Computational identification of maize miRNA and their gene targets involved in biotic and abiotic stresses

Plant interactions with biotic and abiotic stresses are complex and entail changes at the transcriptional, cellular and physiological level. MicroRNAs (miRNAs) are small (similar to 20-24 nt), non-coding RNAs that play a vital role in wide range of biological processes involved in regulation of gene expression through translation inhibition or degradation of their target mRNAs during stress conditions. Therefore, identification of miRNAs and their targets are of immense value in understanding the regulatory networks triggered during stress. Advancement in computational approaches has opened up ways for the prediction of miRNAs and their possible targets with functional pathways. Our objective was to identify miRNA and their potential targets involved in both biotic and abiotic stresses in maize. A total of 2,019,524 downloaded ESTs from dbEST were processed and trimmed by Seq Clean. The program trashed 264,000 and trimmed 284,979 sequences and the resulting 1,755,534 sequences were submitted for clustering and assembled to RepeatMasker and TGICL. A total of 30 miRNAs were found to hybridize with the potential targets of gene families such as CoA ligase, lipoxygenase 1, Terpenoideyclases, Zn finger, transducing, etc. Ten of the identified miRNAs targeted cytochrome c1 family. Zm_miR23 class targeted 11 different genes. The identified targets are involved in the plant growth and development during biotic and abiotic stresses in maize. These miRNAs may be further used for functional analysis. Furthermore, four and two of the miRNA targets were validated in response to waterlogging tolerance and southern leaf blight resistance, respectively, to understand the miRNA-assisted regulation of target miRNAs. The functional annotation of the predicted targets indicated that these stress-responsive miRNAs regulate cellular function; molecular function and biological process in maize at the post-transcriptional level. The present results have paved way towards better understanding the role of miRNAs in the mechanism of stress tolerance in maize.