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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Research Project #441868

Research Project: Development of Pathogen- and Plant-Based Genetic Tools and Disease Mitigation Methods for Tropical Perennial Crops

Location: Sustainable Perennial Crops Laboratory

Project Number: 8042-21220-258-000-D
Project Type: In-House Appropriated

Start Date: Mar 28, 2022
End Date: Mar 27, 2027

Objective 1: Characterize the genetic diversity of pathogens of cacao and other tropical perennial crops to improve understanding of how pathogen diversity impacts plant/pathogen interactions. (NP303, C1, PS1A, C2, PS2B). Sub-objective 1.A: Sequence the genome and transcriptome of fungal species causing thread blight on cacao in Ghana (years 1-3). (Non-hypothesis-driven). Sub-objective 1.B: Sequence the genomes and transcriptomes of Rosellinia species causing black root rot of cacao in Colombia, Ecuador and Peru (years 1-3). (Non-hypothesis-driven). Objective 2: Integrate genetic resources of pathogens and hosts for use in breeding disease tolerance in cacao and other tropical perennial crops. (NP303, C2, PS2B, C3, PS3A, NP301, C2, PS2A). Sub-objective 2.A: Detailed genome assembly and analysis of cacao clones showing tolerance and susceptibility to P. palmivora/P. megakarya. (years 1-3). (Non-hypothesis-driven). Sub-objective 2.B: Transient gene expression of candidate cacao defense genes and tissue-specific gene promoters for use in the GAANTRY system in cacao. (years 2-3). (Non-hypothesis-driven). Sub-objective 2.C: Stable transformation of cacao using the GAANTRY gene stacking system. (years 3-5). (Non-hypothesis-driven). Objective 3: Develop novel strategies for managing diseases of cacao and other tropical perennial crops. (NP303, C2, PS2B, C3, PS3A). (Hypothesis-driven).

Black pod rot of cacao, caused by Phytophthora spp., has the greatest negative impact on cacao production globally while coffee leaf rust, caused by Hemileia vastatrix, causes severe yield reduction wherever it occurs on coffee. Although these two diseases are being studied extensively because of their global concerns, other diseases like thread blight (basidiomycete disease complex) and black root rot (Rosellinia species) of cacao are much less studied because of their local/regional distributions. Disease mitigation methodologies continue to have limited success in managing these and other diseases in cacao and coffee. While progress is being made in breeding tolerance to some diseases in these crops, these efforts continue to be hindered by our limited knowledge of pathogen genetics and host genes conferring disease tolerance. Therefore, this project will continue developing tools with applications to managing plant diseases. The genome and transcriptomes of established and emerging cacao pathogens, including those causing thread blight and black root rot, will be sequenced. New knowledge of cacao genes that contribute to disease resistance against Phytophthora spp. will be acquired through functional analysis. A transient gene expression system will be exploited to identify condition and tissue-specific cacao gene promoters and candidate cacao defense genes for inclusion in a stable multigene transformation system (GAANTRY) validating its use in cacao. New methodologies with potential for mitigating cacao and coffee disease losses will be developed. LED-based UV light technologies will be tested for efficacy in mitigating of both black pod rot in cacao and coffee leaf rust. The objectives of this project target specific plant/pathogen interactions using multiple approaches. Still, there is a high probability the findings of these studies will have applicability to additional plant/pathogen interactions.