Genome-wide mRNA and small RNA transcriptome profiles uncover cultivar- and tissue-specific changes induced by cadmium in Brassica parachinensis

One of the main pathways for cadmium (Cd) transfer from the environment to the humans is through the consumption of leafy vegetables, and Brassica leafy crops tend to be Cd hyper-accumulators. To investigate Brassica response strategies to Cd, two cultivars with different Cd tolerance were used to perform transcriptomic studies under Cd treatments. Genes related to vacuolar sequestration (such as ABCCs and YSL family genes) and detoxification (such as GST, SAT and APS) were up-regulated in both cultivars but exhibited different temporal expression profiles in leaves of the two cultivars, which may underlie their different Cd tolerance. Analyses of microRNAs (miRNAs) and their target genes by small RNA and degradome sequencing not only revealed Cd-induced changes in miRNAs but also implicated the existence of a regulatory cascade involving two miRNAs, bra-miR156 and bra-miR397, and their corresponding targets, SPLs and LACs, in Cd stress responses. This cascade down-regulates the expression of several LACs particularly in roots under Cd stress, and it is proposed to be a mechanism to maintain root growth under Cd stress through regulating cell wall lignification. In addition, Cd induced a drastic reduction of a 22-nt small RNA, the footprint of a pentatricopeptide repeat (PPR) protein on the chloroplast ndhB transcript and the concomitant down-regulation of the ndhB transcript. A global reduction in the expression of PPR genes was found, revealing previously unknown effects of Cd on organellar gene expression. The present findings help uncover the impact of Cd stress on the transcriptome of B. parachinensis and reveal the strategies used by B. parachinensis in dealing with Cd stress. It also provides candidate genes and miRNAs for further investigation.