Transcriptome Analysis of Diurnal Gene Expression in Chinese Cabbage

Abstract

Plants have developed timing mechanisms that enable them to maintain synchrony with daily environmental events. These timing mechanisms, i.e., circadian clocks, include transcriptional/translational feedback loops that drive 24 h transcriptional rhythms, which underlie oscillations in protein abundance, thus mediating circadian rhythms of behavior, physiology, and metabolism. Circadian clock genes have been investigated in the diploid model plant Arabidopsis thaliana. Crop plants with polyploid genomes—such as Brassica species—have multiple copies of some clock-related genes. Over the last decade, numerous studies have been aimed at identifying and understanding the function of paralogous genes with conserved sequences, or those that diverged during evolution. Brassica rapa’s triplicate genomes retain sequence-level collinearity with Arabidopsis. In this study, we used RNA sequencing (RNAseq) to profile the diurnal transcriptome of Brassica rapa seedlings. We identified candidate paralogs of circadian clock-related genes and assessed their expression levels. These genes and their related traits that modulate the diurnal rhythm of gene expression contribute to the adaptation of crop cultivars. Our findings will contribute to the mechanistic study of circadian clock regulation inherent in polyploidy genome crops, which differ from those of model plants, and thus will be useful for future breeding studies using clock genes.