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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Research Project #434576

Research Project: Developing Pathogen and Plant Based Genetic Tools for Breeding Disease Resistance in Theobroma Cacao

Location: Sustainable Perennial Crops Laboratory

Project Number: 8042-21220-255-08-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: May 21, 2018
End Date: May 20, 2021

Objective:
This project will address the critical need in understanding functional diversity in sources of disease resistance, new genes or alleles for breeders and an improved understanding of the disease process during the cacao swollen shoot virus (CSSV) disease interaction. So far the efforts in characterization and evaluation of germplasm have received much less attention than germplasm maintenance. Most of the phenotyping in this collection has been limited in morphological descriptors. Only a small fraction of the germplasm held in the international collections has been evaluated for disease resistance. Within the genebank holdings, there remains a significant amount of untapped wild germplasm, which may harbor new sources of variations in resistance to diseases and pests. Through this project, we would like to evaluate diseases resistance and analyze the susceptible and resistance mechanisms in a specific set of clones. Results of this project will contribute to more efficient management and use of cacao germplasm for varietal development through the identification of new sources of resistance to cacao. The new disease resistance genes identified can be used by cacao breeders to improve breeding programs.

Approach:
Genetic diversity and phenotypic trait analysis of the International Cocoa Quarantine Centre (ICQC) at the University of Reading. Phenotypic traits related to diseases resistance will be evaluated from a set of specific clones for CSSV disease interaction including susceptible and resistant material. Technology of next generation sequencing and candidate gene markers will be used to evaluate the disease responses. The evaluation will utilize RNA-Seq technology, cacao clones with varying levels of resistance to CSSV, a virus pathogen that caused cacao swollen shoot will be infected. Plants will be produced from 8 clones to develop a replicated 2 time-point experiment with 5 reps/time point/clone-plus controls. A total of 20 plants per clone will be produced for a total of 160 samples. The clones will be inoculated with CSSV isolates and the infected material will be harvested at the 2 time points, representing one early and late time point in the disease cycle. The material will be frozen in liquid nitrogen and kept at -80C. The RNA will be extracted from 3 reps/time point/clone plus controls for a total of 96 samples. A decision will be made later to determine if leaves or stems are the most useful material based on RNA extractions and gene expression. Once completed the RNA (or frozen material will be shipped to Beltsville or directly to BGI for sequencing. Molecular evaluation of this collection, through a multiparty collaboration, will greatly improve the understanding of viral disease interactions and resistance to CSSV. Comprehensive characterization of a working subset of the whole collection is a promising approach to document the disease resistance in the ICQC, as well as providing potential opportunities for cacao genetic improvement in Africa.