Molecular characterization of tomato-infecting begomoviruses in Central America and development of DNA-based detection methods

Begomoviruses cause great losses of tomato crops in Central America. Eight begomoviruses were identified by sequencing PCR fragments. Four of these were new viruses: Tomato severe leaf curl virus (ToSLCV, AF130415), Tomato golden mottle virus (ToGMoV, AF132852), Tomato mild mottle virus (ToMiMoV, AF131071) and Tomato yellow mottle virus (ToYMoV, AF112981) and four were previously characterized: Pepper golden mosaic virus (PepGMV, AF136404) Tomato mosaic Havana virus (ToMHV, AF139078), Tomato leaf curl Sinaloa virus (ToLCSinV, AF131213) and Pepper huasteco yellow vein virus (PHYVV). A general probe, consisting of the most conserved region of the CP gene of Bean yellow golden mosaic virus (BGYMV, M91604), was used in non-radioactive hybridization methods to detect these viruses. Specific probes, which consisted primarily of the common region for each virus, were developed. Specific primers for PCR identification were designed for each virus, and the PCR fragments obtained from plant samples with these begomovirus-specific primer sets were sequenced to confirm the primers' specificity. ToSLCV, ToMHV and ToMiMoV were present in tomatoes from Comayagua, Honduras. ToYMoV and ToLCSinV were present only in samples from Costa Rica. ToSLCV, ToGMoV, ToMiMoV, ToMHV, PepGMV, ToLCSinV and PHYVV were detected in tomatoes in one valley in Guatemala. ToSLCV only existed in mixed infections with another bipartite begomovirus, and no DNA-B was ever identified for this virus. These detection methods were used to monitor begomoviruses in tomato-breeding lines being developed in Guatemala for resistance to these viruses.