Predicting Function of Unknown Genes


Recent advances in plant genomics have identified many new genes, but many are of unknown function. Experimental determination of the function of individual genes is difficult because gene duplication occurs frequently among plants so large, functionally redundant gene families are common. Researchers at the DOE Joint BioEnergy Institute have used a phylogenetic (evolutionary relatedness) approach to computationally predict the biological function of individual genes within the very large (1,508-member) rice kinase gene family by combining gene expression data from various rice tissues and different experimental conditions with protein interaction data and looking for similarities. Function could be inferred for genes showing similar patterns in diverse tissues and conditions. Certain members of the kinase gene family regulate the responses of plants to a range of stresses such as drought and pathogens, as well as being involved in other signaling cascades. Rice can be used as a model for bioenergy grass crops such as sorghum and switchgrass, thus integration of gene data from these plants could facilitate functional predictions of genes important for bioenergy-relevant traits.


Jung, K-H., P. Cao, Y-S. Seo, C. Dardick, and P.C. Ronald. 2010. “The Rice Kinase Phylogenomics Database: A Guide for Systematic Analysis of the Rice Kinase Super-family,” Trends in Plant Science 15(11), 595-99.