Transcriptome Analysis of Cassava Brown Streak Virus (CBSV) Infected Susceptible and Resistant Cassava (Manihot esculenta L.)

Cassava brown streak disease (CBSD), caused by cassava brown streak viruses (CBSV), represents a major threat to cassava production, as infection of tuberous roots results in substantial yield losses. Certain South American cassava germplasm genotypes exhibit virus resistance, which can either be characterized as complete immunity by preventing virus replication and movement, or restrict viral replication to phloem companion cells and limit root infection. To investigate the molecular basis of these resistance responses and identify candidate resistance genes, a time-course RNA-seq experiment was conducted. Gene expression in the virus-susceptible cassava line TMS 96/0304 was compared with that in the root-restricted line DSC 260, which keeps above-ground tissues symptom-free and allows virus accumulation mainly in tuberous roots, and the immune line DSC 167, which does not support virus replication. Differential expression analyses across leaves, stems, and roots revealed pronounced differences between susceptible and resistant genotypes. Temporal analysis indicated substantial variation in the number of differentially expressed genes (DEGs) at one day after inoculation (DAI), with resistant lines DSC 167 and DSC 260 showing strong differential expression, whereas significant expression changes in TMS 96/0304 were only detected at 10 DAI. In resistant genotypes, several DEGs were associated with proteins involved in hormone regulation, defense and immunity, transcriptional control, stress responses, cell structure, and signal transduction. Heat shock proteins were upregulated in stem and root tissues of DSC 167 but downregulated in root tissues of DSC 260 and TMS 96/0304, highlighting molecular differences in root tissues between root-restricted and highly resistant genotypes. Additionally, phloem enrichment analyses were conducted to identify genes involved in virus restriction in resistant cassava. RNA-seq comparisons of laser-microdissected internal and external phloem tissues across the three genotypes revealed five major differentially expressed genes encoding characterized proteins, while the remaining DEGs were annotated as uncharacterized. One uncharacterized gene displayed notably strong expression, requiring further functional investigation. The findings of this study provide valuable insights for the identification of resistant genotypes and the development of strategies to control CBSD in Africa.