Detection of multiple Begomoviruses in chilli crop in the five agro-climatic zones of Tamil Nadu state of India

Chilli, an important vegetable cum spice crop in India, is affected by various biotic and abiotic factors, which leads to a significant reduction in the growth and yield of the chilli crop. One of the most prominent biotic factors posing threat to chilli production in southern parts of India especially, in Tamil Nadu is begomoviruses (Family Geminiviridae). Begomoviruses are transmitted by the insect vector, whitefly (Bemisia tabaci) and they cause curling, yellowing, puckering, and reduction in the size of the leaf in the infected chilli plants. In this study, molecular (PCR) diagnostics were used to detect the presence of begomovirus, betasatellite, and six begomovirus species viz tomato leaf curl New Delhi virus (ToLCNDV), tomato leaf curl Bangalore virus (ToLCBV), tomato leaf curl Palampur virus (ToLCPalV), tomato leaf curl Gujarat virus (ToLCGV), tomato leaf curl Joydebpur virus (ToLCJoV) and chilli leaf curl virus (ChiLCV), in the chilli samples collected from the major chilli growing areas of all the five agro-climatic zones of Tamil Nadu state of India. A total number of 833 samples collected from different locations in Tamil Nadu during the period of 2018-2022 were analysed by generic as well as species-specific PCR. The PCR results of 833 samples showed positive amplification of 20.5% for generic, 13.4% for beta satellite, 42.1% for ChiLCV, 17.8% (ToLCNDV), 16.6% (ToLCGV), 6.7% (ToLCBV), 2.2% (ToLCPalV), and 0.7% for ToLCJoV specific primers respectively. The percentage of mixed infection of two or more than two begomoviruses among the total samples is 39.2. Our study has shown that the ChiLCV and multiple tomato-infecting begomoviruses were prevalent in the major chilli-growing areas of Tamil Nadu. The present study also showed that species of begomovirus infecting chilli plants in Northern and Southern India have a differential distribution.