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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Agricultural Systems Laboratory » Research » Publications at this Location » Publication #353691
Title: Co-Expression analysis of miRNAs and target NBS-LRR genes in Cucumis sativus

Author
item ZAHOOR, SARWAT - University Of Agriculture - Pakistan
item CHEEMA, HAFIZA MASOOMA - University Of Agriculture - Pakistan
item KHAN, ASIF - University Of Agriculture - Pakistan
item REHMAN, MUHAMMAD - University Of Agriculture - Pakistan
item Mattoo, Autar

Submitted to: International Journal of Agriculture and Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/18/2017
Publication Date: 1/1/2018
Citation: Zahoor, S., Cheema, H., Khan, A.A., Rehman, M.N., Mattoo, A.K. 2018. Co-Expression analysis of miRNAs and target NBS-LRR genes in Cucumis sativus. International Journal of Agriculture and Biology. 20(1):100-108. https://doi.org/10.17957/IJAB/15.0441.
DOI: https://doi.org/10.17957/IJAB/15.0441

Interpretive Summary: In recent years, it has become apparent that small cellular RNAs, called miRNA, regulate the plant developmental machinery. Whether these miRNAs play a significant role in preparing plants to cope with biotic stress is still being determined. In this study, the role of miRNAs in the regulation of plant defense R-proteins was ascertained. Forty miRNAs were retrieved from the miRBase database and analyzed further using bioinformatics tools. In collaboration with scientists in Pakistan, we dissected the co-expression of miRNAs and NBS-LRR-containing R-protein genes in non-infected (control) and infected tissue using cucumber as a model plant. All NBS-LRR genes were highly expressed in the infected tissue and miRNA was not detected. In control plants, mature miRNAs were detected while there was no expression of NBS-LRR genes. These results suggest that the identified miRNAs could be involved in downregulating/silencing the target NBS-LRR genes in the absence of infection. The tight control of transcription by miRNAs might give way upon infection, and the plant can then combat the infection with the help of the ‘R’ genes. These findings are important to plant pathologists, agriculture scientists, industry and academicians for containing plant diseases.

Technical Abstract: Plants react against their biological enemies by activating the innate immune system. Their defense system comprises of various R-protein, which usually contain NBS-LRR domain. MicroRNAs (miRNAs) are important molecules of 2nd layer of plant defense and play pivotal role behind the scene. To support such endeavors, this study was carried out to dissect the co-expression of miRNAs and NBS-LRR genes upon viral infection. Bioinformatics prediction of miRNAs which were targeting the NBS-LRR genes was conducted by TAPIR and miRU softwares. After analyzing the results from two software tools only those miRNAs were selected for co-expression analysis, whose interaction with NBS-LRR genes was predicted by both softwares. The results revealed that the complementation of only ten miRNAs with NBS-LRR genes was affirmed by two tools used in this study. The expression of miRNAs and NBS-LRR genes was evaluated through RT-PCR from CMV (cucumber mosaic virus) infected and non-infected plants. All NBS-LRR genes showed high levels of expression in response to viral infection, while miRNA couldn’t be detected by stem loop RT-PCR in the infected plants. But mature miRNAs were detected in the control plants with no expression of NBS-LRR genes. After analyzing the results, it was concluded that these miRNAs might be involved in downregulating/silencing the target NBS-LRR genes in the absence of any infection. This tight control of transcription by miRNAs might be relaxed upon infection, so that a plant can combat its enemy with the help of resistance genes.