The Transcriptome Response of African and South American Cassava ( <scp> <i>Manihot esculenta</i> </scp> ) to Infection by East African Cassava Mosaic Virus‐Uganda

ABSTRACT Cassava mosaic begomoviruses (CMBs) cause the economically important cassava mosaic disease (CMD) in cassava. In this research, we investigated potential new sources of resistance to CMD. Fourteen cassava varieties were tested for resistance to the major CMB, East African cassava mosaic virus‐Uganda (EACMV‐Ug). Six African cassava varieties (72‐TME 14, TME 204, TZ 130, Nase 1, Nase 3 and Nase 14) expressed no or mild disease symptoms with low viral load and therefore have been classified as resistant. South American varieties showed severe leaf symptoms and supported high viral load. Nase 3 (resistant), TZ 130 (resistant) and Ebwanateraka (susceptible) were subjected to RNA‐sequencing (RNA‐Seq) to identify putative CMD resistance genes and mechanisms. Transcriptome analysis of three cassava varieties at 2, 4, 7, and 28 days after grafting (DAG) revealed the largest number of differentially expressed genes (DEGs) upon virus infection in Nase 3 (4228) with 1725 genes uniquely over‐expressed. Additionally, early induction of heat shock proteins and transcription factors such as ethylene‐responsive transcription factor (ERF), teosinte‐like, cycloidea and PCF1 (TCPs), heat stress transcription factor and basic leucine zipper were observed in the resistant varieties. These results suggest that resistant varieties maintain a low titre of EACMV‐Ug by activating specific stress‐response genes early. The role of these genes in plants remains to be investigated but offers insights into the molecular mechanism of resistance to CMD.