Differential and developmental stage specific abundance of Zmdreb2a mRNA transcripts under drought stress and root development in Zea mays (L.)

Environmental stress constraints like temperature, drought and salinity affect plant growth, development and productivity negatively. In maize (Zea mays L.) water-deficiency affects flowering, pollination and embryo development. Transgenic plants having drought tolerance is a priority target in maize breeding programs worldwide. Various transcription factors play a key role in plant development and stress management. DRE-Binding Protein 2A (DREB2A) has been shown to play a central role in drought tolerance in Arabidopsis thaliana. The homologue of dreb2a in Zea mays is Zmdreb2a, a well-known transcription factor regulating genes induced under stress conditions. Studies indicated that Zmdreb2a transgenic plants show not only stress tolerance but also growth retardation. It is a major targeted gene for transgenesis to produce drought-tolerant plants. However, to make construct for transgenic plants, there is need to consider functional transcripts and regulating mechanism of Zmdreb2a mRNAs under drought condition. We have analyzed publicly available RNASeq data of leaf meristem, ovary and developing root and used a host of FastQC, Tophat, Cufflinks, Cuffmerge, Cuffdiff and ‘R’ packages to functionally characterize the differentially expressed genes (DEGs). In addition, prediction of protein structure, nuclear localization signals and transactivation domain were performed using cNLS mapper and 9aaTAD prediction tools. Alternative splicing of Zmdreb2a pre-mRNA was shown to be strongly associated with developmental stage and isoforms show fluctuating expression under stress. This study provides putative functional transcripts of Zmdreb2a, and NMD as a regulating mechanism to control their abundance.