Researchers discover novel and valuable plant gene modules from large-scale RNA-seq samples

The complex cellular networks underlying phenotypes are formed by the interacting gene modules. Building and analyzing genome-wide and high-quality Gene Co-expression Networks (GCNs) is useful for uncovering these modules and understanding the phenotypes of an organism.

Using large-scale RNA-seq samples, researchers at the Chinese Academy of Sciences constructed high coverage and confident GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed gene modules. Taking rice as an example, they discovered many interesting and valuable modules, for instance, pollen-specific modules and starch biosynthesis module. The researchers explored the regulatory mechanism of modules and revealed synergistic effects of gene expression regulation. In addition, they discovered that the modules conserved among plants participated in basic biological processes, whereas the species-specific modules were involved in spatiotemporal-specific processes linking genotypes to phenotypes. This study suggests gene regulatory relationships and modules relating to cellular activities and agronomic traits in several model and crop plants, and thus providing a valuable data source for plant genetics research and breeding.

An example of Module #30 related to panicle flower in rice


A, Subnetwork of Module #30. Red nodes indicate the known genes associating with panicle flower development collected in Q-TARO database and literature; Pink nodes represent the genes which may be involved in panicle flower development recorded in; Light green nodes indicate that the genes are function unknown or annotated with irrelevant functions; The size of node was proportional to the number of connected genes. B, Violin plot of expression of module genes in different types of tissues. We can observe that the genes in this module was highly expressed in reproductive organs.

Availability: The analyzed gene expression data, reconstructed GCNs, modules and detailed annotations can be freely downloaded from

Yu H, Lu L, Jiao B, Liang C. (2018) Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples. Bioinformatics [Epub ahead of print]. [abstract]

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