Investigating resistance breakdown and alternative management strategies for tomato yellow leaf curl virus

Abstract

Tomato yellow leaf curl virus (TYLCV), a single-stranded DNA virus in the Begomovirus genus, is transmitted by whitefly Bemisia tabaci in a persistent, circulative manner. This virus poses a significant threat to global tomato production. In Australia, TYLCV-Israel (TYLCV-IL) was first detected in 2006 in southeast Queensland and later spread to northern Queensland, causing substantial economic impact. Introducing TYLCV-resistant tomato hybrids containing the Ty-1 resistance gene has effectively managed the virus in Queensland for several years. However, recently, resistance breakdown has been observed in Bundaberg. To investigate the factors contributing to this and explore alternative management strategies, PCR was conducted on samples collected from symptomatic plants of the TYLCV-resistant variety SV0215TH collected in Bundaberg in 2023. In addition, Sanger sequencing was conducted to obtain the genome sequence of the TYLCV 2023 isolate (AU23) for phylogenetic and severity prediction analysis using the machine learning software IML-TYLCVs. The results showed no detectable mixed infection of tomato leaf curl virus (ToLCV), tomato chlorosis virus, or ToLCV betasatellite. Although AU23 was predicted to be a mild isolate based on amino acid sequence, the phylogenetic analysis revealed that the pairwise distance of the nucleotide sequence of AU23 is far from that of the other Australian isolates retrieved from the NCBI virus database. Subsequently, spray-induced RNA interference (RNAi) was evaluated to protect tomato plants from AU23. Plants treated with dsRNA targeting the viral transcripts V1 and C3, combined with an 41 additive, showed reduced symptom expression and virus titre. Further research is needed to identify the major factors affecting the resistance breakdown, providing insights into developing new protection strategies for reemerging viruses.