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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #353941

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

Location: Subtropical Horticulture Research

Title: The previously unidentified, divergent badnavirus species, cacao red vein-banding virus, is associated with cacao swollen shoot disease in Nigeria

Author
item Chingandu, Nomatter - University Of Arizona
item Dongo, Lelia - Cocoa Research Institute Of Nigeria
item Gutierrez, Osman
item Brown, Judith - University Of Arizona

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/27/2018
Publication Date: 12/31/2018
Citation: Chingandu, N., Dongo, L., Gutierrez, O.A., Brown, J.K. 2018. The previously unidentified, divergent badnavirus species, cacao red vein-banding virus, is associated with cacao swollen shoot disease in Nigeria. Plant Disease. https://doi.org/10.1094/PDIS-09-18-1561-RE.
DOI: https://doi.org/10.1094/PDIS-09-18-1561-RE

Interpretive Summary: Cacao production is concentrated in the tropical regions of the world, with West Africa accounting for 70% and Cote d’Ivoire, Ghana, Cameroon, and Cacao production is concentrated in the tropical regions of the world, with West Africa accounting for 70% and Cote d’Ivoire, Ghana, Cameroon, and Nigeria being the main producers. Cacao swollen shoot disease has been relentlessly affecting the cacao production in West Africa since the late 1930s. It was first observed in Nigeria in 1944. Cacao swollen shoot virus disease eradication programs have been conducted since these early years; however, they have not been very successful. Due to the lack of diagnostic tools to detect infected trees before symptom are visible, thousands of trees die within three years after they become infected. In addition, the disease continues to expand to new cacao-growing areas, frequently triggering serious outbreaks. Up to the present time, no genetic characterization of the viruses causing Cacao swollen shoot disease in Nigeria have been conducted. The main goal of this research was to sequence and describe the badnavirus genomes associated with Cacao swollen shoot disease in Nigeria because this will help in the development of new assays that are able to detect all the swollen shoot virus shoot virus strains in Nigeria and other cacao producing countries in West Africa. Genome sequence and phylogenetic analysis results showed the presence of a new species that has been designated Cacao red vein-banding virus (CRVBV). Newly designed polymerase chain reaction tests demonstrated that this new virus species and several other isolates are present in the area. This molecular assay using primers designed based on the CRVBV genome sequences was able to detect all Nigerian virus isolates, and additional isolates from seven samples.

Technical Abstract: Although cacao swollen shoot disease (CSSD) of Theobroma cacao has been documented in Nigeria since 1944, no badnavirus has been associated with diseased trees. Degenerate primers were designed and used to amplify a 500-base pair (bp) fragment of the intergenic region from 32 CSSD-symptomatic samples collected in Osun and Oyo states, Nigeria, during 2016. The aligned sequences were used to design abutting primers, which were used to PCR-amplify and sequence a full-length badnavirus genome of ~7.0 kbp from 9 of 18 field samples that encoded four open reading frames and shared 86-99% nucleotide (nt) identity. Pairwise distance analysis with 21 CSSD badnavirus sequences (GenBank) indicated that the Nigerian isolates shared 71 -75% and 72-76% nt identity with the complete genome and RT-RNase H (1230 bp) sequences, respectively. Phylogenetic analyses of the full-length genome sequences indicated the CSSD-Nigerian isolates were highly divergent from, but most closely related to, other West African CSSD-badnaviruses. Based on sequence analyses the CSSD-Nigerian isolates represent a new badnavirus species, Cacao red vein-banding virus (CRVBV), among the now five recognized CSSD-badnavirus species. Using primers based on the CRVBV sequences, 16 of 18 symptomatic leaf samples collected in Nigeria during 2017, were positive for CRVBV.