Genetic diversity and identification of cocoa swollen shoot virus detected in tolerant cocoa trees (Theobroma cacao L.) in west and central west department of Côte d'Ivoire

Abstract

Abstract Swollen shoot virus disease (CSSVD) is responsible of production losses and destruction of cocoa plantations. Since its resurgence in Côte d'Ivoire in 2003, it has caused a real threat to Ivorian cocoa production. The aim of this study was to highlight the genetic diversity of isolates from potentially CSSV-tolerant cocoa trees. The methodology used involved PCR detection of the presence of virus on 168 potentially CSSVD-tolerant and susceptible cocoa accessions collected from seven CSSVD-infected departments of Côte d'Ivoire. This step was followed by DNA sequencing to identify isolates. The results of this study show 32 viral sequences (clones) were obtained after PCR. Three groups of isolates were identified. Group B (species CSSTBV), including the BC subgroup, group D (species CSSCDV) and a new group S, never before observed in west and central west of Côte d'Ivoire. The groups of isolates identified were not assigned to the phenotypic groups evaluated. These results indicate the need for further molecular diagnosis of asymptomatic cocoa trees present in infected cocoa farms in Côte d'Ivoire.