Sugarcane mosaic virus mediated changes in cytosine methylation pattern and differentially transcribed fragments in resistance-contrasting sugarcane genotypes

Abstract

Sugarcane mosaic virus (SCMV) is the causal agent of sugarcane mosaic disease (SMD) in Brazil; it is mainly controlled by using resistant cultivars. Studies on the changes in sugarcane transcriptome provided the first insights about the molecular basis underlying the genetic resistance to SMD; nonetheless, epigenetic modifications such as cytosine methylation is also informative, considering its roles in gene expression regulation. In our previous study, differentially transcribed fragments (DTFs) were obtained using cDNA-amplified fragment length polymorphism by comparing mock- and SCMV-inoculated plants from two sugarcane cultivars with contrasting responses to SMD. In this study, the identification of unexplored DTFs was continued while the same leaf samples were used to evaluate SCMV-mediated changes in the cytosine methylation pattern by using methylation-sensitive amplification polymorphism. This analysis revealed minor changes in cytosine methylation in response to SCMV infection, but distinct changes between the cultivars with contrasting responses to SMD, with higher hypomethylation events 24 and 72 h post-inoculation in the resistant cultivar. The differentially methylated fragments (DMFs) aligned with transcripts, putative promoters, and genomic regions, with a preponderant distribution within CpG islands. The transcripts found were associated with plant immunity and other stress responses, epigenetic changes, and transposable elements. The DTFs aligned with transcripts assigned to stress responses, epigenetic changes, photosynthesis, lipid transport, and oxidoreductases, in which the transcriptional start site is located in proximity with CpG islands and tandem repeats. Real-time quantitative polymerase chain reaction results revealed significant upregulation in the resistant cultivar of aspartyl protease and VQ protein, respectively, selected from DMF and DTF alignments, suggesting their roles in genetic resistance to SMD and supporting the influence of cytosine methylation in gene expression. Thus, we identified new candidate genes for further validation and showed that the changes in cytosine methylation may regulate important mechanisms underlying the genetic resistance to SMD.

Turnip mosaic virus manipulates DRM2 expression to regulate host CHH and CHG methylation for robust infection

“…Previous studies showed that the infection of potyviruses, e.g., TuMV and SCMV caused comprehensive changes of DNA methylation in host plant (da Silva et al 2020;Corrêa et al 2020). In this study, we further analyzed the methylome change in virus-infected cells to insight the arms race between virus and host at the DNA methylation level.…”

Multiomic investigation of sugarcane mosaic virus resistance in sugarcane

“…Similarly, a heavy metal-associated isoprenylated plant protein was shown to interact with the Pomovirus movement protein, affecting virus long-distance movement (Cowan et al ., 2018). Interestingly, transcripts of two chaperones and a heavy metal-associated isoprenylated protein differentially accumulated in response to SCMV in sugarcane (da Silva et al, 2020). Another protein annotated in the present study that has been shown to interact with the potyviral movement protein P3N-PIPO is a beta-glucosidase, possibly facilitating viral spread through the plant (Song et al ., 2016); beta-glucosidase genes have also been found in QTLs for resistance to SCMV and other potyviruses (Gustafson et al ., 2018; Rubio et al ., 2019).…”

“…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.…”

“…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).…”