1. Gene networks for Arabidopsis & plants

OverviewGenes never work alone. They interact with each other and form gene modules to execute biological functions. Gene network captures the functional interaction between genes and has become an essential tool to understand biological systems. Large biological datasets have accumulated explosively in the past decade. These Big Data provide golden opportunities for gene networks analysis and open a new era of biological discovery.

We have constructed a gene network AtGGM2014 for the model plant species Arabidopsis thaliana, using a large amount of gene expression data. The network contains 18,068 genes and is divided into 622 gene modules, as shown in the right figure.

2. Gene modules functioning in various plant processes

Many gene modules were identified from the plant genes networks. These gene modules function in a variety of development, metabolism, stress response, hormonal signaling, and house-keeping pathways. Shown here are an overview of the network.  Shown here on the right are a handful of examples. Besides known genes, these modules contain uncharacterized genes that serve as ideal candidates for future functional studies. These modules are valuable resources for plant systems biology research. A software was developed to query and utilize the network. It can be downloaded from here.

Currently, we are studying how gene expression are regulated within the modules. We are also working on a group of stress-related gene modules and trying to identify novel regulators.

3. Plant nutrients uptake & utilization

We are using the gene modules identified from the gene networks to study the molecular mechanisms of nutrients uptake & utilization in plants. As an example, nitrogen uptake and utilization is a complex process involving multiple steps. From the gene networks, we identified gene modules functioning in these different steps, and plan to study the key genes’ functions within these modules. We hope our findings can help to improve crops’ nutrient use efficiency.

4. Natural variation in plant stresses response

Being sessile organisms, plants face many different types of abiotic/biotic stresses throughout their life. They develop diverse strategies to counteract these stresses and adapt to their native growth habitat. Arabidopsis thaliana is an ideal species to study such adaptation. More than 1,000 different ecotypes of Arabidopsis grow in different areas around the world (shown in the right figure), each facing different kinds of environmental stresses. The ecotypes from northern Europe are more tolerant to cold stress, while those from central Asia are more resistant to drought stress. We are using the Arabidopsis gene network and its modules as tools to study the molecular mechanisms responsible for such adaptation. Our ultimate goal is to develop crops with enhanced stress tolerance by leveraging the knowledge learned from Arabidopsis.