Genome-wide analysis of gene expression to distinguish photoperiod-dependent and -independent flowering in Brassicaceae

Photoperiod is the most important environmental cue for the regulation of flowering time, a highly important agronomic trait for crop productivity. To help elucidate the photoperiodic control of flowering in Brassicaceae, we performed microarray experiments using species-specific oligo-arrays with the long day (LD) plant Arabidopsis thaliana and the photoperiod-independent plant rapid cycling Brassica rapa (RCBr). Enrichment analysis of the gene ontologies of differentially expressed genes (DEGs) did not uncover clear differences in gene expression between photoperiod-dependent and -independent plants. Most genes that were up-regulated under LD conditions in Arabidopsis were also up-regulated in RCBr. In addition, most genes associated with light signaling and the circadian clock showed similar expression patterns between Arabidopsis and RCBr, implying that most components known to be key regulators in the photoperiodic flowering pathway are not responsible for the photoperiod independence of RCBr. Nonetheless, we identified one clock-associated gene, PSEUDO-RESPONSE REGULATOR9 (PRR9), as a candidate gene explaining the photoperiod independence of RCBr. The mechanism underlying the role of PRR9 in photoperiodic control and genomic polymorphisms should be further explored using different B. rapa species.