Cassava production in Ivory Coast is hampered by cassava mosaic disease (CMD), which is caused by several begomovirus species. To increase cassava production and conserve genetic resources, the Centre National de Recherche Agronomique (CNRA) maintains a germplasm collection of 610 cassava accessions of various origins, which is kept in open fields in Bouaké and Man. We carried out an epidemiological assessment of the collection and a molecular characterization of the viruses infecting the CNRA cassava germplasm. The field in Man was less affected by CMD (incidence 49.78%, severity 2.23, whitefly infection 2.23%), despite the abundant whitefly populations (1.34 per plant), compared to Bouaké (incidence 74.54%, severity 2.92, whitefly infection 8.04% and whitefly population of 0.34 per plant). However, the predominant mode of CMD transmission was through infected cassava cuttings at both sites. PCR analysis showed that the East African cassava mosaic Cameroon virus (EACMCMV) was always found in co‐infection with African cassava mosaic virus (ACMV), which also occurred in single infection. Co‐infections of EACMCMV and ACMV were more prevalent in Bouaké (52.64%) than Man (13.87%). Eleven complete genome sequences of cassava mosaic begomoviruses infecting the CNRA germplasm were obtained, and phylogenetic analysis showed that they are closely related to ACMV and EACMCMV isolates from Ghana, Burkina Faso and Nigeria. The results of this study will assist breeders to screen accurately for CMD resistance in progeny resulting from parental lines, enabling the strategic distribution of new clean cassava planting materials to reduce the impact of CMD.

Cassava is the staple food crop for hundreds of millions of people in Africa. In Côte d'Ivoire, it is a main source of calories for over 26 million people. However, cassava mosaic disease (CMD), caused by cassava mosaic geminiviruses (CMGs) threaten its production. The development, adoption, and use of CMD resistant varieties remain a key CMD management strategy. Therefore, 610 accessions from the Côte d'Ivoire national cassava germplasm maintained by Centre National de Recherche Agronomique (CNRA) research stations in the cities of Man and Bouaké were characterized to assess their resistance to CMD. We found 72 accessions which were symptomless at both sites. Thirty five out of these 72 accessions were infected by African cassava mosaic virus (ACMV) without any CMD symptoms and 37 were virus free. None of the 72 symptomless accessions were infected by East African cassava mosaic Cameroon virus (EACMCMV). The remaining 538 accessions were CMD infected and displayed clear CMD symptoms. The promising 72 accessions (10 locals and 62 improved) were then tested for the presence of resistance genes, CMD1, CMD2 or CMD3. Except for 2 accessions for which no resistance gene was found, the remaining 70 accessions contained one or more resistance genes. Genotyping of the 69 symptomless accessions revealed that 56 were unique genotypes and 13 were potential duplicates. Accessions were structured in three groups with the variabilities at the individual's level. These findings reveal the existence of potential tolerant/resistant cassava accessions in CNRA's germplasm, which can contribute to CMD control and the increase of cassava production in Côte d'Ivoire.