Comparative Transcriptome Analysis of Cassava Plants Differing in Their Resistance Level to Cassava Brown Streak Virus

Cassava (Manihot esculenta) is a major food staple in Africa, which is severely affected by cassava brown streak disease and for which resistance sources are not available. In order to identify and understand the mechanism of resistance, three cassava varieties; Kaleso, Kiroba and Albert were inoculated with Cassava brown streak virus (CBSV) by grafting. Nine months after virus inoculation, Kaleso was found resistant to the disease with low virus loads and mild symptoms, Kiroba was tolerant as it expressed severe leaf but milder root symptoms, while Albert was susceptible with severe symptoms and high virus titer.  To uncover the genetic basis of this resistance, transcriptome analysis was used on the resistant and susceptible cassavsa using Illumina RNA-sequencing. Pariwise comparisons of virus infected and healthy plants uncovered 745 and 235 genes overexpressed in the resistant and susceptible cassava respectively. Surprisingly none of these genes belong to characterized pathways of virus resistance but 5 NAC-domain protein homologs were confirmed by qPCR to be overexpressed. The differentially expressed genes identified in this study have potential to improve our understanding of the mechanisms of resistance for CBSV in cassava and for developing functional markers that could be used in marker assisted selection for accelerated breeding.