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Minio A, Figueroa-Balderas R, Cohen SP, Ali SS, Carriel D, Britto D, Stack C, Baruah IK, Marelli JP, Cantu D, Bailey BA. Clonal reproduction of Moniliophthora roreri and the emergence of unique lineages with distinct genomes during range expansion. G3 (BETHESDA, MD.) 2023; 13:jkad125. [PMID: 37337677 PMCID: PMC10468315 DOI: 10.1093/g3journal/jkad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 04/27/2023] [Accepted: 05/30/2023] [Indexed: 06/21/2023]
Abstract
The basidiomycete Moniliophthora roreri causes frosty pod rot of cacao (Theobroma cacao) in the western hemisphere. Moniliophthora roreri is considered asexual and haploid throughout its hemibiotrophic life cycle. To understand the processes driving genome modification, using long-read sequencing technology, we sequenced and assembled 5 high-quality M. roreri genomes out of a collection of 99 isolates collected throughout the pathogen's range. We obtained chromosome-scale assemblies composed of 11 scaffolds. We used short-read technology to sequence the genomes of 22 similarly chosen isolates. Alignments among the 5 reference assemblies revealed inversions, translocations, and duplications between and within scaffolds. Isolates at the front of the pathogens' expanding range tend to share lineage-specific structural variants, as confirmed by short-read sequencing. We identified, for the first time, 3 new mating type A locus alleles (5 in total) and 1 new potential mating type B locus allele (3 in total). Currently, only 2 mating type combinations, A1B1 and A2B2, are known to exist outside of Colombia. A systematic survey of the M. roreri transcriptome across 2 isolates identified an expanded candidate effector pool and provided evidence that effector candidate genes unique to the Moniliophthoras are preferentially expressed during the biotrophic phase of disease. Notably, M. roreri isolates in Costa Rica carry a chromosome segment duplication that has doubled the associated gene complement and includes secreted proteins and candidate effectors. Clonal reproduction of the haploid M. roreri genome has allowed lineages with unique genome structures and compositions to dominate as it expands its range, displaying a significant founder effect.
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Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA
- Genome Center, University of California Davis, 95616 Davis, CA, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA
| | - Stephen P Cohen
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
| | - Shahin S Ali
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
| | - Denny Carriel
- Mars La Chola (MLCH), Mars Inc., Guayaquil 090103, Ecuador
| | - Dahyana Britto
- Mars Center for Cocoa Science, Mars Inc., Fazenda Almirante, Caixa Postal 55, Itajuípe, BA, CEP 45630-000, Brazil
| | - Conrad Stack
- Mars Digital Technologies, Mars Inc., Chicago 60642, IL, USA
| | - Indrani K Baruah
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
| | | | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis 95616, CA, USA
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville 20705, MD, USA
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de Novais DPS, Batista TM, Costa EA, Pirovani CP. Genomic and Pathogenicity Mechanisms of the Main Theobroma cacao L. Eukaryotic Pathogens: A Systematic Review. Microorganisms 2023; 11:1567. [PMID: 37375069 DOI: 10.3390/microorganisms11061567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
A set of diseases caused by fungi and oomycetes are responsible for large losses in annual world cocoa production. Managing the impact caused by these diseases is very complex because a common solution has yet to be found for different pathogens. In this context, the systematic knowledge of Theobroma cacao L. pathogens' molecular characteristics may help researchers understand the possibilities and limitations of cocoa disease management strategies. This work systematically organized and summarized the main findings of omics studies of T. cacao eukaryotic pathogens, focusing on the plant-pathogen interaction and production dynamics. Using the PRISMA protocol and a semiautomated process, we selected papers from the Scopus and Web of Science databases and collected data from the selected papers. From the initial 3169 studies, 149 were selected. The first author's affiliations were mostly from two countries, Brazil (55%) and the USA (22%). The most frequent genera were Moniliophthora (105 studies), Phytophthora (59 studies) and Ceratocystis (13 studies). The systematic review database includes papers reporting the whole-genome sequence from six cocoa pathogens and evidence of some necrosis-inducing-like proteins, which are common in T. cacao pathogen genomes. This review contributes to the knowledge about T. cacao diseases, providing an integrated discussion of T. cacao pathogens' molecular characteristics, common mechanisms of pathogenicity and how this knowledge is produced worldwide.
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Affiliation(s)
- Diogo Pereira Silva de Novais
- Department of Biological Sciences, Center for Biotechnology and Genetics, State University of Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil
- Bahia Federal Institute of Education, Science and Technology (IFBA), Porto Seguro 45810-000, BA, Brazil
| | - Thiago Mafra Batista
- Environmental Science Training Center, Federal University of Southern Bahia (UFSB), Porto Seguro 45810-000, BA, Brazil
| | - Eduardo Almeida Costa
- Department of Biological Sciences, Center for Biotechnology and Genetics, State University of Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil
| | - Carlos Priminho Pirovani
- Department of Biological Sciences, Center for Biotechnology and Genetics, State University of Santa Cruz (UESC), Ilhéus 45662-900, BA, Brazil
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Audi L, Shallow G, Robertson E, Bobo D, Ragone D, Gardner EM, Jhurree-Dussoruth B, Wajer J, Zerega NJC. Linking breadfruit cultivar names across the globe connects histories after 230 years of separation. Curr Biol 2023; 33:287-297.e3. [PMID: 36608689 DOI: 10.1016/j.cub.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/07/2022] [Accepted: 12/01/2022] [Indexed: 01/07/2023]
Abstract
Every crop has a story. The story of breadfruit (Artocarpus altilis), an increasingly valued staple crop in tropical agroforestry systems, is filled with intrigue, oppression, and remains incomplete. The Caribbean is a major producer and consumer of breadfruit, yet most breadfruit there came from a single 1793 introduction aimed at providing a cheap food source for slaves forced to work on British plantations. St. Vincent was the first significant point of Caribbean introduction and played a vital role in subsequent breadfruit distribution throughout the region. Hundreds of cultivars are documented in breadfruit's native Oceania. It remains a mystery, however, which ones were introduced to the Caribbean 230 years ago-still comprising the vast diversity found there today. Integrating local knowledge, historical documents and specimens, morphological data, and DNA, we identify eight major global breadfruit lineages-five of which are found in the Caribbean and likely represent the original 1793 introduction. Genetic data were able to match two Caribbean cultivar names confidently to their Oceania counterparts. Genetics and morphology together enabled additional possible matches. Many other named cultivars within lineages are too genetically similar to differentiate, highlighting difficulties of defining and identifying variation among clonally propagated triploid crops. Breadfruit is important in resilient agroforestry in tropical islands predicted to be especially affected by climate change. Findings reveal global links, building upon collective knowledge that can be used to inform breadfruit management. Results are also summarized in a brochure about breadfruit history and diversity in St. Vincent, and the Caribbean more broadly.
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Affiliation(s)
- Lauren Audi
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL 60022, USA; Program in Plant Biology and Conservation, Northwestern University, Evanston, IL 60201, USA; Institute for Comparative Genomics. American Museum of Natural History, New York, NY 10024, USA
| | - Gordon Shallow
- St. Vincent Botanical Garden, Kingstown 5Q8C+4W2, Saint Vincent and the Grenadines; The Ministry of Tourism, National Parks, Rivers and Beaches Authority, Kingstown 5Q6C+F6R, St. Vincent and the Grenadines
| | - Erasto Robertson
- The Ministry of Tourism, National Parks, Rivers and Beaches Authority, Kingstown 5Q6C+F6R, St. Vincent and the Grenadines
| | - Dean Bobo
- Institute for Comparative Genomics. American Museum of Natural History, New York, NY 10024, USA; The Department of Ecology Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
| | - Diane Ragone
- Breadfruit Institute, National Tropical Botanical Garden, Kalaheo, HI 96765, USA
| | - Elliot M Gardner
- International Center for Tropical Botany, Institute of Environment, Florida International University, Miami, FL 33133, USA; National Tropical Botanical Garden, Kalaheo, HI 96765, USA
| | | | - Jacek Wajer
- Natural History Museum, Cromwell Road London SW7 5BD, UK
| | - Nyree J C Zerega
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, IL 60022, USA; Program in Plant Biology and Conservation, Northwestern University, Evanston, IL 60201, USA.
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Jiménez-Zapata DL, Quiroga-Pérez M, Quiroz-Yepes M, Marulanda-Tobón A, Álvarez JC, Mosquera-López S. Development of a Method for Detecting and Estimating Moniliophthora roreri Spore Loads Based on Spore Traps and qPCR. J Fungi (Basel) 2022; 9:jof9010047. [PMID: 36675868 PMCID: PMC9862605 DOI: 10.3390/jof9010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/19/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022] Open
Abstract
Frosty pod rot, caused by Moniliophthora roreri, is the most damaging disease of cacao in Latin America and, to better comprehend its epidemiology, we must understand its dissemination and proliferation. However, we do not know how M. roreri spores loads fluctuate in time and space due to the lack of a reliable technique to quantify M. roreri spores in the fields. Therefore, we developed a method that relies on spore traps and qPCR to detect and quantify M. roreri spore loads. This study demonstrated that the qPCR protocol can detect down to 0.025 ng of M. roreri DNA and quantify between 0.006 ng and 60 ng. Moreover, it demonstrated that qPCR protocol can detect and quantify DNA extracted from spore suspension and spore traps containing at least 2.9 × 104 M. roreri spores. However, the variability of the estimates for spore samples was high. Finally, we described a spore-trap device designed to carry spore traps in the field. The qPCR protocol and spore-trap device here developed will help in the understanding of the M. roreri dissemination patterns since they can be used to assess the environmental loads of M. roreri spore in cacao fields.
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Affiliation(s)
- Diana L. Jiménez-Zapata
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
| | - Manuela Quiroga-Pérez
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
| | - Manuela Quiroz-Yepes
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- GEMA Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
| | - Alejandro Marulanda-Tobón
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- GEMA Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
| | - Javier C. Álvarez
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- Correspondence:
| | - Sandra Mosquera-López
- Division of Natural Systems and Sustainability, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín 050021, Colombia
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Jaimes Y, Gonzalez C, Rojas J, Rivera JJ, Cilas C, Argout X. Population Structure of Moniliophthora perniciosa in the Main Cacao Producing Departments of Colombia. PLANT DISEASE 2022; 106:1492-1501. [PMID: 34879729 DOI: 10.1094/pdis-12-20-2679-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The witches' broom (Moniliophthora perniciosa) is considered as one of the main threats for cacao production and, consequently, for chocolate production worldwide. In this work, the genetic diversity and population structure of M. perniciosa were analyzed for 59 isolates collected in five departments of Colombia and using 10 microsatellite markers. Analyses revealed 35 multilocus genotypes and clonal populations structure according to linkage disequilibrium analysis. One of the objectives of this study was to determine whether populations were differentiated by geographic origin or Theobroma cacao host genotype. Analysis of molecular variance, discriminant analysis of principal components, and Bruvo genetic distance suggested that the genetic structure was driven by geographic origin and not by T. cacao genotype. The results of this study were consistent with previous findings obtained in other cocoa-producing countries. Important insights were discussed regarding the dispersal patterns of the pathogen in Colombia and the genetic change of its populations because of different environmental conditions.
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Affiliation(s)
- Yeirme Jaimes
- Corporación Colombiana de Investigación Agropecuaria - Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación La Suiza, Rionegro, Santander 687511, Colombia
| | - Carolina Gonzalez
- Corporación Colombiana de Investigación Agropecuaria - Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Tibaitatá, Bogotá, Cundinamarca 0130, Colombia
| | - Jairo Rojas
- Corporación Colombiana de Investigación Agropecuaria - Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación La Suiza, Rionegro, Santander 687511, Colombia
| | - Jessica Johana Rivera
- Corporación Colombiana de Investigación Agropecuaria - Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación La Suiza, Rionegro, Santander 687511, Colombia
| | - Christian Cilas
- French Agricultural Research Centre for International Development (CIRAD), Deputy Director General for Research and Strategy, Université Félix Houphouët-Boigny, Cocody, 01 BP 6483 Abidjan, Côte d'Ivoire
| | - Xavier Argout
- Corporación Colombiana de Investigación Agropecuaria - Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Centro de Investigación Palmira, Palmira, Valle del Cauca 763531, Colombia
- French Agricultural Research Centre for International Development (CIRAD), UMR AGAP, Palmira 763532, Colombia
- AGAP, French Agricultural Research Centre for International Development (CIRAD), the French National Institute for Agriculture, Food, and Environment (INRAE), Institut Agro, Université Montpellier, 34398 Montpellier, France
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Ali SS, Amoako-Attah I, Shao J, Kumi-Asare E, Meinhardt LW, Bailey BA. Mitochondrial Genomics of Six Cacao Pathogens From the Basidiomycete Family Marasmiaceae. Front Microbiol 2021; 12:752094. [PMID: 34777305 PMCID: PMC8581569 DOI: 10.3389/fmicb.2021.752094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/01/2021] [Indexed: 11/23/2022] Open
Abstract
Thread blight disease has recently been described as an emerging disease on cacao (Theobroma cacao) in Ghana. In Ghana, thread blight disease is caused by multiple species of the Marasmiaceae family: Marasmius tenuissimus, M. crinis-equi, M. palmivorus, and Marasmiellus scandens. Interestingly, two additional members of the Marasmiaceae; Moniliophthora roreri (frosty pod rot) and Moniliophthora perniciosa (witches’ broom disease), are major pathogens of cacao in the Western hemisphere. It is important to accurately characterize the genetic relationships among these economically important species in support of their disease management. We used data from Illumina NGS-based genome sequencing efforts to study the mitochondrial genomes (mitogenomes) of the four cacao thread blight associated pathogens from Ghana and compared them with published mitogenomes of Mon. roreri and Mon. perniciosa. There is a remarkable interspecies variation in mitogenome size within the six cacao-associated Marasmiaceae species, ranging from 43,121 to 109,103 bp. The differences in genome lengths are primarily due to the number and lengths of introns, differences in intergenic space, and differences in the size and numbers of unidentified ORFs (uORF). Among seven M. tenuissimus mitogenomes sequenced, there is variation in size and sequence pointing to divergent evolution patterns within the species. The intronic regions show a high degree of sequence variation compared to the conserved sequences of the 14 core genes. The intronic ORFs identified, regardless of species, encode GIY-YIG or LAGLIDADG domain-containing homing endonuclease genes. Phylogenetic relationships using the 14 core proteins largely mimic the phylogenetic relationships observed in gene order patterns, grouping M. tenuissimus with M. crinis-equi, and M. palmivorus with Mon. roreri and Mon. perniciosa, leaving Mar. scandens as an outlier. The results from this study provide evidence of independent expansion/contraction events and sequence diversification in each species and establish a foundation for further exploration of the evolutionary trajectory of the fungi in Marasmiaceae family.
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Affiliation(s)
- Shahin S Ali
- Sustainable Perennial Crops Laboratory, U. S. Department of Agriculture (USDA)/Agricultural Research Service (ARS), Beltsville Agricultural Research Center-West, Beltsville, MD, United States.,Department of Viticulture and Enology, University of California, Davis, Davis, CA, United States
| | | | - Jonathan Shao
- U. S. Department of Agriculture (USDA)/Agricultural Research Service (ARS), Beltsville, MD, United States
| | | | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, U. S. Department of Agriculture (USDA)/Agricultural Research Service (ARS), Beltsville Agricultural Research Center-West, Beltsville, MD, United States
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, U. S. Department of Agriculture (USDA)/Agricultural Research Service (ARS), Beltsville Agricultural Research Center-West, Beltsville, MD, United States
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Ali SS, Asman A, Shao J, Firmansyah AP, Susilo AW, Rosmana A, McMahon P, Junaid M, Guest D, Kheng TY, Meinhardt LW, Bailey BA. Draft genome sequence of fastidious pathogen Ceratobasidium theobromae, which causes vascular-streak dieback in Theobroma cacao. Fungal Biol Biotechnol 2019; 6:14. [PMID: 31583107 PMCID: PMC6767637 DOI: 10.1186/s40694-019-0077-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/12/2019] [Indexed: 12/22/2022] Open
Abstract
Background Ceratobasidium theobromae, a member of the Ceratobasidiaceae family, is the causal agent of vascular-streak dieback (VSD) of cacao, a major threat to the chocolate industry in the South-East Asia. The fastidious pathogen is very hard to isolate and maintain in pure culture, which is a major bottleneck in the study of its genetic diversity and genome. Result This study describes for the first time, a 33.90 Mbp de novo assembled genome of a putative C. theobromae isolate from cacao. Ab initio gene prediction identified 9264 protein-coding genes, of which 800 are unique to C. theobromae when compared to Rhizoctonia spp., a closely related group. Transcriptome analysis using RNA isolated from 4 independent VSD symptomatic cacao stems identified 3550 transcriptionally active genes when compared to the assembled C. theobromae genome while transcripts for only 4 C. theobromae genes were detected in 2 asymptomatic stems. De novo assembly of the non-cacao associated reads from the VSD symptomatic stems uniformly produced genes with high identity to predicted genes in the C. theobromae genome as compared to Rhizoctonia spp. or genes found in Genbank. Further analysis of the predicted C. theobromae transcriptome was carried out identifying CAZy gene classes, KEGG-pathway associated genes, and 138 putative effector proteins. Conclusion These findings put forth, for the first time, a predicted genome for the fastidious basidiomycete C. theobromae causing VSD on cacao providing a model for testing and comparison in the future. The C. theobromae genome predicts a pathogenesis model involving secreted effector proteins to suppress plant defense mechanisms and plant cell wall degrading enzymes.
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Affiliation(s)
- Shahin S Ali
- 1Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD 20705 USA.,2Department of Viticulture & Enology, University of California, Davis, CA 95616 USA
| | - Asman Asman
- 3Department of Plant Pests and Diseases, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, 90245 Indonesia.,4Cocoa Research Group, Faculty of Agriculture, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, 90245 Indonesia
| | | | - Amanda P Firmansyah
- 6Faculty of Agriculture, Muhammadiyah University of Makassar, Makassar, Sulawesi Selatan 90221 Indonesia
| | - Agung W Susilo
- 7Indonesian Coffee and Cocoa Research Institute, Jl. PB Sudirman 90, Jember, 68118 Indonesia
| | - Ade Rosmana
- 3Department of Plant Pests and Diseases, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, 90245 Indonesia.,4Cocoa Research Group, Faculty of Agriculture, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, 90245 Indonesia
| | - Peter McMahon
- 8Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Muhammad Junaid
- 3Department of Plant Pests and Diseases, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, 90245 Indonesia.,4Cocoa Research Group, Faculty of Agriculture, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, 90245 Indonesia
| | - David Guest
- 8Sydney Institute of Agriculture, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006 Australia
| | - Tee Yei Kheng
- 9Cocoa Upstream Technology Department, Malaysian Cocoa Board, P.O. Box 30, Sg. Dulang Road, Sg. Sumun, Perak Malaysia
| | - Lyndel W Meinhardt
- 1Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD 20705 USA
| | - Bryan A Bailey
- 1Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD 20705 USA
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Jaimes YY, Ribeyre F, Gonzalez C, Rojas J, Furtado EL, Cilas C. Factors Affecting the Dynamics of Frosty Pod Rot in the Main Cocoa Areas of Santander State, Colombia. PLANT DISEASE 2019; 103:1665-1673. [PMID: 31094657 DOI: 10.1094/pdis-10-18-1761-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Frosty pod rot (FPR) caused by Moniliophthora roreri is the primary disease affecting cacao production in the major producing countries of the Americas and is one of the major threats to cacao worldwide. The incidence of FPR on clones with different levels of resistance was investigated in four localities of Santander State, Colombia, between July 2013 and May 2015. Dynamics of diseased pods were modeled using boosted regression trees, a machine learning technique that allows regressions to be performed without prior statistical assumptions. The results suggested that FPR epidemics varied according to plot location, clone, weeks of observation, and total pods produced. Dynamics in the phenology of pods had an effect on the epidemics, and this dynamic could partially explain the difference in resistance among clones. Although not total, partial resistance of ICS 95 was confirmed. An important wilt effect was observed, particularly in the resistant clones; consequently, differences in harvested pods were not significant among clones. Pod stripping remains a good practice for the management of the disease and this practice could also have an effect on the pod dynamics and wilt phenomenon.
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Affiliation(s)
- Yeirme Y Jaimes
- 1 AGROSAVIA, Research Center La Suiza, Rionegro-Santander, Colombia
| | - Fabienne Ribeyre
- 2 CIRAD, UPR Bioagresseurs, F-34398 Montpellier, France. Bioagresseurs, Univ Montpellier, CIRAD, Montpellier, France
| | | | - Jairo Rojas
- 1 AGROSAVIA, Research Center La Suiza, Rionegro-Santander, Colombia
| | - Edson L Furtado
- 4 Plant Protection Department, Faculty of Agricultural Sciences, São Paulo State University, Botucatu, SP, Brasil
| | - Christian Cilas
- 2 CIRAD, UPR Bioagresseurs, F-34398 Montpellier, France. Bioagresseurs, Univ Montpellier, CIRAD, Montpellier, France
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Bailey BA, Evans HC, Phillips‐Mora W, Ali SS, Meinhardt LW. Moniliophthora roreri, causal agent of cacao frosty pod rot. MOLECULAR PLANT PATHOLOGY 2018; 19:1580-1594. [PMID: 29194910 PMCID: PMC6638017 DOI: 10.1111/mpp.12648] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 06/07/2023]
Abstract
Taxonomy: Moniliophthora roreri (Cif.) H.C. Evans et al. ; Phylum Basidiomycota; Class Agaricomycetes; Order Agaricales; Family Marasmiaceae; Genus Moniliophthora. Biology: Moniliophthora roreri attacks Theobroma and Herrania species causing frosty pod rot. Theobroma cacao (cacao) is the host of major economic concern. Moniliophthora roreri is a hemibiotroph with a long biotrophic phase (45-90 days). Spore masses, of apparent asexual origin, are produced on the pod surface after initiation of the necrotrophic phase. Spores are spread by wind, rain and human activity. Symptoms of the biotrophic phase can include necrotic flecks and, in some cases, pod malformation, but pods otherwise remain asymptomatic. Relationship to Moniliophthora perniciosa: Moniliophthora roreri and Moniliophthora perniciosa, causal agent of witches' broom disease of cacao, are closely related. Their genomes are similar, including many of the genes they carry which are considered to be important in the disease process. Moniliophthora perniciosa, also a hemibiotroph, has a typical basidiomycete lifestyle and morphology, forming clamp connections and producing mushrooms. Basidiospores infect meristematic tissues including flower cushions, stem tips and pods. Moniliophthora roreri does not form clamp connections or mushrooms and infects pods only. Both pathogens are limited to the Western Hemisphere and are a threat to cacao production around the world. Agronomic importance: Disease losses caused by frosty pod rot can reach 90% and result in field abandonment. Moniliophthora roreri remains in the invasive phase in the Western Hemisphere, not having reached Brazil, some islands within the Caribbean and a few specific regions within otherwise invaded countries. DISEASE MANAGEMENT The disease can be managed by a combination of cultural (for example, maintenance of tree height and removal of infected pods) and chemical methods. These methods benefit from regional application, but can be cost prohibitive. Breeding for disease resistance offers the greatest potential for frosty pod rot management and new tolerant materials are becoming available.
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Affiliation(s)
- Bryan A. Bailey
- Sustainable Perennial Crops Laboratory, United States Department of AgricultureAgricultural Research ServiceBeltsvilleMD 20705USA
| | | | - Wilbert Phillips‐Mora
- Tropical Agricultural Research and Higher Education Center (CATIE)Turrialba 7170Costa Rica
| | - Shahin S. Ali
- Sustainable Perennial Crops Laboratory, United States Department of AgricultureAgricultural Research ServiceBeltsvilleMD 20705USA
| | - Lyndel W. Meinhardt
- Sustainable Perennial Crops Laboratory, United States Department of AgricultureAgricultural Research ServiceBeltsvilleMD 20705USA
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Bailey BA, Ali SS, Strem MD, Meinhardt LW. Morphological variants of Moniliophthora roreri on artificial media and the biotroph/necrotroph shift. Fungal Biol 2018; 122:701-716. [PMID: 29880205 DOI: 10.1016/j.funbio.2018.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 03/07/2018] [Accepted: 03/12/2018] [Indexed: 11/24/2022]
Abstract
Moniliophthora roreri (Mr) causes frosty pod rot of Theobroma cacao in a hemibiotrophic association. The Mr biotroph-like phase has not been studied in culture. Mr spores (isolates Co12, Co52, and B3) were germinated on high (V8) and low (BPMM) nutrients with different media hardness (0.5% to 3% agarose). Germination was high on V8 media. Hardness affected germination on BPMM. Most colonies on V8 were slow-growing, failing to sporulate. Colony morphology depended on the isolate. On BPMM, exaggerated mycelia formed of limited length with enlarged cells. On agarose, rapidly expanding sporulating necrotrophic colonies formed rarely. Co12 and B3 spores were germinated on V8 and BPMM with low melting point (LMP) agarose. Slow-growing colonies of B3 on BPMM were unstable on LMP agarose, often forming slow-growing/rapidly expanding hybrids. Slow-growing colonies are hypothesized to represent the biotrophic phase. One nucleus was common in Mr cells, other than spores. Binucleate cells were occasionally observed in aged cells of slow-growing mycelia. Co52 cells often had more than two nuclei per cell after germination. Mr mycelia cells typically carry a single nucleus, being considered haploid. Biotroph- and necrotroph-like mycelia displayed differential gene expression but results were inconsistent with published in vivo results and require further study.
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Affiliation(s)
- Bryan A Bailey
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville, MD, 20705, United States.
| | - Shahin S Ali
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville, MD, 20705, United States
| | - Mary D Strem
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville, MD, 20705, United States
| | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, USDA/ARS, Beltsville, MD, 20705, United States
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Jaimes YY, Gonzalez C, Rojas J, Cornejo OE, Mideros MF, Restrepo S, Cilas C, Furtado EL. Geographic Differentiation and Population Genetic Structure of Moniliophthora roreri in the Principal Cocoa Production Areas in Colombia. PLANT DISEASE 2016; 100:1548-1558. [PMID: 30686241 DOI: 10.1094/pdis-12-15-1498-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Frosty pod rot (FPR) disease on cocoa, caused by Moniliophthora roreri, is one of the most devastating cocoa disease in the Western Hemisphere. In Colombia, the disease is particularly severe in the Magdalena Valley, which is considered the possible center of origin for the pathogen species. We analyzed the genetic diversity of isolates from the departments of Santander, Antioquia, Tolima, and Huila in Colombia using 23 simple-sequence repeats (SSR) markers. In total, 117 different multilocus genotypes were found among 120 isolates, each one representing a unique haplotype. High mutation rates in the SSR and gene flow can explain the high levels of diversity. Also, the observed and standardized indexes of association (IA and řd) indicate that the populations of M. roreri are clonal. Furthermore, given the high haplotype diversity and the significant linkage disequilibrium observed, we hypothesize that M. roreri could be a primarily asexual species undergoing sporadic recombination or partial recombination through parasexuality. A Bayesian clustering analysis implemented by STRUCTURE showed that the most probable number of genetic groups in the data was three, confirming the geographical differentiation among isolates. Similar results were obtained by a discriminant analysis of principal components, a principal coordinate analysis, and a neighbor-joining tree from microsatellite loci base on Nei distance. Cacao genotypes and environmental variables did contribute to the genetic differentiation of the groups. We discuss how this information could be used to improve the management of FPR at the regional level.
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Affiliation(s)
- Yeirme Y Jaimes
- Corpoica, Research Center La Suiza, Rionegro-Santander, Colombia; CAPES PEC-PG Fellow; and Plant Protection Department, Faculty of Agricultural Sciences, São Paulo State University, Botucatu, SP, Brasil
| | | | | | - Omar E Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Maria F Mideros
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Silvia Restrepo
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Christian Cilas
- CIRAD, UR Bioagresseurs, Campus de Baillarguet, TA A-106/D, 34398 Montpellier Cedex 5, France
| | - E L Furtado
- CNPq Fellow, Plant Protection Department, Faculty of Agricultural Sciences, São Paulo State University, Botucatu, SP, Brasil
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