Gene expression profiling of reactive oxygen species (ROS) and antioxidant defense system following Sugarcane mosaic virus (SCMV) infection

Abstract

Background Viruses are infectious pathogens, and plant virus epidemics can have devastating consequences to crop yield and quality. Sugarcane mosaic virus (SCMV, belonging to family Potyviridae) is one of the leading pathogens that affect the sugarcane crop every year. To combat the pathogens’ attack, plants generate reactive oxygen species (ROS) as the first line of defense whose sophisticated balance is achieved through well-organized antioxidant scavenging pathways. Results In this study, we investigated the changes occurring at the transcriptomic level of ROS associated and ROS detoxification pathways of SCMV resistant (B-48) and susceptible (Badila) sugarcane genotypes, using Saccharum spontaneum L. genome assembly as a reference genome. Transcriptomic data highlighted the significant upregulation of ROS producing genes such as NADH oxidase, malate dehydrogenase and flavin-binding monooxygenase, in Badila genotype after SCMV pathogenicity. To scavenge the ROS, the Badila genotype illustrated a substantial enhancement of antioxidants i.e. glutathione s-transferase (GST), as compared to its resistant counterpart. GST is supposed to be a key indicator of pathogen attacks on the plant. A remarkably lower GST expression in B-48, as compared to Badila, indicated the development of resistance in this genotype. Additionally, we characterized the critical transcription factors (TFs) involved in endowing resistance to B-48. Among these, WRKY, AP2, NAC, bZIP, and bHLH showed enhanced expression in the B-48 genotype. Our results also confirmed the linkage of transcriptomic data with the enzymatic and qPCR data. The estimation of enzymatic activities for superoxide dismutase, catalase, ascorbate peroxidase, and phenylalanine ammonia-lyase supported the transcriptomic data and evinced higher resistance in B-48 genotype. Conclusion The current study supported the efficiency of the B-48 genotype under SCMV infection. Moreover, comparative transcriptomic data has been presented to highlight the role of significant transcription factors conferring resistance to this genotype. This study provides an in-depth knowledge of the expression profiling of defense mechanisms in sugarcane.

Transcriptomics of Biostimulation of Plants Under Abiotic Stress

“…SnRK2.2 is discussed above. MDH encodes malate dehydrogenase, this enzyme is critical in malate metabolism and is related in ROS producing genes ( Akbar et al, 2020 ). WRKY TF family are associated to transduction of stress signaling and play a major role in plant defense to abiotic and biotic stress ( Li et al, 2020c ).…”

Multiomic investigation of sugarcane mosaic virus resistance in sugarcane

“…The copyright holder for this preprint this version posted August 18, 2022. ; https://doi.org/10.1101/2022.08.18.504288 doi: bioRxiv preprint SCMV indeed affects the regulation of genes and proteins involved in these processes (Wu et al, 2013;Chen et al, 2017;Akbar et al, 2020;da Silva et al, 2020). Notably, the results of our coexpression network analyses indicate that the expression of genes identified in the present study as being associated with SCMV resistance are also associated with those controlling such processes; thus, those genes possibly play roles in their regulation during viral infection.…”

“…To do so, RNA-Seq data was employed to annotate the markers identified as being associated with resistance and to construct coexpression networks to further investigate biological processes linked to them. Although RNA-Seq data from sugarcane plants infected with SCMV are available (Akbar et al ., 2020), they include data from only two biological replicates, which equates to a very low sample number for network modeling—the WGCNA developers recommend a minimum of 15 samples to avoid noise and biologically meaningless inferences (Langfelder and Horvath, 2017). The summarization of GO terms from genes close to markers directly associated with SCMV resistance revealed a few general processes previously associated with responses to this virus; these included stress responses and the regulation of transcription and translation (Akbar et al ., 2020; da Silva et al ., 2020).…”

“…According to the results of our analysis, biological processes enriched in SCMV resistance-associated modules included stress responses, regulation of transcription and translation, and a process that has long been known to be affected by SCMV infection (Irvine, 1971) but has not been featured by the analysis of genes directly associated with resistance— photosynthesis. Recent transcriptomic and proteomic studies have shown that infection by SCMV indeed affects the regulation of genes and proteins involved in these processes (Wu et al ., 2013; Chen et al ., 2017; Akbar et al ., 2020; da Silva et al ., 2020). Notably, the results of our coexpression network analyses indicate that the expression of genes identified in the present study as being associated with SCMV resistance are also associated with those controlling such processes; thus, those genes possibly play roles in their regulation during viral infection.…”

The Potential of Molecular Indicators of Plant Virus Infection: Are Plants Able to Tell Us They Are Infected?

“…In addition to sRNA, specific plant host genes may also be useful as molecular markers for virus infection. Recent studies have utilised microarray, transcriptomics, proteomics and metabolomics approaches to identify host genes and molecular signatures that differentially respond to virus infections [35][36][37][38][39][40][41][42]. In Arabidopsis thaliana, suppressor of gene silencing 3 (AtSGS3) has been reported to have a role in the RNA pathway to amplify the dsRNA signal [43] and involved in defence responses against several plant viruses [44].…”