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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #333676

Research Project: Genetic Improvement of Cacao Through Genomics-Assisted Breeding

Location: Subtropical Horticulture Research

Title: Unexpected Genome Variability at Multiple Loci Suggests Cacao Swollen Shoot Virus Comprises Multiple, Divergent Molecular Variants.

item CHINGANDU, NOMATTER - University Of Arizona
item KOUAKOU, KOFFIE - Centre National De Recherche Agronomique (NCAR)
item AKA, ROMAIN - Centre National De Recherche Agronomique (NCAR)
item Gutierrez, Osman
item BROWN, JUDITH - University Of Arizona

Submitted to: Journal of Emerging Diseases and Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/9/2017
Publication Date: 3/15/2017
Citation: Citation: Chingandu N, Kouakou K, Aka R,Gutierrez OA, Brown JK (2017) P Unexpected Genome Variability at Multiple Loci Suggests Cacao Swollen Shoot Virus Comprises Multiple,Divergent Molecular Variants. J Emerg Virol Dis 3(1): doi

Interpretive Summary: Currently, West Africa is responsible for 70% of the cacao production in the world. Cacao swollen shoot virus is severely affecting the cacao production since it causes the death of the tree within three years of the initial infection. Recent virus epidemics have been characterized by an unusually rapid weakening and death of the infected trees. The inability of current available assays to detect the presence of the virus, suggests the presence of new viral strains. Therefore, new viral detection assays are urgently needed. The purpose of this study was to develop new molecular diagnostic tools that are capable of identifying all the swollen shoot virus shoot virus strains in Cote d’Ivoire and Ghana. Genome sequence analysis of viral sequences amplified from infected cacao leaf samples indicated the presence of four distinct viral species groups. Further phylogenetic analysis showed statistical support for up to three separate clades. These results suggest that the cacao swollen shoot virus may be complex of multiple species.

Technical Abstract: Cacao swollen shoot virus (CSSV) [Badnavirus, Caulimoviridae] causes swollen shoot disease of Theobroma cacao L. in West Africa. Since ~2000, various diagnostic tests have failed to detect CSSV in ~50-70% of symptomatic cacao plants, suggesting the possible emergence of new, previously uncharacterized variants of CSSV. The extent of genomic variability was analyzed using polymerase chain reaction (PCR) amplification eight sequence-specific and/or degenerate primer pairs based on the seven CSSV sequences available in GenBank. Amplicons of the expected size, at 350 to 1100 base pairs, were cloned and the DNA sequence was determined for 124 symptomatic cacao or wild relatives of cacao collected in Cote d’Ivoire. The frequency of PCR amplification was variable and dependent upon primer pair-sample combinations. The CSSV was not detected in all of the samples, regardless of primer pair used, and for some samples, although symptomatic, CSSV was undetectable. Maximum likelihood analysis (70% bootstrap, 1000 replicates) of the amplicon sequences obtained using each primer pair resolved two distinct groups containing previously reported CSSV isolates, and a group that contained no previously described CSSV isolates. Based on the badnavirus species cutoff established by the International Committee on Taxonomy of Viruses, at <80% pairwise nucleotide (nt) identity within the RT-RNase H region, the isolates for which the RT-RNase H locus was amplified, represented four distinct species having 80-99% and 66-99% within- and between-species divergence, respectively. Results indicate that CSSV genomic variability is far more extensive than previously reported, and that CSSV may constitute a complex of species.