Identification of maize genes that condition early systemic infection of sugarcane mosaic virus through single-cell transcriptomics

During the early systemic infection of plant pathogens, individual cells can harbor pathogens at various stages of infection, ranging from absent to abundant. Consequently, gene expression levels within these cells in response to the pathogens exhibit significant variability. These variations are pivotal in determining pathogenicity or susceptibility, yet they remain largely unexplored and poorly understood. Sugarcane mosaic virus (SCMV) is a representative member of the monocot-infecting potyviruses with a polyadenylated RNA genome, which can be captured by single-cell RNA sequencing (scRNA-seq). Here, we performed scRNA-seq on SCMV-infected maize leaves during early systemic infection (prior to symptom manifestation) to investigate the co-variation patterns between viral accumulation and intracellular gene expression alterations. We identified five cell types and found that mesophyll-4 (MS4) cells exhibited the highest levels of viral accumulation in most cells. Early systemic infection of SCMV resulted in a greater upregulation of differentially expressed genes, which were mainly enriched in biological processes related to translation, peptide biosynthesis, and metabolism. Co-variation analysis of the altered maize gene expression and viral accumulation levels in MS1, 2, and 4 revealed several patterns, and the co-expression relationships between them were mainly positive. Furthermore, functional studies identified several potential anti- or pro-viral factors that may play crucial roles during the early stage of SCMV systemic infection. These results not only provide new insights into plant gene regulation during viral infection but also offer a foundation for future investigations of host–virus interactions across molecular, cellular, and physiological scales.