A novel recombinant begomovirus isolated in Southeast Asia breaks the Ty-1-mediated resistance in tomato

Abstract Infections by begomoviruses have threatened the global production of multiple crops, including Solanaceae species. Recombination, a phenomenon frequently observed in begomoviruses, has profound effects on virus populations, enabling them to adapt to changing environmental conditions. We previously isolated pepper yellow leaf curl Aceh virus (PepYLCAV) from pepper (Capsicum annuum), tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum) plants in Aceh Province, Indonesia and determined it is a recombinant of the widely distributed pepper yellow leaf curl Indonesia virus (PepYLCIV). To compare PepYLCAV with its major putative parent PepYLCIV in terms of virulence, multiple solanaceous plants (Nicotiana benthamiana, pepper, and tomato) were inoculated with the two viruses. Disease symptom severity, growth inhibition, and viral DNA accumulation were greater for the infection with PepYLCAV than for the infection with PepYLCIV. Furthermore, the inoculation with PepYLCAV revealed the Ty-1-mediated resistance of the begomovirus-resistant tomato cultivar was compromised, resulting in moderate symptoms, which were not detected in the plants infected with PepYLCIV. According to the polymerase chain reaction-based re-analysis of samples collected from fields in Indonesia from 2012 to 2019, PepYLCAV rather than PepYLCIV has been the predominant species since 2017. In conclusion, PepYLCAV, which is a novel recombinant bipartite begomovirus that is more virulent and widespread than its major putative parent (PepYLCIV), can overcome the Ty-1-mediated resistance of commercial F1 hybrid tomato cultivars.