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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Research Project #431487

Research Project: Determining Cacao Swollen Shoot Virus Diversity and Distribution, Understanding its Epidemiology and Designing Genomic Tools for its Identification

Location: Subtropical Horticulture Research

Project Number: 6038-21000-025-13-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2016
End Date: Aug 31, 2020

Objective:
Elucidate swollen shoot badnavirus genomic variability and link to epidemiology in West Africa (identity and distribution): (2) develop/apply molecular diagnostics to track cacao-infected badnaviruses to support quarantine and breeding activities at USDA-ARS Miami and within the program, worldwide. OBJECTIVES: 1. Genomic pathology: Illumina/Sanger DNA/RNA sequencing of CSS-infected cacao and native species to investigate badnavirus genomic variability to inform molecular diagnostic development/validation and identify virus panel to support breeding program. 2. Develop molecular diagnostics for detection of cacao-infecting viruses. 3. Provide cacao DNA to USDA-ARS for SNP analysis to inform panel of cacao genotypes. Relate virus identity with cacao genotype (SNPs) data. 4. Develop infectious clones to support screening of breeding material. 5. Determine if cacao-infecting begomoviruses are integrated into the genome of selected cacao genotypes (from SNP x badnavirus genotype panels).

Approach:
The production of cacao is plagued by decreased productivity, due to a number of new or emergent plant diseases that cause decreased yields and quality. Among the most important disease is Cacao swollen shoot virus (CSSV), caused by a poorly understood, graft- and mealybug-transmitted virus that infects cacao throughout West Africa. Presently, yield losses occur in 25% and 50% of trees within the first and second years after CSSV infection occurs, respectively, and tree death occurs within 3-5 years following infection. Despite this mass devastation to the cacao industry, the reason for the sudden increase in CSSV spread has not been investigated. More, the diversity of the virus (strains, species, or complex?) is not known, only seven viral genomes have been sequenced and are available in the GenBank database. Although a number of mealybug species have been implicated as vectors of CSSV, studies to identify the most important vector species have not been undertaken since the 1940’s and 1950’s, a large gap in time, during which important changes in mealybug vector composition could have occurred that could alter the disease epidemiology, perhaps even selecting for a particular suite of viral genotypes that are most efficiently transmitted. Such changes could be due to the rapidly expanded production of cacao in the region to meet world cacao demands, changes in the cacao genotypes planted since the 1950’s, the effects of extreme weather/climatic factors on virus-vector complexes, the recent effects of drought on the cacao trees, and/or other factors, all unknown at the present. To accomplish objective (1), an east to west sampling transect will be established through cacao growing regions of the country. Sampling will be carried out at designated sites representative of the production zones characterized by: 1) behind the disease front, an area most closely associated with the Ghana-Cote d’Ivoire border; 2) at the front, or the area where the disease has most recently accelerated in spread (central part of the country), and 3) ahead of the front, or the most western part where the rapidly spreading CSSV strains/species and/or their mealybug vector(s) have not yet arrived. Once the samples have been obtained, the following protocol will be used: samples will be collected from designated field sites and preserved in alcohol (mealybug) or glycerol (plant) by our collaborators at CRIG (Ghana) and CNRA (Cote d’Ivore) after the rainy season has facilitated flush growth on cacao trees and native plant species that are known CSSV hosts. It is expected that collections will consist of ~3000 samples year period (~1000 per year), with a second set of samples consisting of 20 samples/site x 10 sites of T. cacao, Adansonia digitata and Bombax brevicuspe, Ceiba pentandra, Cola chlamydantha, C. gigantea, to facilitate population analysis. Samples will be sent to the University of Arizona for processing, RCA/PCR amplification, DNA sequencing (Sanger, capillary; Next-Gen after removal of host DNA), and analysis.