Impact of the Seasons on the Evolution of Tomato-infecting Geminivirus and Identification of Plant Reservoirs Harboring Geminivirus in Burkina Faso

Abstract

Geminiviruses are known as responsible for huge damage to vegetable crops in many tropical, subtropical, and temperate regions. In Burkina Faso, tomato was reported as the most infected vegetable crop with the involvement of several geminivirus species despite its socioeconomic importance. This suggests and underlines the pressing need for additional information on virus population evolution (diversity, prevalence, and host plant reservoirs). Thus, to address this problem, surveys and sample collection were carried out in three localities in Burkina Faso (Goué, Léguéma, and Toussiana). Tomato leaves and those of cultivated and non-cultivated plants around the tomato fields were collected. The total DNA extracted from these samples was subjected to diagnosis based on the polymerase chain reaction (PCR) protocol with or without amplicon sequencing. Results showed that depending on the season and locality, the prevalence of the disease varied from 0 to 53.33% and that of the virus species varied from 0 to 76.67%. The highest prevalence was observed in the dry season. In addition, PepYVMLV was the virus that was widely detected in all three localities in the rainy (18.89%) and dry (52.22%) seasons. The DNA-B molecule associated with this virus was associated with other begomoviruses (ToLCMLV). In addition, out of 200 samples collected in the vicinity of the tomato fields, only 63 were positive based on PCR diagnosis. Amplicon sequencing yielded 63 partial sequences of virus from ten plant species, including six non-cultivated species. Based on phylogenetic analysis, the 63 partial sequences belonged to three phylogenetic groups (the ToLCV group, the PepYVMLV group, and the CLCuGV group). This study allowed a better understanding of the evolution of tomato leaf curl/yellow disease in Burkina Faso and the diversity of plant species serving as reservoirs for involved viruses. This constitutes an important step in the search for adequate control methods.