Transcriptome-wide identification of the genes responding to replanting disease in Rehmannia glutinosa L. roots

The development of the medicinal plant Rehmannia glutinosa L. are severely declined when are replanted on the soil of the preceding crops being themselves. The biological basis of this so called "replanting disease" is unknown. Here, we have exploited the parallel sequencing capacity of both RNA-seq and DGE technology to ascertain what genes are responsive to the replanting disease in roots of R. glutinosa. RNA-seq analysis generated 99,708 non-redundant consensus sequences from the roots of the first year (R1) and the second year (R2) replanted R. glutinosa plants. From this set, a total of 48,616 transcripts containing a complete or partial encoding region was identified. Based on this resource, two DGE tag libraries were established to capture the transcriptome differences between the R1 and R2 libraries. Finally, a set of 2,817 (1,676 up- and 1,141 down-regulated) differentially transcribed genes was screened, and 114 most strongly differentially transcribed genes were identified by DGE analysis between first year and replanted plants. Furthermore, a more detailed examination of 16 selected candidates was carried out by qRT-PCR. The indication was that replanting could promote Ca(2+) signal transduction and ethylene synthesis, resulting in forming of the replanting disease. We analyzed the biomass indexes of replanted R. glutinosa roots by irrigating Ca(2+) signal blockers. The results suggested that the alleviation of the disease impairment could be the decrease of Ca(2+) signal transduction. This study provided a global survey of the root transcriptome in replanted R. glutinosa roots at the tuberous root expansion stage. As a result, a number of candidate genes underlying the replanting disease have been identified.