A network of rice genes associated with stress response and seed development

Abstract

We used a systematic approach to build a network of genes associated with developmental and stress responses in rice by identifying interaction domains for 200 proteins from stressed and developing tissues, by measuring the associated gene expression changes in different tissues exposed to a variety of environmental, biological, and chemical stress treatments, and by localizing the cognate genes to regions of stress-tolerance trait genetic loci. The integrated data set suggests that similar genes respond to environmental cues and stresses, and some may also regulate development. We demonstrate that the data can be used to correctly predict gene function in monocots and dicots. As a result, we have identified five genes that contribute to disease resistance in Arabidopsis.

Figure 1

Protein–protein interactions detected among rice proteins. Arrows indicate interaction direction between DNA-binding domain fused proteins (thick lined boxes or ovals) and activation domain fused proteins. Dotted boxes indicate that the protein occurs at more than one place on the map. Ovals rather than boxes indicate that a protein fused to the DNA-binding domain did not interact with other proteins. Circular arrows indicate self interactions. Dashed arrows indicate interactions described in published literature but not found in our study. Dotted lines refer to amino acid similarity between proteins. QTL and gene expression data, where available, are noted in each box. Box colors denote functional classification: blue, development; rose, biotic stress; orange, abiotic stress; green, chloroplast; black, undefined role.

Figure 2

Titer of P. syringae in A. thaliana leaves 3 days postinoculation. Error bars are standard deviation.