Comparative analysis of pattern-triggered and effector-triggered immunity gene expression in susceptible and tolerant cassava genotypes following begomovirus infection

South African cassava mosaic virus (SACMV) is one of several bipartite begomoviruses that cause cassava mosaic disease (CMD) which reduces the production yield of the cassava (Manihot esculenta Crantz) crop in many tropical and subtropical regions. SACMV DNA-A and DNA-B encoded-proteins act as virulence factors that aid in inducing different disease severity depending on the host response. Recent evidence suggests a mutual potentiation of cell membrane receptor-associated pattern-triggered immunity (PTI) and nucleotide leucine-rich repeat (NLR) effector-associated immunity (ETI) in plant immune responses.This study aimed to compare expression of SACMV virulence factors, and PTI/ETI, in SACMV-infected susceptible T200 and tolerant TME3 cultivars. Expression of SACMV virulence factors differed between SACMV-infected T200 and TME3 plants at 12, 32 and 67 days post infection (dpi). Notably, at the early stage of infection (12 dpi), expression in TME3 of AV1 and AC2 virulence factors were 10-fold and 30-fold down-regulated, respectively, compared to susceptible T200. At systemic infection (32 dpi) AV1 expression was also significantly lower (4-fold) in TME3 compared to T200. Expression of AC2 (that targets host innate immunity), while significantly lower in both T200 and TME3 at 32 dpi compared to 12 dpi, was also significantly down-regulated (16-fold) in TME3 compared to T200. TME3 recovers around 67 dpi and virus load decreases by 33% , while in T200, symptoms and high SACMV replication persist. Identification and comparison of induced PTI and ETI associated genes upon SACMV-infection in susceptible T200 and tolerant/recovery TME3 cassava genotypes was achieved by whole transcriptome sequencing (RNA-seq) and by reverse transcriptase quantitative PCR (RT-qPCR).Analyses revealed reduced expression of PTI-associated signalling and response genes during SACMV systemic/symptomatic infection (32 dpi) in cassava genotypes. In addition, hydrogen peroxide (H2O2) production, a PTI indicator, was significantly reduced in the symptomatic viral infection stage at 32 dpi. Concurrently at 32 dpi, transcription of ETI signalling and response genes as well as SA biosynthesis and response genes, were upregulated during SACMV systemic infection in TME3. These results indicate that SACMV targets PTI-associated genes during systemic infection at 32 dpi to subvert PTI-mediated antiviral immunity in cassava, which results in reduced induction of ROS production. Differential expression of specific NLR-associated genes also differed between susceptible and tolerant cultivars at 12, 32 and 67 dpi. SACMV virulence factors were shown to play a role in symptom severity in T200 and TME3.