Prevalence of Sugarcane Streak Mosaic Virus (SCSMV) in a Sugarcane Germplasm in Northern Côte d’Ivoire

Sugarcane streak mosaic disease (SCSMD) can reduce sugarcane yields by up to 70%. Since the first confirmation of SCSMD in 2018 in Sucrerie d’Afrique de Côte d’Ivoire (SUCAF-CI) plantations in Ferkessédougou, the epidemiology of the disease has never been studied. Therefore, the aim of this work was to evaluate various SCSMD parameters within the SUCAF-CI sugarcane germplasm, which comprises sugarcane varieties from diverse geographic origins. To that end, an epidemiological and molecular assessment was conducted on 548 varieties of SUCAF-CI sugarcane germplasm, preserved at two sites (Ferké 1 and Ferké 2) to evaluate SCSMD incidence and severity, determine the diversity of SCSMV strains infecting sugarcane at SUCAF-CI, identify sugarcane varieties that are potentially resistant to sugarcane streak mosaic virus (SCSMV), and investigate the presence of alternative hosts in SUCAF-CI plantations. The results reveal a very high incidence of the disease three months after planting (91.27 ± 23.28% in Ferké 1; 90.73 ± 22.80% in Ferké 2), followed by a significant increase at eight months (97.32 ± 11.79% and 96.45 ± 15.55%, respectively). The mean severity of the disease was low at both sites, with an average of 1.31 ± 0.02 at Ferké 1 and 1.05 ± 0.02 at Ferké 2. The varieties M292/70 and M700/86, which proved to be potentially resistant in the germplasm, showed symptoms in the industrial plots. Molecular analyses confirmed the presence of SCSMV in the germplasm studied, with a high overall prevalence of 71.32%. The infection rate was lower at Ferké 1 (55.8%) than at Ferké 2 (85.8%). Phylogenetic analysis of the SCSMV sequences obtained in this study showed that they are closely related to sequences from Côte d’Ivoire, India, Iran and Pakistan. No alternative hosts for SCSMV were identified. These findings highlight the critical importance of rigorously monitoring the importation of plant material and establishing a global management strategy that prioritizes the production of certified pathogen-free sugarcane plants.