Genome-wide identification of novel internal control genes for normalization of gene expression during various stages of development in rice

An internal control gene with highly uniform expression throughout the experimental conditions is required for accurate and reliable gene expression results. However, no gene can serve as a universal internal control, implying the need for identification of most suitable internal control gene(s) for experimental conditions being analyzed. In an earlier study, we identified UBQ5 and eEF1-α as the most suitable internal control genes by validating the expression of ten housekeeping genes in rice. The aim of this study was to identify the most suitable novel internal control genes at the whole genome level for normalization of gene expression during various developmental stages in rice, the model crop plant. A systematic analysis of the whole genome microarray data for various stages of vegetative and reproductive development in rice was performed. Several novel internal control genes have been identified, which display highly uniform expression levels in all the developmental stages analyzed and outperform many traditional internal control genes. The expression of these genes ranges from low to very high, which make them suitable for normalization of gene expression over a wide range of transcript levels. The expression stability of the novel genes identified has also been validated by geNORM and NormFinder softwares. The novel genes with highly uniform expression identified in this study can be used for more accurate normalization of transcript levels during various developmental stages in rice and should enable the detection of biologically significant changes in gene expression.