Genomics, Transcriptomics, and Beyond: The Fifteen Years of Cacao’s Witches’ Broom Disease Genome Project

Mondego, Jorge Maurı́cio Costa; Thomazella, Daniela Paula de Toledo; Pereira, Gonçalo

doi:10.1007/978-3-319-24789-2_6

Cited by 4 publications

(3 citation statements)

References 117 publications

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“…outbreaks can destroy all cacao fruit on a single farm. Because diseases are a persistent problem for cacao, improvement of disease resistance through breeding (Gutiérrez et al, 2016 ), biocontrol (Ten Hoopen and Krauss, 2016 ), and biotechnology (Guiltinan and Maximova, 2015 ; Mondego et al, 2016 ) approaches are all active areas of research.…”

Section: Introductionmentioning

confidence: 99%

Transient Expression of CRISPR/Cas9 Machinery Targeting TcNPR3 Enhances Defense Response in Theobroma cacao

et al. 2018

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Theobroma cacao, the source of cocoa, suffers significant losses to a variety of pathogens resulting in reduced incomes for millions of farmers in developing countries. Development of disease resistant cacao varieties is an essential strategy to combat this threat, but is limited by sources of genetic resistance and the slow generation time of this tropical tree crop. In this study, we present the first application of genome editing technology in cacao, using Agrobacterium-mediated transient transformation to introduce CRISPR/Cas9 components into cacao leaves and cotyledon cells. As a first proof of concept, we targeted the cacao Non-Expressor of Pathogenesis-Related 3 (TcNPR3) gene, a suppressor of the defense response. After demonstrating activity of designed single-guide RNAs (sgRNA) in vitro, we used Agrobacterium to introduce a CRISPR/Cas9 system into leaf tissue, and identified the presence of deletions in 27% of TcNPR3 copies in the treated tissues. The edited tissue exhibited an increased resistance to infection with the cacao pathogen Phytophthora tropicalis and elevated expression of downstream defense genes. Analysis of off-target mutagenesis in sequences similar to sgRNA target sites using high-throughput sequencing did not reveal mutations above background sequencing error rates. These results confirm the function of NPR3 as a repressor of the cacao immune system and demonstrate the application of CRISPR/Cas9 as a powerful functional genomics tool for cacao. Several stably transformed and genome edited somatic embryos were obtained via Agrobacterium-mediated transformation, and ongoing work will test the effectiveness of this approach at a whole plant level.

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Section: Introductionmentioning

confidence: 99%

Transient Expression of CRISPR/Cas9 Machinery Targeting TcNPR3 Enhances Defense Response in Theobroma cacao

et al. 2018

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“…This can contribute to reducing spore survival and dissemination within agroecosystems, primarily by reducing wind exposure that is crucial for spore dispersal as observed in agroforestry settings [40]. Moreover, plantains may help minimize spore spread by maintaining constant humidity levels, thereby altering the micro-environment needed for the fungal basidiocarps to develop, which require alternating periods of wet and dry conditions [41,42].…”

Section: Discussionmentioning

confidence: 99%

Optimizing Pathogen Control through Mixed Cocoa–Plantain Agroecosystems in the Ecuadorian Coastal Region

Vera-Velez,

Ramos-Veintimilla,

Grijalva-Olmedo

2024

Agronomy

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Mixed production systems play a vital role in the economic sustainability and ecological balance of agroecosystems. Cocoa and plantain are key crops in Ecuador but face phytosanitary challenges, like witches’ broom and black sigatoka diseases, especially when cultivated under monocropping systems. Combining habitat manipulation with adaptive pathogen management (APM) strategies can mitigate these challenges, but their efficacy in mixed cropping systems remains unclear. This study investigates disease and pest incidence in mixed cocoa–plantain systems during the establishment phase, focusing on the impact of spatial arrangements. Mixed agroecosystems showed a lower witches’ broom incidence in cocoa than monocultures. Whereas, in plantain, there was a consistent black sigatoka incidence across spatial arrangements but a lower infection rate per leaf within mixed systems. We found varied nematode populations with monocultures hosting the highest root damage due to phytoparasitic nematodes. Weevil populations were also influenced by spatial arrangements with monocultures among the highest. Overall, mixed agroecosystems influence disease and pest incidence, potentially hindering pathogen spread. Plantain–cocoa associations reduce disease incidence in cocoa but may not affect the overall incidence of black sigatoka in plantain, at least during the establishment phase. Continued monitoring is crucial for understanding the long-term impacts and microclimatic effects on pest populations that could offer sustainable pest management strategies, reducing the reliance on chemical pesticides.

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“…Some family members also possess the ability to integrate part of their genomes in the form of minichromosomes into the host genome during their replication cycle ( Diop et al, 2018 ). Particularly for T. cacao , the studies mostly focused on symptomatic infections that affect the economic potential of the production with the genus Badnavirus , and correlate to the outbreak of Cacao Swollen Shoot Virus Disease (CSSVD) that started in 1922 in West Africa and is still devastating cacao production in Eastern African regions ( Mondego et al, 2016 ). Thus, 10 species of viruses were described in West Africa or in some Caribbean islands, and most recently, one isolate of CaMMV-BR-like virus was identified in the Bahia state, Brazil, and also one species ( Cacao bacilliform Sri Lanka virus ) from Sri Lanka ( Muller et al, 2021 ; Ramos-Sobrinho et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Expanding the environmental virome: Infection profile in a native rainforest tree species

et al. 2022

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Agroforestry systems (AFS) for cocoa production combine traditional land-use practices with local biodiversity conservation, resulting in both ecological and agricultural benefits. The cacao-cabruca AFS model is widely implemented in regions of the Brazilian Atlantic Forest. Carpotroche brasiliensis (Raddi) A. Gray (Achariaceae) is a tree found in cabruca landscapes that is often used for reforestation and biotechnological applications. Despite its importance, we still lack information about viruses circulating in C. brasiliensis, particularly considering the possibility of spillover that could affect cocoa production. In our study, we analyzed the Carpotroche brasiliensis virome from Atlantic Forest and cacao-cabruca AFS regions using metatranscriptomics from several vegetative and reproductive organs. Our results revealed a diverse virome detecting near-complete or partial coding sequences of single- and double-stranded DNA and RNA viruses classified into at least six families (Botourmiaviridae, Bromoviridae, Caulimoviridae, Genomoviridae, Mitoviridae, and Rhabdoviridae) plus unclassified elements. We described with high confidence the near-complete and the partial genomes of two tentative novel viruses: Carpotroche-associated ilarvirus and Carpotroche-associated genomovirus, respectively. Interestingly, we also described sequences likely derived from a rhabdovirus, which could represent a novel member of the genus Gammanucleorhabdovirus. We observed higher viral diversity in cacao-cabruca AFS and reproductive organs of C. brasiliensis with preferential tropism to fruits, which could directly affect production. Altogether, our results provide data to better understand the virome in this unexplored agroecological interface, such as cacao-cabruca AFS and forest ecosystem, providing information on the aspects of virus–plant interactions.

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Genomics, Transcriptomics, and Beyond: The Fifteen Years of Cacao’s Witches’ Broom Disease Genome Project

Cited by 4 publications

References 117 publications

Transient Expression of CRISPR/Cas9 Machinery Targeting TcNPR3 Enhances Defense Response in Theobroma cacao

Transient Expression of CRISPR/Cas9 Machinery Targeting TcNPR3 Enhances Defense Response in Theobroma cacao

Optimizing Pathogen Control through Mixed Cocoa–Plantain Agroecosystems in the Ecuadorian Coastal Region

Expanding the environmental virome: Infection profile in a native rainforest tree species

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