial for adaptation. Overall, we concluded that the exclusive pattern of the network motifs is closely associated with the biological traits of each tissue.