The effect of cadmium on the microRNAome, degradome and transcriptome of rice seedlings

The damage induced by the uptake of cadmium (Cd) into the rice plant is of growing concern. Although many micro-RNAs (miRNAs) and their target genes have been identified in experiments designed to elucidate the molecular impact of exposure to Cd, as yet there has been no attempt to integrate data from sequencing the microRNAome, the degradome and the transcriptome of rice plants exposed to Cd. Here, the abundance of 40 miRNAs was shown to be substantially altered as response to Cd exposure. Of those, 38 (belonging to 22 known miRNA families) were already documented in rice and two (PC-3p-38247_129 and PC-3p-102187_26) are novel. The abundance of 18 genes differentially transcribed as a result of Cd exposure was found to be inversely correlated to that of 18 of the Cd-responsive miRNAs. The majority of the target genes encoded transcription factors, including ARF13, SCL6, various SPLs, NFYA6, GAMYB, and various NACs which encode proteins that participate in signal transduction and abiotic stress resistance. In all, the present study established a fundamental basis for evaluating the regulatory role of miRNA and their targets in plant exposure to Cd stress.