Elucidating the Field Transcriptome of Rice

Understanding the function and regulation of all the rice genes essential for vegetative and reproductive growth is one of the ultimate goals of cereal genomics. To address this goal, we analyzed the rice transcriptome encompassing the entire developmental cycle from transplanting to harvesting in order to establish a profile of the global transcriptional changes triggered by exogenous and endogenous signals under natural field conditions. This large large-scale gene expression profiling strategy clarified the tissue as well as growth-stage specificifity of gene expression signatures across the vegetative and reproductive organs at various stages of development. A gene expression profiling database (RiceXPro) and a co-expression network database (RiceFREND) were developed as resources for visualization and analysis of expression profiles. Additionally, a statistical modeling approach based on the gene expression data and the corresponding atmospheric data was used to predict the genome-wide transcriptional response in accordance with the changes in various environmental conditions. A comprehensive field transcriptome of rice could lead to better understanding of the genomic basis of critical processes that determine productivity and yield improvement of cereal crops.