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Nousias O, Zheng J, Li T, Meinhardt LW, Bailey B, Gutierrez O, Baruah IK, Cohen SP, Zhang D, Yin Y. Three de novo assembled wild cacao genomes from the Upper Amazon. Sci Data 2024; 11:369. [PMID: 38605066 PMCID: PMC11009333 DOI: 10.1038/s41597-024-03215-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/03/2024] [Indexed: 04/13/2024] Open
Abstract
Theobroma cacao, the chocolate tree, is indigenous to the Amazon basin, the greatest biodiversity hotspot on earth. Recent advancement in plant genomics highlights the importance of de novo sequencing of multiple reference genomes to capture the genome diversity present in different cacao populations. In this study, three high-quality chromosome-level genomes of wild cacao were constructed, de novo assembled with HiFi long reads sequencing, and scaffolded using a reference-free strategy. These genomes represent the three most important genetic clusters of cacao trees from the Upper Amazon region. The three wild cacao genomes were compared with two reference genomes of domesticated cacao. The five cacao genetic clusters were inferred to have diverged in the early and middle Pleistocene period, approximately 1.83-0.69 million years ago. The results shown here serve as an example of understanding how the Amazonian biodiversity was developed. The three wild cacao genomes provide valuable resources for studying genetic diversity and advancing genetic improvement of this species.
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Affiliation(s)
- Orestis Nousias
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tang Li
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lyndel W Meinhardt
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA
| | - Bryan Bailey
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA
| | - Osman Gutierrez
- U.S. Department of Agriculture, Subtropical Horticulture Research Station, Miami, FL, USA
| | - Indrani K Baruah
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA
| | - Stephen P Cohen
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA
| | - Dapeng Zhang
- U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA.
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
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Purificacion M, Shah RBM, De Meeûs T, Bakar SB, Savantil AB, Yusof MM, Amalin D, Nguyen H, Sulistyowati E, Budiman A, Ekayanti A, Niogret J, Ravel S, Vreysen MJB, Abd-Alla AMM. Development and characterization of microsatellite markers for population genetics of the cocoa pod borer Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae). PLoS One 2024; 19:e0297662. [PMID: 38603675 PMCID: PMC11008836 DOI: 10.1371/journal.pone.0297662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 01/09/2024] [Indexed: 04/13/2024] Open
Abstract
The cocoa pod borer (CPB) Conopomorpha cramerella (Snellen) (Lepidoptera: Gracillaridae) is one of the major constraints for cocoa production in South East Asia. In addition to cultural and chemical control methods, autocidal control tactics such as the Sterile Insect Technique (SIT) could be an efficient addition to the currently control strategy, however SIT implementation will depend on the population genetics of the targeted pest. The aim of the present work was to search for suitable microsatellite loci in the genome of CPB that is partially sequenced. Twelve microsatellites were initially selected and used to analyze moths collected from Indonesia, Malaysia, and the Philippines. A quality control verification process was carried out and seven microsatellites found to be suitable and efficient to distinguish differences between CPB populations from different locations. The selected microsatellites were also tested against a closely related species, i.e. the lychee fruit borer Conopomorpha sinensis (LFB) from Vietnam and eight loci were found to be suitable. The availability of these novel microsatellite loci will provide useful tools for the analysis of the population genetics and gene flow of these pests, to select suitable CPB strains to implement the SIT.
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Affiliation(s)
- Marynold Purificacion
- Biological Control Research Unit, Center for Natural Science and Environmental Research, De La Salle University, Manila, Philippines
| | - Roslina Binti Mohd Shah
- Centre for Cocoa Biotechnology Research, Malaysian Cocoa Board, Kota Kinabalu, Sabah, Malaysia
| | - Thierry De Meeûs
- Intertryp, Univ Montpellier, Cirad, IRD, Montpellier, France
- IRD, UMR Intertryp, Cirad, Campus International de Baillarguet, Montpellier, France
| | | | - Anisah Bintil Savantil
- Centre for Cocoa Biotechnology Research, Malaysian Cocoa Board, Kota Kinabalu, Sabah, Malaysia
| | - Meriam Mohd Yusof
- Centre for Cocoa Biotechnology Research, Malaysian Cocoa Board, Kota Kinabalu, Sabah, Malaysia
| | - Divina Amalin
- Biological Control Research Unit, Center for Natural Science and Environmental Research, De La Salle University, Manila, Philippines
| | - Hien Nguyen
- Plant Protection Research Institute, Duc Thang, Hanoi, Vietnam
| | | | - Aris Budiman
- Indonesian Coffee and Cocoa Research Institute, Jember, Indonesia
| | - Arni Ekayanti
- Mars Cocoa Research Centre, Mars Wrigley, Sulawesi Selatan, Indonesia
| | - Jerome Niogret
- Mars Wrigley, Centre for Tropical Environmental & Sustainability Science, James Cook University Nguma-bada Campus, Smithfield, Australia
| | - Sophie Ravel
- Intertryp, Univ Montpellier, Cirad, IRD, Montpellier, France
| | - Marc J. B. Vreysen
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - Adly M. M. Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, Vienna, Austria
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Porcel M, Miranda TC, Pisco-Ortiz C, Camargo H, Moreno J, Gutiérrez Y. A scarab beetle (Coleoptera: Scarabaeidae) causes tree mortality, delayed growth, and yield reduction in cacao with genotype-specific susceptibility to herbivory. Pest Manag Sci 2024; 80:2179-2187. [PMID: 38158649 DOI: 10.1002/ps.7957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/26/2023] [Accepted: 12/30/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND This study explored the impact of Leucothyreus femoratus, a previously unreported folivorous pest in cacao cultivation, on cacao tree survival, development, and yield. The study was conducted in an experimental cacao plot in the Colombian plains, it featured 20 cacao genotypes in an agroforestry system, with plantain and Mexican sunflower providing temporary shade, and yopo offering permanent shade. RESULTS We found an infestation rate of 2.9 ± 0.3 adult beetles per cacao tree. L. femoratus larvae were discovered in association with the roots of all plants within the agroforestry arrangement; however, yopo and plantain exhibited the highest incidence of root-feeding larvae among these associated plants. Interestingly, male and female L. femoratus displayed distinct leaf consumption patterns in the laboratory, with females consuming more foliage relative to their body weight. Moreover, field observations highlighted the detrimental impact of L. femoratus herbivory on cacao tree survival and growth, leading to leaf skeletonization, reduced plant height, and stem diameter. Trees with over 50% leaf consumption suffered more than 20% mortality. Additionally, herbivory negatively affected cacao yield, correlating higher leaf surface damage with a decrease in harvested pods. The study also identified varying antixenotic resistance in different cacao genotypes, with some consistently displaying resistance while others showed variable levels during tree establishment and production stages. CONCLUSION This research underscores the significant role of L. femoratus as a cacao pest, emphasizing its adverse effects on cacao tree survival, development, and yield. Consequently, implementing effective control measures is vital for ensuring sustainable cacao cultivation. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Mario Porcel
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación La Libertad, Km. 17 vía Puerto López, Villavicencio, Meta, Colombia
- Instituto de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica, Centro Málaga, Cortijo de la Cruz S/N, Málaga, 29140, Spain
| | - Tatiana C Miranda
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación La Libertad, Km. 17 vía Puerto López, Villavicencio, Meta, Colombia
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Sede Central, Km 14 vía Bogotá - Mosquera, Mosquera, Colombia
| | - Carolina Pisco-Ortiz
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación La Libertad, Km. 17 vía Puerto López, Villavicencio, Meta, Colombia
- Programa de plagas y enfermedades, Centro de Investigación en Palma de Aceite (Cenipalma), Bogotá, D.C., Colombia
| | - Hebert Camargo
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación La Libertad, Km. 17 vía Puerto López, Villavicencio, Meta, Colombia
| | - Jessica Moreno
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación La Libertad, Km. 17 vía Puerto López, Villavicencio, Meta, Colombia
| | - Yeisson Gutiérrez
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación La Libertad, Km. 17 vía Puerto López, Villavicencio, Meta, Colombia
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Araújo MS, Chaves SFS, Pereira GR, Guimarães MHD, Alves AKS, Dias LAS, Souza CAS, Aguilar MAG. Multi-trait selection for nutritional and physiological quality of cacao genotypes in irrigated and non-irrigated environments. Sci Rep 2024; 14:6368. [PMID: 38493219 DOI: 10.1038/s41598-024-56556-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/07/2024] [Indexed: 03/18/2024] Open
Abstract
Water is a scarce, strategic resource and the most important input for economic development, especially in agricultural countries such as Brazil. Cocoa production is directly related to water availability, and, as climate changes, selecting drought-tolerant genotypes is vital to keep cacao crops sustainable. Here, we evaluated cacao genotypes under irrigated and water-stressed conditions and selected drought-tolerant ones based on nutritional and physiological traits. Thirty-nine genotypes were monitored for three years for agronomic traits and higher fruit yield. After this evaluation, the 18 most promising genotypes were evaluated in a randomized block design, under a 2 (with and without irrigation) × 18 (genotypes) factorial arrangement, with three replicates and five plants per plot. We evaluated seven physiological and 11 nutritional traits, selecting genotypes based on the Genotype-by-Trait Biplot approach. Significant effects (p < 0.05) were observed for the nutritional traits N, P, Mg, S, Zn, Cu, Mn and for the physiological traits CO2 assimilation rate (A), stomatal conductance (gs), transpiration (E), intercellular and atmospheric CO2 concentrations (Ci/Ca), intrinsic water use efficiency (A/gs), instantaneous water use efficiency (A/E), and instantaneous carboxylation efficiency (A/Ci), as determined by analysis of variance. The genotype × irrigation treatment interaction was significant (p < 0.05) for the traits A, gs, and E. Genotypes CP 41, CP 43, and CCN 51 exhibited superior performance for both nutritional and physiological traits (A, gs, and E). In the irrigated environment, CP 41 showed superiority in traits such as P, A/E, A/gs, Mn, S, and Zn. Conversely, under non-irrigated conditions, CP 43 exhibited better performance in nutritional properties, specifically Mn, Mg, and Zn. Notably, in both irrigated and non-irrigated environments, CCN 51 excelled in key physiological traits, including A/Ci, A/E, and A/gs. This robust performance across diverse conditions suggests that these three genotypes possess physiological mechanisms to endure water-stressed conditions. Our research can generate valuable insights into these genotypes informing suitable choices for cocoa cultivation, especially in the context of global climate change.
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Affiliation(s)
- Maurício S Araújo
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil.
| | - Saulo F S Chaves
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Guilherme R Pereira
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Matheus H D Guimarães
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Andressa K S Alves
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Luiz Antônio S Dias
- Department of Agronomy, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Carlos A S Souza
- Filogonio Peixoto Experimental Station (ESFIP), Cocoa Research Center, CEPLAC, Augusto Pestana Street, Linhares, Espírito Santo, 29990-192, Brazil
| | - Marco A G Aguilar
- Filogonio Peixoto Experimental Station (ESFIP), Cocoa Research Center, CEPLAC, Augusto Pestana Street, Linhares, Espírito Santo, 29990-192, Brazil
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Lanaud C, Vignes H, Utge J, Valette G, Rhoné B, Garcia Caputi M, Angarita Nieto NS, Fouet O, Gaikwad N, Zarrillo S, Powis TG, Cyphers A, Valdez F, Olivera Nunez SQ, Speller C, Blake M, Valdez FJ, Raymond S, Rowe SM, Duke GS, Romano FE, Loor Solórzano RG, Argout X. A revisited history of cacao domestication in pre-Columbian times revealed by archaeogenomic approaches. Sci Rep 2024; 14:2972. [PMID: 38453955 PMCID: PMC10920634 DOI: 10.1038/s41598-024-53010-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 01/25/2024] [Indexed: 03/09/2024] Open
Abstract
Humans have a long history of transporting and trading plants, contributing to the evolution of domesticated plants. Theobroma cacao originated in the Neotropics from South America. However, little is known about its domestication and use in these regions. In this study, ceramic residues from a large sample of pre-Columbian cultures from South and Central America were analyzed using archaeogenomic and biochemical approaches. Here we show, for the first time, the widespread use of cacao in South America out of its native Amazonian area of origin, extending back 5000 years, likely supported by cultural interactions between the Amazon and the Pacific coast. We observed that strong genetic mixing between geographically distant cacao populations occurred as early as the middle Holocene, in South America, driven by humans, favoring the adaptation of T. cacao to new environments. This complex history of cacao domestication is the basis of today's cacao tree populations and its knowledge can help us better manage their genetic resources.
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Affiliation(s)
- Claire Lanaud
- CIRAD, AGAP Institut, Avenue Agropolis, F-34398, Montpellier, France.
- AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - Hélène Vignes
- CIRAD, AGAP Institut, Avenue Agropolis, F-34398, Montpellier, France
- AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - José Utge
- UMR 7206 Eco-anthropologie, Département Homme et Environnement, MNHN-CNRS-Université Paris Cité, Paris, France
| | - Gilles Valette
- Institut des Biomolécules Max Mousseron - (UMR IBMM), Université de Montpellier, Montpellier, France
| | - Bénédicte Rhoné
- CIRAD, AGAP Institut, Avenue Agropolis, F-34398, Montpellier, France
- AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | | | - Olivier Fouet
- CIRAD, AGAP Institut, Avenue Agropolis, F-34398, Montpellier, France
- AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | | | - Sonia Zarrillo
- Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Terry G Powis
- Department of Geography and Anthropology, Kennesaw State University, Kennesaw, USA
| | - Ann Cyphers
- Universidad Nacional Autónoma de México (UNAM), México, México
| | - Francisco Valdez
- Institut de Recherche pour le Développement (IRD), UMR 208 PALOC, MNHN-IRD, Paris, France
| | | | - Camilla Speller
- Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Michael Blake
- Department of Anthropology, University of British Columbia, Vancouver, Canada
| | | | - Scott Raymond
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Canada
| | - Sarah M Rowe
- The University of Texas Rio Grande Valley, Edinburg, TX, USA
| | - Guy S Duke
- The University of Texas Rio Grande Valley, Edinburg, TX, USA
| | | | | | - Xavier Argout
- CIRAD, AGAP Institut, Avenue Agropolis, F-34398, Montpellier, France
- AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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6
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Llanos-Gómez KJ, Aime MC, Díaz-Valderrama JR. The surface of leaves and fruits of Peruvian cacao is home for several Hannaella yeast species, including the new species Hannaella theobromatis sp. nov. Antonie Van Leeuwenhoek 2024; 117:43. [PMID: 38413427 DOI: 10.1007/s10482-024-01936-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/28/2024] [Indexed: 02/29/2024]
Abstract
As part of a long-term study aiming to isolate and identify yeast species that inhabit the surface of leaves and fruits of native fine-aroma cacao in the department of Amazonas, Peru, we obtained multiple isolates of Hannaella species. Yeasts of the genus Hannaella are common inhabitants of the phyllosphere of natural and crop plants. On the basis of morphological, and physiological characteristics, and sequence analysis of the D1/D2 domains of the large subunit rRNA gene (LSU) and the internal transcribed spacer region (ITS), we identified five species of Hannaella from the phyllosphere of Peruvian cacao. Four have been previously described: H. phyllophila (isolates KLG-073, KLG-091), H. pagnoccae (KLG-076), H. sinensis (KLG-121), and H. taiwanensis (KLG-021). A fifth, represented by eight isolates (KLG-034, KLG-063, KLG-074, KLG-078, KLG-79, KLG-082, KLG-084, KLG-085), is not conspecific with any previously described Hannaella species, and forms the sister clade to H. surugaensis in the phylogenetic analysis. It has 2.6-3.9% (18-27 substitutions, 2-4 deletions, and 1-3 insertions in 610-938 bp-long alignments), and 9.8-10.0% nucleotide differences (37 substitutions and 14 insertions in 511-520 bp-long alignments) in the LSU and ITS regions, respectively, to H. surugaensis type strain, CBS 9426. Herein, the new species Hannaella theobromatis sp. nov. is described and characterised. The species epithet refers to its epiphytic ecology on its host Theobroma cacao.
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Affiliation(s)
- Kelvin J Llanos-Gómez
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Amazonas, Perú
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Jorge R Díaz-Valderrama
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Amazonas, Perú.
- Facultad de Ingeniería y Ciencias Agrarias, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Amazonas, Perú.
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7
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Winters NP, Wafula EK, Knollenberg BJ, Hämälä T, Timilsena PR, Perryman M, Zhang D, Sheaffer LL, Praul CA, Ralph PE, Prewitt S, Leandro-Muñoz ME, Delgadillo-Duran DA, Altman NS, Tiffin P, Maximova SN, dePamphilis CW, Marden JH, Guiltinan MJ. A combination of conserved and diverged responses underlies Theobroma cacao's defense response to Phytophthora palmivora. BMC Biol 2024; 22:38. [PMID: 38360697 PMCID: PMC10870529 DOI: 10.1186/s12915-024-01831-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Plants have complex and dynamic immune systems that have evolved to resist pathogens. Humans have worked to enhance these defenses in crops through breeding. However, many crops harbor only a fraction of the genetic diversity present in wild relatives. Increased utilization of diverse germplasm to search for desirable traits, such as disease resistance, is therefore a valuable step towards breeding crops that are adapted to both current and emerging threats. Here, we examine diversity of defense responses across four populations of the long-generation tree crop Theobroma cacao L., as well as four non-cacao Theobroma species, with the goal of identifying genetic elements essential for protection against the oomycete pathogen Phytophthora palmivora. RESULTS We began by creating a new, highly contiguous genome assembly for the P. palmivora-resistant genotype SCA 6 (Additional file 1: Tables S1-S5), deposited in GenBank under accessions CP139290-CP139299. We then used this high-quality assembly to combine RNA and whole-genome sequencing data to discover several genes and pathways associated with resistance. Many of these are unique, i.e., differentially regulated in only one of the four populations (diverged 40 k-900 k generations). Among the pathways shared across all populations is phenylpropanoid biosynthesis, a metabolic pathway with well-documented roles in plant defense. One gene in this pathway, caffeoyl shikimate esterase (CSE), was upregulated across all four populations following pathogen treatment, indicating its broad importance for cacao's defense response. Further experimental evidence suggests this gene hydrolyzes caffeoyl shikimate to create caffeic acid, an antimicrobial compound and known inhibitor of Phytophthora spp. CONCLUSIONS Our results indicate most expression variation associated with resistance is unique to populations. Moreover, our findings demonstrate the value of using a broad sample of evolutionarily diverged populations for revealing the genetic bases of cacao resistance to P. palmivora. This approach has promise for further revealing and harnessing valuable genetic resources in this and other long-generation plants.
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Affiliation(s)
- Noah P Winters
- IGDP Ecology, The Pennsylvania State University, 422 Huck Life Sciences Building, University Park, PA, 16803, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | | | - Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Prakash R Timilsena
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Melanie Perryman
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, USA
| | - Lena L Sheaffer
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Craig A Praul
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Paula E Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sarah Prewitt
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Naomi S Altman
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Siela N Maximova
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Claude W dePamphilis
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
- IGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA
| | - James H Marden
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Mark J Guiltinan
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
- Department of Biology, The Pennsylvania State University, University Park, PA, USA.
- IGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA.
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.
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8
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Septiani P, Pramesti Y, Ningsih DU, Pancaningtyas S, Meitha K. Identification of self- and pathogen-targeted miRNAs from resistant and susceptible Theobroma cacao variety to black pod disease. Sci Rep 2024; 14:3272. [PMID: 38332251 PMCID: PMC10853554 DOI: 10.1038/s41598-024-53685-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Cacao (Theobroma cacao) is a highly valuable crop with growing demand in the global market. However, cacao farmers often face challenges posed by black pod disease caused by Phytophthora spp., with P. palmivora being the most dominant. Regulations of various gene expressions influence plant resistance to pathogens. One mechanism involves targeting the mRNA of virulence genes in the invading pathogens, suppressing their infection. However, resistance also could be suppressed by plant-derived miRNAs that target their own defence genes. The objective of this study is to identify differentially expressed miRNAs in black pod-resistant and susceptible cacao varieties and to predict their targets in T. cacao and P. palmivora transcripts. Extracted miRNA from resistant and susceptible varieties of T. Cacao was sequenced, identified, and matched to host and pathogen mRNA. In total, 54 known miRNAs from 40 miRNA families and 67 novel miRNAs were identified. Seventeen miRNAs were differentially expressed in susceptible variety compared to resistant one, with 9 miRNAs upregulated and 8 miRNAs downregulated. In T. cacao transcripts, the upregulated miRNAs were predicted to target several genes, including defence genes. The suppression of these defense genes can lead to a reduction in plant resistance against pathogen infection. In P. palmivora transcripts, the upregulated miRNAs were predicted to target several genes, including P. palmivora effector genes. In the future, limiting expression of miRNAs that target T. cacao's defence genes and applying miRNAs that target P. palmivora effector genes hold promise for enhancing cacao plant resistance against P. palmivora infection.
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Affiliation(s)
- Popi Septiani
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Yonadita Pramesti
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Devi Ulfa Ningsih
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia
| | - Sulistyani Pancaningtyas
- Indonesian Coffee and Cocoa Research Institute (ICCRI), Jl. PB. Sudirman 90, Jember, 68118, Indonesia
| | - Karlia Meitha
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jl. Ganesha No. 10, Bandung, 40132, Indonesia.
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9
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Huamán-Pilco AF, Ramos-Carrasco TA, Franco MEE, Tineo-Flores D, Estrada-Cañari R, Romero PE, Aguilar-Rafael V, Ramírez-Orrego LA, Tincopa-Marca R, Márquez FR, Oliva-Cruz M, Díaz-Valderrama JR. Morphological, phylogenetic, and genomic evidence reveals the causal agent of thread blight disease of cacao in Peru is a new species of Marasmius in the section Neosessiles, Marasmius infestans sp. nov. F1000Res 2024; 12:1327. [PMID: 38680601 PMCID: PMC11053350 DOI: 10.12688/f1000research.140405.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 05/01/2024] Open
Abstract
The thread blight disease (TBD) of cacao ( Theobroma cacao) in the department of Amazonas, Peru was recently reported to be caused by Marasmius tenuissimus (sect. Neosessiles). This same species is known to be the main causal agent of TBD in West Africa. However, some morphological characteristics, such as the presence of rhizomorphs, the almost exclusively white color, and pileus sizes less than 5 mm, among others, differ to the description of M. tenuissimus. Therefore, we aimed to conduct a taxonomic revision of the cacao-TBD causal agent in Peru, by using thorough micro and macro morphological, phylogenetic, and nuclear and mitochondrial genomic approaches. We showed that the causal agent of TBD of cacao in Amazonas, Peru, belongs to a new species, Marasmius infestans sp. nov. This study enriches our knowledge of species in the sect. Neosessiles, and strongly suggests that the M. tenuissimus species complex is highly diverse.
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Affiliation(s)
- Angel Fernando Huamán-Pilco
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
| | - Tito Ademir Ramos-Carrasco
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
| | - Mario Emilio Ernesto Franco
- Sustainable Plant Protection Programme, Institute of Agrifood Research and Technology (IRTA), 25198 Lieda, Spain
- Department of Soil, Plant and Food Sciences, Universita degli Studi di Bari Aldo Moro, Bari, Apulia, 70126, Italy
| | - Daniel Tineo-Flores
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
- Centro Experimental Yanayacu, Dirección de Supervisión y Monitoreo en las Estaciones Experimentales Agrarias, Instituto Nacional de Innovación Agraria, Jaén 06801, Calamarca, Peru
| | - Richard Estrada-Cañari
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria, Lima, Lima, Peru
| | - Pedro Eduardo Romero
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima District, Lima Region, Peru
| | - Vilma Aguilar-Rafael
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
| | - Lourdes Adriana Ramírez-Orrego
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
| | - Rosalina Tincopa-Marca
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
| | - Fanny-Rosario Márquez
- Escuela Profesional de Ingeniería Agronómica Tropical, Universidad Nacional Intercultural de Quillabamba, Quillabamba, Cusco, Peru
| | - Manuel Oliva-Cruz
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
| | - Jorge Ronny Díaz-Valderrama
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
- Facultad de Ingeniería y Ciencias Agrarias, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
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10
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Hernández-Delgado HE, Zamora-Briseño JA, Figueroa-Yáñez LJ, Urrea-López R. Vacuum-Forced Agroinfiltration for In planta Transformation of Recalcitrant Plants: Cacao as a Case Study. J Vis Exp 2023. [PMID: 38047562 DOI: 10.3791/66024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
Transient in planta transformation is a fast and cost-effective alternative for plant genetic transformation. Most protocols for in planta transformation rely on the use of Agrobacterium-mediated transformation. However, the protocols currently in use are standardized for small-sized plants due to the physical and economic constraints of submitting large-sized plants to a vacuum treatment. This work presents an effective protocol for localized vacuum-based agroinfiltration customized for large-sized plants. To assess the efficacy of the proposed method, we tested its use in cacao plants, a tropical plant species recalcitrant to genetic transformation. Our protocol allowed applying up to 0.07 MPa vacuum, with repetitions, to a localized aerial part of cacao leaves, making it possible to force the infiltration of Agrobacterium into the intercellular spaces of attached leaves. As a result, we achieved the Agrobacterium-mediated transient in planta transformation of attached cacao leaves expressing for the RUBY reporter system. This is also the first Agrobacterium-mediated in planta transient transformation of cacao. This protocol would allow the application of the vacuum-based agroinfiltration method to other plant species with similar size constraints and open the door for the in planta characterization of genes in recalcitrant woody, large-size species.
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Affiliation(s)
- Hilda E Hernández-Delgado
- Unidad de Biotecnología Vegetal, Centro de Investigación Y Asistencia en Tecnología Y Diseño del Estado de Jalisco (CIATEJ)
| | | | - Luis Joel Figueroa-Yáñez
- Unidad de Biotecnología Industrial, Centro de Investigación Y Asistencia en Tecnología Y Diseño del Estado de Jalisco (CIATEJ)
| | - Rafael Urrea-López
- Unidad de Biotecnología Vegetal, Centro de Investigación Y Asistencia en Tecnología Y Diseño del Estado de Jalisco (CIATEJ);
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11
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Schmidt JE, Puig AS, DuVal AE, Pfeufer EE. Phyllosphere microbial diversity and specific taxa mediate within-cultivar resistance to Phytophthora palmivora in cacao. mSphere 2023; 8:e0001323. [PMID: 37603690 PMCID: PMC10597403 DOI: 10.1128/msphere.00013-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/08/2023] [Indexed: 08/23/2023] Open
Abstract
The oomycete pathogen Phytophthora palmivora, which causes black pod rot (BPR) on cacao (Theobroma cacao L.), is responsible for devastating yield losses worldwide. Genetic variation in resistance to Phytophthora spp. is well documented among cacao cultivars, but variation has also been observed in the incidence of BPR even among trees of the same cultivar. In light of evidence that the naturally occurring phyllosphere microbiome can influence foliar disease resistance in other host-pathogen systems, it was hypothesized that differences in the phyllosphere microbiome between two field accessions of the cultivar Gainesville II 164 could be responsible for their contrasting resistance to P. palmivora. Bacterial alpha diversity was higher but fungal alpha diversity was lower in the more resistant accession MITC-331, and the accessions harbored phyllosphere microbiomes with distinct community compositions. Six bacterial and 82 fungal amplicon sequence variants (ASVs) differed in relative abundance between MITC-333 and MITC-331, including bacterial putative biocontrol agents and a high proportion of fungal pathogens, and nine fungal ASVs were correlated with increased lesion development. The roles of contrasting light availability and host mineral nutrition, particularly potassium, are also discussed. Results of this preliminary study can be used to guide research into microbiome-informed integrated pest management strategies effective against Phytophthora spp. in cacao. IMPORTANCE Up to 40% of the world's cacao is lost each year to diseases, the most devastating of which is black pod rot, caused by Phytophthora palmivora. Though disease resistance is often attributed to cacao genotypes (i.e., disease-resistant rootstocks), this study highlights the role of the microbiome in contributing to differences in resistance even among accessions of the same cacao cultivar. Future studies of plant-pathogen interactions may need to account for variation in the host microbiome, and optimizing the cacao phyllosphere microbiome could be a promising new direction for P. palmivora resistance research.
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Affiliation(s)
| | - Alina S. Puig
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Fort Detrick, Frederick, Maryland, USA
| | | | - Emily E. Pfeufer
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Fort Detrick, Frederick, Maryland, USA
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12
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De Oliveira AC, Muhovski Y, Rogez H, Debode F. DNA Isolation from Cocoa-Derived Products and Cocoa Authentication by TaqMan Real-Time PCR. Methods Mol Biol 2023; 2967:75-83. [PMID: 37608104 DOI: 10.1007/978-1-0716-3358-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Cocoa (Theobroma cacao L.) is an international commodity used as an ingredient in the manufacturing of chocolate making its authentication a key issue in the cocoa chain. Various molecular techniques have been increasingly applied for quality requirements. These issues highlight the need for techniques that allow the extraction and detection of cocoa DNA from highly processed cocoa products and chocolate. The applicability of real-time PCR to highly processed cocoa-derived products for authentication purposes depends on the possibility of extracting high-quality and amplifiable DNA and further developing efficient PCR tests. This methodology herein describes the use of a classical CTAB method providing DNA suitable for TaqMan real-time PCR amplification. Real-time PCR is a simple and fast method, with a high potential application in a wide range of food products. The main features of this technique are focused on two DNA targets, one located in the nuclear genome (vicilin-li PCR test) and a second one based on chloroplast DNA (lipids PCR test), which successfully passed the performance criteria considering the specificity, sensitivity, efficiency of amplification, robustness, and applicability in processed cocoa-derived products and chocolate.
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Affiliation(s)
- Ana Caroline De Oliveira
- Department of Life Sciences, Unit Bioengineering, Walloon Agricultural Research Centre (CRA-W), Gembloux, Belgium.
| | - Yordan Muhovski
- Department of Life Sciences, Unit Bioengineering, Walloon Agricultural Research Centre (CRA-W), Gembloux, Belgium
| | - Herve Rogez
- Centre for Valorisation of Amazonian Bioactive Compounds (CVACBA) & Universidade Federal Do Pará, Belém, Pará, Brazil
| | - Frédéric Debode
- Department of Life Sciences, Unit Bioengineering, Walloon Agricultural Research Centre (CRA-W), Gembloux, Belgium
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13
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de Souza Araújo DM, de Almeida AAF, Pirovani CP, Mora-Ocampo IY, Lima Silva JP, Valle Meléndez RR. Molecular, biochemical and micromorphological responses of cacao seedlings of the Parinari series, carrying the lethal gene Luteus-Pa, in the presence and absence of cotyledons. Plant Physiol Biochem 2023; 194:550-569. [PMID: 36525937 DOI: 10.1016/j.plaphy.2022.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Investigations of the compatibility between cacao genotypes of the population of the Parinari series (Pa), resulting from the reciprocal crossing of Pa 30 × Pa 169 and Pa 121 × Pa 169, allowed the verification of the occurrence of the recessive lethal single character called Luteus-Pa. These genotypes have this gene in heterozygosity, which when intercross or self-fertilize, segregate in a 3:1 ratio. Normal (NS) and mutant (MS) seedlings grow normally and, after a period of approximately 30 days of age, MS leaves begin to show a metallic yellow color, followed by necrotic spots, and death of the entire seedling, approximately 40 days after the emergency. The work evaluate the molecular, biochemical and micromorphological responses in NS and MS, with and without cotyledons, resulting from the crossing of the Pa 30 × Pa 169 cacao genotypes, aiming to elucidate the possible lethal mechanisms of the homozygous recessive Luteus-Pa. The presence of the lethal gene Luteus-Pa in the seedlings of the cacao genotypes of the population of the Parinari (Pa), with and without cotyledons, resulting from the crossing of Pa 30 × Pa 169, in addition to regulating the synthesis of proteins related to the photosynthetic and stress defense processes, promoted an increase in the synthesis of proteins involved in the glycolic pathway, induced oxidative stress, altered the mobilization of cotyledonary reserves, the integrity of cell membranes, leaf micromorphology and induced the death of seedlings, soon after depletion of protein and carbohydrate reserves, especially in the absence of cotyledons.
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Affiliation(s)
- D'avila Maria de Souza Araújo
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - Alex-Alan Furtado de Almeida
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil.
| | - Carlos Priminho Pirovani
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - Irma Yuliana Mora-Ocampo
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - João Paulo Lima Silva
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - Raúl René Valle Meléndez
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil; Executive Commission for the Cacao farming Plan, km 22 Jorge Amado Highway, 45650-780, Ilhéus, BA, Brazil
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14
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Hou S, Zhang Q, Chen J, Meng J, Wang C, Du J, Guo Y. Genome-Wide Identification and Analysis of the GRAS Transcription Factor Gene Family in Theobroma cacao. Genes (Basel) 2022; 14:57. [PMID: 36672798 PMCID: PMC9858872 DOI: 10.3390/genes14010057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/28/2022] Open
Abstract
GRAS genes exist widely and play vital roles in various physiological processes in plants. In this study, to identify Theobroma cacao (T. cacao) GRAS genes involved in environmental stress and phytohormones, we conducted a genome-wide analysis of the GRAS gene family in T. cacao. A total of 46 GRAS genes of T. cacao were identified. Chromosomal distribution analysis showed that all the TcGRAS genes were evenly distributed on ten chromosomes. Phylogenetic relationships revealed that GRAS proteins could be divided into twelve subfamilies (HAM: 6, LISCL: 10, LAS: 1, SCL4/7: 1, SCR: 4, DLT: 1, SCL3: 3, DELLA: 4, SHR: 5, PAT1: 6, UN1: 1, UN2: 4). Of the T. cacao GRAS genes, all contained the GRAS domain or GRAS superfamily domain. Subcellular localization analysis predicted that TcGRAS proteins were located in the nucleus, chloroplast, and endomembrane system. Gene duplication analysis showed that there were two pairs of tandem repeats and six pairs of fragment duplications, which may account for the rapid expansion in T. cacao. In addition, we also predicted the physicochemical properties and cis-acting elements. The analysis of GO annotation predicted that the TcGRAS genes were involved in many biological processes. This study highlights the evolution, diversity, and characterization of the GRAS genes in T. cacao and provides the first comprehensive analysis of this gene family in the cacao genome.
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Affiliation(s)
- Sijia Hou
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Qianqian Zhang
- Chinese Institute for Brain Research, Beijing 102206, China
- College of Biological Science, China Agricultural University, Beijing 100193, China
| | - Jing Chen
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jianqiao Meng
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Cong Wang
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Junhong Du
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yunqian Guo
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China
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15
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Colonges K, Seguine E, Saltos A, Davrieux F, Minier J, Jimenez JC, Lahon MC, Calderon D, Subia C, Sotomayor I, Fernández F, Fouet O, Rhoné B, Argout X, Lebrun M, Costet P, Lanaud C, Boulanger R, Loor Solorzano RG. Diversity and determinants of bitterness, astringency, and fat content in cultivated Nacional and native Amazonian cocoa accessions from Ecuador. Plant Genome 2022; 15:e20218. [PMID: 36065790 DOI: 10.1002/tpg2.20218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Cocoa (Theobroma cacao L.) is the only tree that can produce cocoa. Cocoa beans are highly sought after by chocolate makers to produce chocolate. Cocoa can be fine aromatic, characterized by floral and fruity notes, or it can be described as standard cocoa with a more pronounced cocoa aroma and bitterness. In this study, the genetic and biochemical determinants of sensorial notes and nonvolatile compounds related to bitterness, astringency, fat content, and protein content will be investigated in two populations: a cultivated modern Nacional population and a population of cocoa accessions collected recently in the Ecuadorian South Amazonia area of origin of the Nacional ancestral variety. For this purpose, a genome-wide association study (GWAS) was carried out on both populations, with results of biochemical compounds evaluated by near-infrared spectroscopy (NIRS) assays and with sensory evaluations. Twenty areas of associations were detected for sensorial data especially bitterness and astringency. Fifty-three areas of associations were detected linked to nonvolatile compounds. A total of 81 candidate genes could be identified in the areas of the association.
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Affiliation(s)
- Kelly Colonges
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR Qualisud, Montpellier, F-34398, France
- Qualisud, Univ. Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Edward Seguine
- Seguine Cacao/Guittard Chocolate Co, Arroyo Grande, CA, USA
| | - Alejandra Saltos
- Instituto Nacional de Investigacion Agropecurias, INIAP, Quito, Ecuador
| | - Fabrice Davrieux
- Qualisud, Univ. Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- Cirad, UMR Qualisud, Réunion, F-97400, France
| | - Jérôme Minier
- Qualisud, Univ. Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
- Cirad, UMR Qualisud, Réunion, F-97400, France
| | | | - Marie-Christine Lahon
- CIRAD, UMR Qualisud, Montpellier, F-34398, France
- Qualisud, Univ. Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Darío Calderon
- Instituto Nacional de Investigacion Agropecurias, INIAP, Quito, Ecuador
| | - Cristian Subia
- Instituto Nacional de Investigacion Agropecurias, INIAP, Quito, Ecuador
| | - Ignacio Sotomayor
- Instituto Nacional de Investigacion Agropecurias, INIAP, Quito, Ecuador
| | - Fabián Fernández
- Instituto Nacional de Investigacion Agropecurias, INIAP, Quito, Ecuador
| | - Olivier Fouet
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Bénédicte Rhoné
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Xavier Argout
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Marc Lebrun
- CIRAD, UMR Qualisud, Montpellier, F-34398, France
- Qualisud, Univ. Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | | | - Claire Lanaud
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- AGAP Institut, Univ. Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Renaud Boulanger
- CIRAD, UMR Qualisud, Montpellier, F-34398, France
- Qualisud, Univ. Montpellier, Avignon Université, CIRAD, Institut Agro, IRD, Université de La Réunion, Montpellier, France
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16
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Lopes UV, Pires JL, Gramacho KP, Grattapaglia D. Genome-wide SNP genotyping as a simple and practical tool to accelerate the development of inbred lines in outbred tree species: An example in cacao (Theobroma cacao L.). PLoS One 2022; 17:e0270437. [PMID: 36288356 PMCID: PMC9604995 DOI: 10.1371/journal.pone.0270437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Cacao is a globally important crop with a long history of domestication and selective breeding. Despite the increased use of elite clones by cacao farmers, worldwide plantations are established mainly using hybrid progeny material derived from heterozygous parents, therefore displaying high tree-to-tree variability. The deliberate development of hybrids from advanced inbred lines produced by successive generations of self-pollination has not yet been fully considered in cacao breeding. This is largely due to the self-incompatibility of the species, the long generation cycles (3–5 years) and the extensive trial areas needed to accomplish the endeavor. We propose a simple and accessible approach to develop inbred lines based on accelerating the buildup of homozygosity based on regular selfing assisted by genome-wide SNP genotyping. In this study we genotyped 90 clones from the Brazilian CEPEC´s germplasm collection and 49 inbred offspring of six S1 or S2 cacao families derived from self-pollinating clones CCN-51, PS-13.19, TSH-1188 and SIAL-169. A set of 3,380 SNPs distributed across the cacao genome were interrogated on the EMBRAPA multi-species 65k Infinium chip. The 90 cacao clones showed considerable variation in genome-wide SNP homozygosity (mean 0.727± 0.182) and 19 of them with homozygosity ≥90%. By assessing the increase in homozygosity across two generations of self-pollinations, SNP data revealed the wide variability in homozygosity within and between S1 and S2 families. Even in small families (<10 sibs), individuals were identified with up to ~1.5 standard deviations above the family mean homozygosity. From baseline homozygosities of 0.476 and 0.454, offspring with homozygosities of 0.862 and 0.879 were recovered for clones TSH-1188 and CCN-51 respectively, in only two generations of selfing (81–93% increase). SNP marker assisted monitoring and selection of inbred individuals can be a practical tool to optimize and accelerate the development of inbred lines of outbred tree species. This approach will allow a faster and more accurate exploitation of hybrid breeding strategies in cacao improvement programs and potentially in other perennial fruit and forest trees.
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Affiliation(s)
| | | | | | - Dario Grattapaglia
- Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, Brasilia, Brazil
- * E-mail:
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Du J, Zhang Q, Hou S, Chen J, Meng J, Wang C, Liang D, Wu R, Guo Y. Genome-Wide Identification and Analysis of the R2R3-MYB Gene Family in Theobroma cacao. Genes (Basel) 2022; 13:genes13091572. [PMID: 36140738 PMCID: PMC9498333 DOI: 10.3390/genes13091572] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
The MYB gene family is involved in the regulation of plant growth, development and stress responses. In this paper, to identify Theobroma cacao R2R3-MYB (TcMYB) genes involved in environmental stress and phytohormones, we conducted a genome-wide analysis of the R2R3-MYB gene family in Theobroma cacao (cacao). A total of 116 TcMYB genes were identified, and they were divided into 23 subgroups according to the phylogenetic analysis. Meanwhile, the conserved motifs, gene structures and cis-acting elements of promoters were analyzed. Moreover, these TcMYB genes were distributed on 10 chromosomes. We conducted a synteny analysis to understand the evolution of the cacao R2R3-MYB gene family. A total of 37 gene pairs of TcMYB genes were identified through tandem or segmental duplication events. Additionally, we also predicted the subcellular localization and physicochemical properties. All the studies showed that TcMYB genes have multiple functions, including responding to environmental stresses. The results provide an understanding of R2R3-MYB in Theobroma cacao and lay the foundation for a further functional analysis of TcMYB genes in the growth of cacao.
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Affiliation(s)
- Junhong Du
- Center for Computational Biology, College of Biological Science and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
| | - Qianqian Zhang
- Chinese Institute for Brain Research, Beijing 102206, China
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Sijia Hou
- Center for Computational Biology, College of Biological Science and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
| | - Jing Chen
- Center for Computational Biology, College of Biological Science and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
| | - Jianqiao Meng
- Center for Computational Biology, College of Biological Science and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
| | - Cong Wang
- Center for Computational Biology, College of Biological Science and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
| | - Dan Liang
- Center for Computational Biology, College of Biological Science and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Science and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
| | - Yunqian Guo
- Center for Computational Biology, College of Biological Science and Technology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
- Correspondence:
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La-Rostami F, Wax N, Druschka M, Adams E, Albert C, Fischer M. In Vitro CRISPR-Cpf1 Assay for Differentiation of Fine and Bulk Cocoa ( Theobroma cacao L.). J Agric Food Chem 2022; 70:8819-8826. [PMID: 35786882 DOI: 10.1021/acs.jafc.2c02537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cocoa cultivation is dominated by the clone "Colleción Castro Naranjal 51" (CCN-51). In contrast, CCN-51 is the expensive and aromatic fine cocoa "Arriba Nacional" from Ecuador. The differences in the overall quality of the beans and in the prices show that it is necessary to develop a rapid and accurate method to distinguish these varieties and prevent food fraud. To this end, we used a CRISPR-Cpf1 assay suitable for AT-rich targets such as the chloroplast genome (cpGenome). SNPs in cocoa plastid genomes were selected to replace the canonical PAM sequence of Cpf1 (5'-TTTV-3'). We developed two assay systems to digest both Arriba and CCN-51. The results were tested qualitatively by agarose gel electrophoresis and quantitatively by capillary gel electrophoresis. Using the assay described here, we were able to reliably detect admixtures of 5% CCN-51 (P < 0.01) and 10% Arriba (P < 0.05). The application to processed cocoa products was also successful.
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Affiliation(s)
- Farshad La-Rostami
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Nils Wax
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Michael Druschka
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Elena Adams
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Chenyang Albert
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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Paschoal D, Costa JL, da Silva EM, da Silva FB, Capelin D, Ometto V, Aricetti JA, Carvalho GG, Pimpinato RF, de Oliveira RF, Carrera E, López-Díaz I, Rossi ML, Tornisielo V, Caldana C, Riano-Pachon DM, Cesarino I, Teixeira PJPL, Figueira A. Infection by Moniliophthora perniciosa reprograms tomato Micro-Tom physiology, establishes a sink, and increases secondary cell wall synthesis. J Exp Bot 2022; 73:3651-3670. [PMID: 35176760 DOI: 10.1093/jxb/erac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Witches' broom disease of cacao is caused by the pathogenic fungus Moniliophthora perniciosa. By using tomato (Solanum lycopersicum) cultivar Micro-Tom (MT) as a model system, we investigated the physiological and metabolic consequences of M. perniciosa infection to determine whether symptoms result from sink establishment during infection. Infection of MT by M. perniciosa caused reductions in root biomass and fruit yield, a decrease in leaf gas exchange, and down-regulation of photosynthesis-related genes. The total leaf area and water potential decreased, while ABA levels, water conductance/conductivity, and ABA-related gene expression increased. Genes related to sugar metabolism and those involved in secondary cell wall deposition were up-regulated upon infection, and the concentrations of sugars, fumarate, and amino acids increased. 14C-glucose was mobilized towards infected MT stems, but not in inoculated stems of the MT line overexpressing CYTOKININ OXIDASE-2 (35S::AtCKX2), suggesting a role for cytokinin in establishing a sugar sink. The up-regulation of genes involved in cell wall deposition and phenylpropanoid metabolism in infected MT, but not in 35S::AtCKX2 plants, suggests establishment of a cytokinin-mediated sink that promotes tissue overgrowth with an increase in lignin. Possibly, M. perniciosa could benefit from the accumulation of secondary cell walls during its saprotrophic phase of infection.
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Affiliation(s)
- Daniele Paschoal
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Juliana L Costa
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Eder M da Silva
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Fábia B da Silva
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Diogo Capelin
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Vitor Ometto
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Juliana A Aricetti
- Laboratório Nacional de Biorrenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, 13083-100, Brazil
| | - Gabriel G Carvalho
- Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Rodrigo F Pimpinato
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Ricardo F de Oliveira
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Esther Carrera
- Universitat Politècnica de València (UPV), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Isabel López-Díaz
- Universitat Politècnica de València (UPV), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Mônica L Rossi
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Valdemar Tornisielo
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Camila Caldana
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Diego M Riano-Pachon
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
| | - Igor Cesarino
- Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Paulo J P L Teixeira
- Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, SP, 13400-970, Brazil
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Hong La V. Genome-Wide Identification and Analysis of Heat Shock Protein 70 Family in Theobroma cacao. Pak J Biol Sci 2022; 25:608-618. [PMID: 36098167 DOI: 10.3923/pjbs.2022.608.618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
<b>Background and Objective:</b> In plants, the 70 kDa heat shock proteins (Hsp70-s) play important roles during growth and development and in response to stresses. This study aimed to provide comprehensive information on the <i>Hsp70 </i>family in cocoa (<i>Theobroma cacao</i>), one of the most important tropical perennial cash crops worldwide. <b>Materials and Methods:</b> A basic local alignment search tool (TBLASTN) against the cocoa genome was performed using <i>Arabidopsis</i> Hsp70-s as queries to detect TcHsp70-s. Sequence analyses were carried out by various bioinformatics tools. <b>Results:</b> A total of 18 members of the <i>Hsp70</i> family has been detected and characterized in the cocoa genome. All general properties, such as physic-chemical parameters, gene structure, phylogenetic tree and sub-cellular localization, were determined using a variety of bioinformatics tools. The expression patterns of the <i>TcHsp70</i> genes in different stages of the zygotic and somatic embryos were investigated. In addition, expression profiles of the <i>TcHsp70</i> genes under <i>Phytophthora megakarya</i> inoculation were analyzed. <b>Conclusion:</b> The results of this study revealed the features and expression analyses of <i>Hsp70</i> genes in cocoa. These findings could provide a strong foundation for further research of the <i>TcHsp70</i> family, which could aid in the development and stress tolerance of cocoa species.
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Colonges K, Jimenez JC, Saltos A, Seguine E, Loor Solorzano RG, Fouet O, Argout X, Assemat S, Davrieux F, Cros E, Lanaud C, Boulanger R. Integration of GWAS, metabolomics, and sensorial analyses to reveal novel metabolic pathways involved in cocoa fruity aroma GWAS of fruity aroma in Theobroma cacao. Plant Physiol Biochem 2022; 171:213-225. [PMID: 34863583 DOI: 10.1016/j.plaphy.2021.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/03/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
Nacional is a variety of cocoa tree known for its "Arriba" aroma characterised mainly by fruity, floral, and spicy aromatic notes. In this study, the genetic basis of the fruity aroma of modern Nacional cocoa was investigated. GWAS studies have been conducted on biochemical and sensorial fruity traits and allowed to identify a large number of association zones. These areas are linked to both the volatile compounds known to provide fruity flavours and present in the beans before and after roasting, and to the fruity notes detected by sensorial analysis. Five main metabolic pathways were identified as involved in the fruity traits of the Nacional population: the protein degradation pathway, the sugar degradation pathway, the fatty acid degradation pathway, the monoterpene pathway, and the L-phenylalanine pathway. Candidate genes involved in the biosynthetic pathways of volatile compounds identified in association areas were detected for a large number of associations.
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Affiliation(s)
- Kelly Colonges
- Cirad, UMR AGAP, F-34398, Montpellier, France; AGAP Institut, Univ Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France; Cirad, UMR Qualisud, F-34398 Montpellier, France; Qualisud, Univ Montpellier, Avignon Université, Cirad, Institut Agro, IRD, Université de La Réunion, Montpellier, France.
| | | | - Alejandra Saltos
- Instituto Nacional de Investigacion Agropecurias, INIAP, Ecuador
| | | | | | - Olivier Fouet
- Cirad, UMR AGAP, F-34398, Montpellier, France; AGAP Institut, Univ Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Xavier Argout
- Cirad, UMR AGAP, F-34398, Montpellier, France; AGAP Institut, Univ Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Sophie Assemat
- Cirad, UMR Qualisud, F-34398 Montpellier, France; Qualisud, Univ Montpellier, Avignon Université, Cirad, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Fabrice Davrieux
- Cirad, UMR Qualisud, F-34398 Montpellier, France; Qualisud, Univ Montpellier, Avignon Université, Cirad, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Emile Cros
- Cirad, UMR Qualisud, F-34398 Montpellier, France; Qualisud, Univ Montpellier, Avignon Université, Cirad, Institut Agro, IRD, Université de La Réunion, Montpellier, France
| | - Claire Lanaud
- Cirad, UMR AGAP, F-34398, Montpellier, France; AGAP Institut, Univ Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Renaud Boulanger
- Cirad, UMR Qualisud, F-34398 Montpellier, France; Qualisud, Univ Montpellier, Avignon Université, Cirad, Institut Agro, IRD, Université de La Réunion, Montpellier, France.
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Jaimez RE, Barragan L, Fernández-Niño M, Wessjohann LA, Cedeño-Garcia G, Sotomayor Cantos I, Arteaga F. Theobroma cacao L. cultivar CCN 51: a comprehensive review on origin, genetics, sensory properties, production dynamics, and physiological aspects. PeerJ 2022; 10:e12676. [PMID: 35036091 PMCID: PMC8742540 DOI: 10.7717/peerj.12676] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/02/2021] [Indexed: 01/07/2023] Open
Abstract
Many decades of improvement in cacao have aided to obtain cultivars with characteristics of tolerance to diseases, adaptability to different edaphoclimatic conditions, and higher yields. In Ecuador, as a result of several breeding programs, the clone CCN 51 was obtained, which gradually expanded through the cacao-production regions of Ecuador, Colombia, Brazil and Peru. Recognized for its high yield and adaptability to different regions and environments, it has become one of the most popular clones for breeding programs and cultivation around the world. This review aims to summarize the current evidence on the origin, genetics, morphological, volatile compounds, and organoleptic characteristics of this clone. Physiological evidence, production dynamics, and floral biology are also included to explain the high yield of CCN 51. Thus, characteristics such as osmotic adjustment, long pollen longevity, and fruit formation are further discussed and associated with high production at the end of the dry period. Finally, the impact of this popular clone on the current and future cacao industry will be discussed highlighting the major challenges for flavor enhancement and its relevance as a platform for the identification of novel genetic markers for cultivar improvement in breeding programs.
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Affiliation(s)
- Ramon E. Jaimez
- Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Manabí, Ecuador
| | | | - Miguel Fernández-Niño
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Ludger A. Wessjohann
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Halle (Saale), Germany
| | - George Cedeño-Garcia
- Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Manabí, Ecuador
| | - Ignacio Sotomayor Cantos
- Estación Experimental Tropical Pichilingue, Instituto Nacional de Investigaciones Agropecuarias (INIAP), Los Ríos, Ecuador
| | - Francisco Arteaga
- Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Manabí, Ecuador
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Vázquez-Alcántara L, Oliart-Ros RM, García-Bórquez A, Peña-Montes C. Expression of a Cutinase of Moniliophthora roreri with Polyester and PET-Plastic Residues Degradation Activity. Microbiol Spectr 2021; 9:e0097621. [PMID: 34730414 PMCID: PMC8567236 DOI: 10.1128/spectrum.00976-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Cutinases are enzymes produced by phytopathogenic fungi like Moniliophthora roreri. The three genome-located cutinase genes of M. roreri were amplified from cDNA of fungi growing in different induction culture media for cutinase production. The mrcut1 gene was expressed in the presence of a cacao cuticle, while the mrcut2 and mrcut3 genes were expressed when an apple cuticle was used as the inducer. The sequences of all genes were obtained and analyzed by bioinformatics tools to determine the presence of signal peptides, introns, glycosylation, and regulatory sequences. Also, the theoretical molecular weight and pI were obtained and experimentally confirmed. Finally, cutinase 1 from M. roreri (MRCUT1) was selected for heterologous expression in Escherichia coli. Successful overexpression of MRCUT1 was observed with the highest enzyme activity of 34,036 U/mg under the assay conditions at 40°C and pH 8. Furthermore, the degradation of different synthetic polyesters was evaluated; after 21 days, 59% of polyethylene succinate (PES), 43% of polycaprolactone (PCL), and 31% of polyethylene terephthalate (PET) from plastic residues were degraded. IMPORTANCE Plastic pollution is exponentially increasing; even the G20 has recognized an urgent need to implement actions to reduce it. In recent years, searching for enzymes that can degrade plastics, especially those based on polyesters such as PET, has been increasing as they can be a green alternative to the actual plastic degradation process. A promising option in recent years refers to biological tools such as enzymes involved in stages of partial and even total degradation of some plastics. In this context, the MRCUT1 enzyme can degrade polyesters contained in plastic residues in a short time. Besides, there is limited knowledge about the biochemical properties of cutinases from M. roreri. Commonly, fungal enzymes are expressed as inclusion bodies in E. coli with reduced activity. Interestingly, the successful expression of one cutinase of M. roreri in E. coli with enhanced activity is described.
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Affiliation(s)
- Laura Vázquez-Alcántara
- Tecnológico Nacional de México/IT Veracruz, Unidad de Investigación y Desarrollo en Alimentos, Veracruz, México
| | - Rosa María Oliart-Ros
- Tecnológico Nacional de México/IT Veracruz, Unidad de Investigación y Desarrollo en Alimentos, Veracruz, México
| | - Arturo García-Bórquez
- Instituto Politécnico Nacional, Escuela Superior de Física y Matemáticas, UPALM, Mexico City, México
| | - Carolina Peña-Montes
- Tecnológico Nacional de México/IT Veracruz, Unidad de Investigación y Desarrollo en Alimentos, Veracruz, México
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Zhang Q, Hou S, Sun Z, Chen J, Meng J, Liang D, Wu R, Guo Y. Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Theobroma cacao. Genes (Basel) 2021; 12:genes12111799. [PMID: 34828404 PMCID: PMC8622960 DOI: 10.3390/genes12111799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023] Open
Abstract
The MADS-box family gene is a class of transcription factors that have been extensively studied and involved in several plant growth and development processes, especially in floral organ specificity, flowering time and initiation and fruit development. In this study, we identified 69 candidate MADS-box genes and clustered these genes into five subgroups (Mα: 11; Mβ: 2; Mγ: 14; Mδ: 9; MIKC: 32) based on their phylogenetical relationships with Arabidopsis. Most TcMADS genes within the same subgroup showed a similar gene structure and highly conserved motifs. Chromosomal distribution analysis revealed that all the TcMADS genes were evenly distributed in 10 chromosomes. Additionally, the cis-acting elements of promoter, physicochemical properties and subcellular localization were also analyzed. This study provides a comprehensive analysis of MADS-box genes in Theobroma cacao and lays the foundation for further functional research.
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Affiliation(s)
- Qianqian Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Sijia Hou
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Zhenmei Sun
- Institute of Marine Materials Science and Engineering, College of Ocean Science and Engineering, Shanghai Maritime University, Shanghai 201306, China;
| | - Jing Chen
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Jianqiao Meng
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Dan Liang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
| | - Yunqian Guo
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Q.Z.); (S.H.); (J.C.); (J.M.); (D.L.); (R.W.)
- Correspondence:
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Chen G, Liu Z, Li S, Qanmber G, Liu L, Guo M, Lu L, Ma S, Li F, Yang Z. Genome-wide analysis of ZAT gene family revealed GhZAT6 regulates salt stress tolerance in G. hirsutum. Plant Sci 2021; 312:111055. [PMID: 34620449 DOI: 10.1016/j.plantsci.2021.111055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/05/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
High salt environments can induce stress in different plants. The genes containing the ZAT domain constitute a family that belongs to a branch of the C2H2 family, which plays a vital role in responding to abiotic stresses. In this study, we identified 169 ZAT genes from seven plant species, including 44 ZAT genes from G. hirsutum. Phylogenetic tree analysis divided ZAT genes in six groups with conserved gene structure, protein motifs. Two C2H2 domains and an EAR domain and even chromosomal distribution on At and Dt sub-genome chromosomes of G. hirsutum was observed. GhZAT6 was primarily expressed in the root tissue and responded to NaCl and ABA treatments. Subcellular localization found that GhZAT6 was located in the nucleus and demonstrated transactivation activity during a transactivation activity assay. Arabidopsis transgenic lines overexpressing the GhZAT6 gene showed salt tolerance and grew more vigorously than WT on MS medium supplemented with 100 mmol NaCl. Additionally, the silencing of the GhZAT6 gene in cotton plants showed more obvious leaf wilting than the control plants, which were subjected to 400 mmol NaCl treatment. Next, the expressions of GhAPX1, GhFSD1, GhFSD2, and GhSOS3 were significantly lower in the GhZAT6-silenced plants treated with NaCl than the control. Based on these findings, GhZAT6 may be involved in the ABA pathway and mediate salt stress tolerance by regulating ROS-related gene expression.
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Affiliation(s)
- Guoquan Chen
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Zhao Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Shengdong Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Le Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Mengzhen Guo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Lili Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Shuya Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Li F, Wu B, Yan L, Qin X, Lai J. Metabolome and transcriptome profiling of Theobroma cacao provides insights into the molecular basis of pod color variation. J Plant Res 2021; 134:1323-1334. [PMID: 34420146 DOI: 10.1007/s10265-021-01338-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
The Theobroma cacao presents a wide diversity in pod color among different cultivars. Although flavonoid biosynthesis has been studied in many plants, molecular mechanisms governing the diversity of coloration in cacao pods are largely unknown. The flavonoid metabolite profiles and flavonoid biosynthetic gene expression in the pod exocarps of light green pod 'TAS 410' (GW), green pod 'TAS 166' (GF), and mauve pod 'TAS 168' (PF) were determined. Changes in flavonoid metabolites, particularly the anthocyanins (cyanidin 3-O-galactoside, cyanidin 3-O-glucoside, and cyanidin O-syringic acid) were significantly up-accumulated in the mauve phenotype (PF) compared to the light green or green phenotypes, endowing the pod color change from light green or green to mauve. Consistently, the PF phenotype showed different expression patterns of flavonoid biosynthetic structural genes in comparison with GW/GF phenotypes. The expression level of LAR and ANR in GW/GF was significantly higher than PF, while the expression level of UFGT in GW/GF was lower than PF. These genes likely generated more anthocyanins in the exocarps samples of PF than that of GW/GF. Simultaneously, colorless flavan-3-ols (catechin, epicatechin and proanthocyanidin) content in the exocarp samples of PF was lower than GW/GF. Additionally, MYB (gene18079) and bHLH (gene5045 and gene21575) may participate in the regulation of the pod color. This study sheds light on the molecular basis of cacao pod color variation, which will contribute to breeding cacao varieties with enhanced flavonoid profiles for nutritional applications.
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Affiliation(s)
- Fupeng Li
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, 571533, Hainan, China
| | - Baoduo Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, 571533, Hainan, China
| | - Lin Yan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, 571533, Hainan, China
| | - Xiaowei Qin
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, Hainan, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, 571533, Hainan, China
| | - Jianxiong Lai
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, Hainan, China.
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, 571533, Hainan, China.
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Hernandez CE, Granados L. Quality differentiation of cocoa beans: implications for geographical indications. J Sci Food Agric 2021; 101:3993-4002. [PMID: 33421139 DOI: 10.1002/jsfa.11077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 01/03/2021] [Accepted: 01/09/2021] [Indexed: 06/12/2023]
Abstract
Geographical indications may stimulate collective actions of governance for quality control, trade and marketing as well as innovation based on the use of local resources and regional biodiversity. Cocoa production, however, dominated by small family agriculture in tropical regions, has rarely made use of such strategies. This review is aimed at understanding major research interests and emerging technologies helpful for the origin differentiation of cocoa quality. Results from literature search and cited references of publications on cocoa research were imported into VOSviewer for data analysis, which aided in visualizing major research hotpots. Co-occurrence analysis yielded major research clusters which guided the discussion of this review. Observed was a consensus recognizing cocoa quality resulting from the interaction of genotype, fermentation variables and geographical origin. A classic view of cocoa genetics based on the dichotomy of 'fine versus bulk' has been reexamined by a broader perspective of human selection and cocoa genotype evolution. This new approach to cocoa genetic diversity, together with the understanding of complex microbiome interactions through fermentation, as well as quality reproducibility challenged by geographical conditions, have demonstrated the importance of terroir in the production of special attributes. Cocoa growing communities around the tropics have been clearly enabled by new omics and chemometrics to systematize producing conditions and practices in the designation of specifications for the differentiation of origin quality. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Carlos Eduardo Hernandez
- Laboratory of Food Quality Innovation, School of Agricultural Sciences, National University (UNA), Heredia, Costa Rica
| | - Leonardo Granados
- Center for the Development of Denominations of Origin and Agrifood Quality (CADENAGRO), School of Agricultural Sciences, National University (UNA), Heredia, Costa Rica
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Gallego AM, Rojas LF, Valencia WG, Atehortúa L, Urrea AI, Fister AS, Guiltinan MJ, Maximova SN, Pabón-Mora N. Transcriptomic analyses of cacao flavonoids produced in photobioreactors. BMC Genomics 2021; 22:551. [PMID: 34281511 PMCID: PMC8287782 DOI: 10.1186/s12864-021-07871-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 07/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Theobroma cacao is a major source of flavonoids such as catechins and their monomers proanthocyanidins (PAs), widely studied for their potential benefits in cardiovascular diseases. Light has been shown to promote plant secondary metabolite production in vitro. In this study, cacao cells cultured in 7.5 L stirred tank photobioreactors (STPs) were exposed to a change of white to blue LED lights for 28 days (d). RESULTS Transcriptomic analyses were performed in three time points comparing changing expression patterns, after cell exposure to white light (d0-VS-d14), after a shift from white to blue light (d14-VS-d15), and after an extended period of blue light for the following 15 days (d15-VS-d28). Under white light, there was enrichment in metabolic pathways associated with cell growth (carbon, glycolysis, and amino acid biosynthesis) accompanied by a significant increase in the PAs content. In the shift to blue light, further increase in PAs content was observed concomitantly with the significant expression of TWO-COMPONENT RESPONSE REGULATOR genes involved in the early stress responses via circadian clock and hormone pathways. Under blue light exposure, we observed a depletion of PAs content associated with ROS-mediated stress pathways. CONCLUSIONS Light effects on large-scale cell cultures in photobioreactors are complex and pleiotropic; however, we have been able to identify key regulatory players upstream cacao flavonoid biosynthesis in STPs, including TWO-COMPONENT SYSTEM and ROS-signaling genes. The crosstalk between flavonoid biosynthesis and regulatory networks led to understand the dynamics of flavonoid production and degradation in response to light-driven ROS signals. This can be used to optimize the time, and the yield of in vitro targeted metabolites in large-scale culture systems.
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Affiliation(s)
- Adriana M Gallego
- Grupo de Biotecnología, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Luisa F Rojas
- Grupo de Biotransformación, Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Wilmar G Valencia
- Centro de Investigación, Desarrollo y Calidad CIDCA, Compañía Nacional de Chocolates S.A.S, Km 2 Vía Belén autopista, Medellín-Bogotá, Colombia
| | - Lucía Atehortúa
- Grupo de Biotecnología, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Aura I Urrea
- Grupo de Biotecnología, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Andrew S Fister
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
- Present address: Pairwise Plants, 110 TW Alexander Dr, Durham, NC, USA
| | - Mark J Guiltinan
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Siela N Maximova
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA.
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
| | - Natalia Pabón-Mora
- Grupo Evo-Devo en Plantas, Instituto de Biología, Universidad de Antioquia, Medellín, Colombia.
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Prewitt SF, Shalit-Kaneh A, Maximova SN, Guiltinan MJ. Inter-species functional compatibility of the Theobroma cacao and Arabidopsis FT orthologs: 90 million years of functional conservation of meristem identity genes. BMC Plant Biol 2021; 21:218. [PMID: 33990176 PMCID: PMC8122565 DOI: 10.1186/s12870-021-02982-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND In angiosperms the transition to flowering is controlled by a complex set of interacting networks integrating a range of developmental, physiological, and environmental factors optimizing transition time for maximal reproductive efficiency. The molecular mechanisms comprising these networks have been partially characterized and include both transcriptional and post-transcriptional regulatory pathways. Florigen, encoded by FLOWERING LOCUS T (FT) orthologs, is a conserved central integrator of several flowering time regulatory pathways. To characterize the molecular mechanisms involved in controlling cacao flowering time, we have characterized a cacao candidate florigen gene, TcFLOWERING LOCUS T (TcFT). Understanding how this conserved flowering time regulator affects cacao plant's transition to flowering could lead to strategies to accelerate cacao breeding. RESULTS BLAST searches of cacao genome reference assemblies identified seven candidate members of the CENTRORADIALIS/TERMINAL FLOWER1/SELF PRUNING gene family including a single florigen candidate. cDNA encoding the predicted cacao florigen was cloned and functionally tested by transgenic genetic complementation in the Arabidopsis ft-10 mutant. Transgenic expression of the candidate TcFT cDNA in late flowering Arabidopsis ft-10 partially rescues the mutant to wild-type flowering time. Gene expression studies reveal that TcFT is spatially and temporally expressed in a manner similar to that found in Arabidopsis, specifically, TcFT mRNA is shown to be both developmentally and diurnally regulated in leaves and is most abundant in floral tissues. Finally, to test interspecies compatibility of florigens, we transformed cacao tissues with AtFT resulting in the remarkable formation of flowers in tissue culture. The morphology of these in vitro flowers is normal, and they produce pollen that germinates in vitro with high rates. CONCLUSION We have identified the cacao CETS gene family, central to developmental regulation in angiosperms. The role of the cacao's single FT-like gene (TcFT) as a general regulator of determinate growth in cacao was demonstrated by functional complementation of Arabidopsis ft-10 late-flowering mutant and through gene expression analysis. In addition, overexpression of AtFT in cacao resulted in precocious flowering in cacao tissue culture demonstrating the highly conserved function of FT and the mechanisms controlling flowering in cacao.
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Affiliation(s)
- S F Prewitt
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA, USA
| | - A Shalit-Kaneh
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA, USA
| | - S N Maximova
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - M J Guiltinan
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA, USA.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
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30
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de Almeida OGG, Vitulo N, De Martinis ECP, Felis GE. Pangenome analyses of LuxS-coding genes and enzymatic repertoires in cocoa-related lactic acid bacteria. Genomics 2021; 113:1659-1670. [PMID: 33839269 DOI: 10.1016/j.ygeno.2021.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/04/2021] [Accepted: 04/05/2021] [Indexed: 01/15/2023]
Abstract
Lactobacillaceae presents potential for interspecific Quorum Sensing (QS) in spontaneous cocoa fermentation, correlated with high abundance of luxS. Three Brazilian isolates from cocoa fermentation were characterized by Whole Genome Sequencing and luxS gene was surveyed in their genomes, in comparison with public databases. They were classified as Lactiplantibacillus plantarum, Limosilactobacillus fermentum and Pediococcus acidilactici. LuxS genes were conserved in core genomes of the novel isolates, but in some non-cocoa related Lactic Acid Bacteria (LAB) it was accessory and plasmid-borne. The conservation and horizontal acquisition of luxS reinforces that QS is determinant for bacterial adaptation in several environments, especially taking into account the luxS has been correlated with modulation of bacteriocin production, stress tolerance and biofilm formation. Therefore, in this paper, new clade and species-specific primers were designed for future application for screening of luxS gene in LAB to evaluate the adaptive potential to diverse food fermentations.
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Affiliation(s)
| | - Nicola Vitulo
- University of Verona, Department of Biotechnology, Verona, Italy
| | | | - Giovanna E Felis
- University of Verona, Department of Biotechnology, Verona, Italy
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Febrianto NA, Zhu F. Changes in the Composition of Methylxanthines, Polyphenols, and Volatiles and Sensory Profiles of Cocoa Beans from the Sul 1 Genotype Affected by Fermentation. J Agric Food Chem 2020; 68:8658-8675. [PMID: 32662271 DOI: 10.1021/acs.jafc.0c02909] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Sul 1 cacao (Theobroma cacao) genotype has become more popular among cocoa producers due to its resistance toward vascular streak dieback, a devastating dieback disease in cacao plants. Sul 1 cocoa beans were subjected to prolonged fermentation of 10 days (240 h). Changes in the composition of methylxanthines, polyphenols, and volatiles and sensory profiles of the cocoa beans as affected by fermentation were analyzed. The first 48 h of fermentation significantly determined the composition of the methylxanthines and polyphenols in the cocoa beans. A prolonged fermentation (>96 h) period did not further reduce the contents of methylxanthines and polyphenols in the cocoa beans. Important volatiles characteristic of the cocoa/chocolate flavor were mostly developed after 48 h of fermentation. The fermentation for 72 h retained considerable amounts of methylxanthines and polyphenols in the beans while producing cocoa mass with good sensory profiles.
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Affiliation(s)
- Noor Ariefandie Febrianto
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Indonesian Coffee and Cocoa Research Institute (ICCRI), Jl. PB Sudirman No. 90, Jember 68118, East Java, Indonesia
| | - Fan Zhu
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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dos Santos EC, Pirovani CP, Correa SC, Micheli F, Gramacho KP. The pathogen Moniliophthora perniciosa promotes differential proteomic modulation of cacao genotypes with contrasting resistance to witches´ broom disease. BMC Plant Biol 2020; 20:1. [PMID: 31898482 PMCID: PMC6941324 DOI: 10.1186/s12870-019-2170-7] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 11/27/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Witches' broom disease (WBD) of cacao (Theobroma cacao L.), caused by Moniliophthora perniciosa, is the most important limiting factor for the cacao production in Brazil. Hence, the development of cacao genotypes with durable resistance is the key challenge for control the disease. Proteomic methods are often used to study the interactions between hosts and pathogens, therefore helping classical plant breeding projects on the development of resistant genotypes. The present study compared the proteomic alterations between two cacao genotypes standard for WBD resistance and susceptibility, in response to M. perniciosa infection at 72 h and 45 days post-inoculation; respectively the very early stages of the biotrophic and necrotrophic stages of the cacao x M. perniciosa interaction. RESULTS A total of 554 proteins were identified, being 246 in the susceptible Catongo and 308 in the resistant TSH1188 genotypes. The identified proteins were involved mainly in metabolism, energy, defense and oxidative stress. The resistant genotype showed more expressed proteins with more variability associated with stress and defense, while the susceptible genotype exhibited more repressed proteins. Among these proteins, stand out pathogenesis related proteins (PRs), oxidative stress regulation related proteins, and trypsin inhibitors. Interaction networks were predicted, and a complex protein-protein interaction was observed. Some proteins showed a high number of interactions, suggesting that those proteins may function as cross-talkers between these biological functions. CONCLUSIONS We present the first study reporting the proteomic alterations of resistant and susceptible genotypes in the T. cacao x M. perniciosa pathosystem. The important altered proteins identified in the present study are related to key biologic functions in resistance, such as oxidative stress, especially in the resistant genotype TSH1188, that showed a strong mechanism of detoxification. Also, the positive regulation of defense and stress proteins were more evident in this genotype. Proteins with significant roles against fungal plant pathogens, such as chitinases, trypsin inhibitors and PR 5 were also identified, and they may be good resistance markers. Finally, important biological functions, such as stress and defense, photosynthesis, oxidative stress and carbohydrate metabolism were differentially impacted with M. perniciosa infection in each genotype.
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Affiliation(s)
- Everton Cruz dos Santos
- Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), State University of Santa Cruz (UESC), Rodovia Ilhéus-Itabuna km 16, Ilhéus, Bahia 45652-900 Brazil
- Stem Cell Laboratory, Bone Marrow Transplantation Center (CEMO), National Cancer Institute (INCA), Rio de Janeiro, RJ Brazil
| | - Carlos Priminho Pirovani
- Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), State University of Santa Cruz (UESC), Rodovia Ilhéus-Itabuna km 16, Ilhéus, Bahia 45652-900 Brazil
| | - Stephany Cristiane Correa
- Stem Cell Laboratory, Bone Marrow Transplantation Center (CEMO), National Cancer Institute (INCA), Rio de Janeiro, RJ Brazil
| | - Fabienne Micheli
- Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), State University of Santa Cruz (UESC), Rodovia Ilhéus-Itabuna km 16, Ilhéus, Bahia 45652-900 Brazil
- CIRAD, UMR AGAP, F-34398, Montpellier, France
| | - Karina Peres Gramacho
- Department of Biological Science (DCB), Center of Biotechnology and Genetics (CBG), State University of Santa Cruz (UESC), Rodovia Ilhéus-Itabuna km 16, Ilhéus, Bahia 45652-900 Brazil
- Molecular Plant Pathology Laboratory, Cocoa Research Center (CEPEC), CEPLAC, Km 22 Rod. Ilhéus-Itabuna, Ilhéus, Bahia 45600-970 Brazil
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Shen S, Zhang Q, Shi Y, Sun Z, Zhang Q, Hou S, Wu R, Jiang L, Zhao X, Guo Y. Genome-Wide Analysis of the NAC Domain Transcription Factor Gene Family in Theobroma cacao. Genes (Basel) 2019; 11:genes11010035. [PMID: 31905649 PMCID: PMC7017368 DOI: 10.3390/genes11010035] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/24/2019] [Accepted: 12/26/2019] [Indexed: 12/27/2022] Open
Abstract
As a plant-specific transcription factor, the NAC (NAM, ATAF1/2 and CUC2) domain protein plays an important role in plant growth and development, as well as stress resistance. Based on the genomic data of the cacao tree, this study identified 102 cacao NAC genes and named them according to their location within the genome. The phylogeny of the protein sequence of the cacao tree NAC family was analyzed using various bioinformatic methods, and then divided into 12 subfamilies. Then, the amino-acid composition, physicochemical properties, genomic location, gene structure, conserved domains, and promoter cis-acting elements were analyzed. This study provides information on the evolution of the TcNAC gene and its possible functions, laying the foundation for further research on the NAC family.
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Affiliation(s)
- Shiya Shen
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Qianru Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yu Shi
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhenmei Sun
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Qianqian Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Sijia Hou
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiyang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150000, China
| | - Yunqian Guo
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Correspondence:
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Li F, Wu B, Yan L, Hao C, Qin X, Lai J, Song Y. Transcriptional profiling reveals differentially expressed genes involved in lipid biosynthesis during cacao seed development. Sci Rep 2019; 9:17263. [PMID: 31754164 PMCID: PMC6872657 DOI: 10.1038/s41598-019-53959-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/05/2019] [Indexed: 11/09/2022] Open
Abstract
Theobroma cacao is a plant of economic value due to the use of its seed lipid for chocolate, confectionery, and cosmetic industries. The seed lipid contains a stable ratio of saturated and unsaturated fatty acids, which determines its unique melting temperature. However, little is known about the molecular mechanism determining the fatty acid ratio and lipid content in cacao. To gain insight into the unique properties of lipid synthesis in cacao, biochemical and transcriptomic approaches were used to compare the lipid accumulation between high and low lipid content cacao accessions. Lipid accumulation rates and lipid content were different between the two accessions. Moreover, differentially expressed genes were detected between high and low lipid content cacao accessions. The data allowed the identification of distinct candidate genes and furthered our understanding of lipid accumulation, potentially explaining the differences in lipid content between various cacao accessions. The results might be used to develop molecular tools and engineer alternative pathways for cacao breeding with improved lipid production potentials.
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Affiliation(s)
- Fupeng Li
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China
| | - Baoduo Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China
| | - Lin Yan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China
| | - Xiaowei Qin
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China
| | - Jianxiong Lai
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China
| | - Yinghui Song
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China.
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Abstract
Composition of bioactive compounds in cocoa beans is critical to the sensory and nutritional quality of cocoa based products. Twenty-six cocoa bean genotypes were freshly collected from the same plantation location in Indonesia. The bioactive compounds in these raw cocoa genotypes were identified and quantified. The results showed a great diversity in the composition of bioactive compounds among the 26 cocoa samples. The concentrations of methylxanthines, epicatechin, proanthocyanidin (PA) B-type oligomers, clovamide, and anthocyanins were important variables that differentiated these genotypes. MCC 01, SUL 3, ICCRI 03, and ICS 60 genotypes had the highest contents of flavan-3-ols including PAs and have the potential to be developed for "healthy" product formulations. Some genotypes such as DR 1, DR 2, DR 38, ICS 13, KPC 1, KW 617, RCC 71, and TSH 858 could be favored by industries due to the potential to be made into end-products with brighter appearance.
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Affiliation(s)
- Noor Ariefandie Febrianto
- School of Chemical Sciences , University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand
- Indonesian Coffee and Cocoa Research Institute (ICCRI) , Jl. PB Sudirman No. 90 Jember , East Java 68118 , Indonesia
| | - Fan Zhu
- School of Chemical Sciences , University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand
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36
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Engbersen N, Gramlich A, Lopez M, Schwarz G, Hattendorf B, Gutierrez O, Schulin R. Cadmium accumulation and allocation in different cacao cultivars. Sci Total Environ 2019; 678:660-670. [PMID: 31078857 DOI: 10.1016/j.scitotenv.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 04/14/2023]
Abstract
Cadmium (Cd) is a biologically non-essential heavy metal that can cause toxic effects in plants, animals and humans already at low concentrations compared to other metals. After Cd concentrations in cacao beans of various provenances, particularly from Latin America, were found to exceed the new regulations enforced by the European Union in 2019, there is an urgent need to find measures to lower Cd accumulation in cacao beans to acceptable values. In this research, the long-term cacao cultivar trial CEDEC-JAS in northern Honduras was used to investigate differences between 11 cultivars in Cd uptake and translocation. Sampling of various plant parts, including rootstocks, scions, leaves and beans, from three replicate trees per cultivar and the soil around each tree was conducted at this site. Results indicate that concentrations of available soil Cd were more closely correlated with Cd concentrations of the rootstocks (R2 = 0.56), scions (R2 = 0.59) and leaves (R2 = 0.46) than with bean Cd concentrations (R2 = 0.26). In addition, Cd concentrations of rootstocks, scions and leaves showed close relationships to available soil Cd concentrations, with no significant differences between the cultivars. In contrast, bean Cd concentrations showed only weak correlations to available soil Cd and Cd concentrations in the vegetative plant parts, but significant variation among cultivars. Three cultivars, which were analysed in more detail, showed significant differences in Cd concentrations of mature beans, but not of immature beans. These results suggest that cultivar-related differences in bean Cd concentrations primarily result from differences in Cd loading during bean maturation, possibly due to cultivar-specific differences in the xylem-to-phloem transfer of Cd. The results show that selection of cultivars with low Cd transfer from vegetative parts into the beans has high potential to keep Cd accumulation in cacao beans at levels that are safe for consumption.
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Affiliation(s)
- Nadine Engbersen
- Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland.
| | - Anja Gramlich
- Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland
| | - Marlon Lopez
- Honduran Foundation for Agricultural Research (FHIA), La Lima, Cortés, Honduras
| | - Gunnar Schwarz
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8052 Zürich, Switzerland
| | - Bodo Hattendorf
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1, 8052 Zürich, Switzerland
| | - Osman Gutierrez
- USDA-ARS Subtropical Horticulture Research Station, 13601 Old Cutler Road, Miami, FL, USA
| | - Rainer Schulin
- Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland
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37
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Li ZK, Chen B, Li XX, Wang JP, Zhang Y, Wang XF, Yan YY, Ke HF, Yang J, Wu JH, Wang GN, Zhang GY, Wu LQ, Wang XY, Ma ZY. A newly identified cluster of glutathione S-transferase genes provides Verticillium wilt resistance in cotton. Plant J 2019; 98:213-227. [PMID: 30561788 DOI: 10.1111/tpj.14206] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 05/08/2023]
Abstract
As the largest cultivated fiber crop in the world, cotton (Gossypium hirsutum) is often exposed to various biotic stresses during its growth periods. Verticillium wilt caused by Verticillium dahliae is a severe disease in cotton, and the molecular mechanism of cotton resistance for Verticillium wilt needs to be further investigated. Here, we revealed that the cotton genome contains nine types of GST genes. An evolutionary analysis showed that a newly identified cluster (including Gh_A09G1508, Gh_A09G1509 and Gh_A09G1510) located on chromosome 09 of the A-subgenome was under positive selection pressure during the formation of an allotetraploid. Transcriptome analysis showed that this cluster participates in Verticillium wilt resistance. Because the Gh_A09G1509 gene showed the greatest differential expression in the resistant cultivar under V. dahliae stress, we overexpressed this gene in tobacco and found that its overexpression resulted in enhanced Verticillium wilt resistance. Suppression of the gene cluster via virus-induced gene silencing made cotton plants of the resistant cultivar Nongda601 significantly susceptible. These results demonstrated that the GST cluster played an important role in Verticillium wilt resistance. Further investigation showed that the encoded enzymes of the cluster were essential for the delicate equilibrium between the production and scavenging of H2 O2 during V. dahliae stress.
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Affiliation(s)
- Zhi-Kun Li
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Bin Chen
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Xiu-Xin Li
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Jin-Peng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, China
| | - Yan Zhang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Xing-Fen Wang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Yuan-Yuan Yan
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Hui-Feng Ke
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Jun Yang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Jin-Hua Wu
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Guo-Ning Wang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Gui-Yin Zhang
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Li-Qiang Wu
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
| | - Xi-Yin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, 063210, China
| | - Zhi-Ying Ma
- North China Key Laboratory for Germplasm Resources of Education Ministry, Co-Innovation Center for Cotton Industry of Hebei Province, Hebei Agricultural University, Baoding, 071001, China
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38
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Tee YK, Balasundram SK, Ding P, M Hanif AH, Bariah K. Determination of optimum harvest maturity and non-destructive evaluation of pod development and maturity in cacao (Theobroma cacao L.) using a multiparametric fluorescence sensor. J Sci Food Agric 2019; 99:1700-1708. [PMID: 30206959 DOI: 10.1002/jsfa.9359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 09/03/2018] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND A series of fluorescence indices (anthocyanin, flavonol, chlorophyll and nitrogen balance) were deployed to detect the pigments and colourless flavonoids in cacao pods of three commercial cacao (Theobroma cacao L.) genotypes (QH1003, KKM22 and MCBC1) using a fast and non-destructive multiparametric fluorescence sensor. The aim was to determine optimum harvest periods (either 4 or 5 months after pod emergence) of commercial cacao based on fluorescence indices of cacao development and bean quality. RESULTS As pod developed, cacao exhibited a rise with the peak of flavonol occurring at months 4 and 5 after pod maturity was initiated while nitrogen balance showed a decreasing trend during maturity. Cacao pods contained high chlorophyll as they developed but chlorophyll content declined significantly on pods that ripened at month 5. CONCLUSION Cacao pods harvested at months 4 and 5 can be considered as commercially-ready as the beans have developed good quality and comply with the Malaysian standard on cacao bean specification. Thus, cacao pods can be harvested earlier when they reach maturity at month 4 after pod emergence to avoid germinated beans and over fermentation in ripe pods harvested at month 5. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Yei-Kheng Tee
- Cocoa Upstream Technology Department, Malaysian Cocoa Board, Sg. Sumun, Perak, Malaysia
| | - Siva K Balasundram
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Phebe Ding
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Ahmad Husni M Hanif
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Khairul Bariah
- Cocoa Downstream Technology Department, Malaysian Cocoa Board, Cocoa Innovative and Technology Center, Nilai, Negeri Sembilan Darul Khusus, Malaysia
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39
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Pokou DN, Fister AS, Winters N, Tahi M, Klotioloma C, Sebastian A, Marden JH, Maximova SN, Guiltinan MJ. Resistant and susceptible cacao genotypes exhibit defense gene polymorphism and unique early responses to Phytophthora megakarya inoculation. Plant Mol Biol 2019; 99:499-516. [PMID: 30739243 DOI: 10.1007/s11103-019-00832-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 01/24/2019] [Indexed: 05/26/2023]
Abstract
Key genes potentially involved in cacao disease resistance were identified by transcriptomic analysis of important cacao cultivars. Defense gene polymorphisms were identified which could contribute to pathogen recognition capacity. Cacao suffers significant annual losses to the water mold Phytophthora spp. (Oomycetes). In West Africa, P. megakarya poses a major threat to farmer livelihood and the stability of cocoa production. As part of a long-term goal to define key disease resistance genes in cacao, here we use a transcriptomic analysis of the disease-resistant cacao clone SCA6 and the susceptible clone NA32 to characterize basal differences in gene expression, early responses to infection, and polymorphisms in defense genes. Gene expression measurements by RNA-seq along a time course revealed the strongest transcriptomic response 24 h after inoculation in the resistant genotype. We observed strong regulation of several pathogenesis-related genes, pattern recognition receptors, and resistance genes, which could be critical for the ability of SCA6 to combat infection. These classes of genes also showed differences in basal expression between the two genotypes prior to infection, suggesting that prophylactic expression of defense-associated genes could contribute to SCA6's broad-spectrum disease resistance. Finally, we analyzed polymorphism in a set of defense-associated receptors, identifying coding variants between SCA6 and NA32 which could contribute to unique capacities for pathogen recognition. This work is an important step toward characterizing genetic differences underlying a successful defense response in cacao.
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Affiliation(s)
- Désiré N Pokou
- Centre National de Recherche Agronomique, Laboratoire Central de Biotechnologie, 01 BP 1740, Abidjan 01, Côte d'Ivoire
| | - Andrew S Fister
- Department of Plant Sciences, Life Sciences Building, Pennsylvania State University, University Park, PA, 16802, USA
| | - Noah Winters
- Intercollege Graduate Degree Program in Ecology, Pennsylvania State University, University Park, PA, 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mathias Tahi
- Centre National de Recherche Agronomique, Laboratoire Central de Biotechnologie, 01 BP 1740, Abidjan 01, Côte d'Ivoire
| | - Coulibaly Klotioloma
- Centre National de Recherche Agronomique, Laboratoire Central de Biotechnologie, 01 BP 1740, Abidjan 01, Côte d'Ivoire
| | - Aswathy Sebastian
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - James H Marden
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Siela N Maximova
- Department of Plant Sciences, Life Sciences Building, Pennsylvania State University, University Park, PA, 16802, USA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mark J Guiltinan
- Department of Plant Sciences, Life Sciences Building, Pennsylvania State University, University Park, PA, 16802, USA.
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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40
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Lewis C, Lennon AM, Eudoxie G, Umaharan P. Genetic variation in bioaccumulation and partitioning of cadmium in Theobroma cacao L. Sci Total Environ 2018; 640-641:696-703. [PMID: 29870946 DOI: 10.1016/j.scitotenv.2018.05.365] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/28/2018] [Accepted: 05/28/2018] [Indexed: 05/18/2023]
Abstract
Cadmium (Cd) is a non-essential heavy metal that is toxic to both plants and animals and chocolates have been identified as a contributor to the human dietary Cd intake. One hundred accessions representing the various genetic groups and hybrid populations in Theobroma cacao L. held at the International Cocoa Genebank, Trinidad were evaluated for leaf and bean cadmium levels with three tree replications. Representative samples of soil from the drip zone around each tree were evaluated for bioavailable cadmium. Although there were significant differences (P ≤ 0.05) among genetic groups for leaf and bean Cd much of the variation was between accessions. There was a 13-fold variation in bean Cd and a 7-fold variation in leaf Cd between accessions despite the bioavailable Cd in the soil being uniform. There were differences in the level of partitioning into beans evident by significant variation (P ≤ 0.05) in bean Cd as a percentage of the cumulative leaf and bean Cd concentration (15-52%) between accessions. Although in general there was a higher concentration of cadmium in the testa than the cotyledon of the cocoa bean there was considerable genetic variation. These results point to the potential of using a genetic strategy to mitigate cadmium within cocoa beans either through breeding or through the use of low cadmium uptake rootstocks in grafting. The results will fuel further work into the understanding of mechanisms and genetics of cadmium uptake and partitioning in cocoa.
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Affiliation(s)
- Caleb Lewis
- Cocoa Research Centre, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago; Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine Campus, College Road, Trinidad and Tobago
| | - Adrian M Lennon
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine Campus, College Road, Trinidad and Tobago
| | - Gaius Eudoxie
- Department of Food Production, Faculty of Food and Agriculture, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago
| | - Pathmanathan Umaharan
- Cocoa Research Centre, The University of the West Indies, St. Augustine Campus, Trinidad and Tobago.
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41
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Osorio-Guarín JA, Quackenbush CR, Cornejo OE. Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao. PLoS One 2018; 13:e0203973. [PMID: 30332408 PMCID: PMC6192562 DOI: 10.1371/journal.pone.0203973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/04/2018] [Indexed: 12/18/2022] Open
Abstract
As the source of chocolate, cacao has become one of the most important crops in the world. The identification of molecular markers to understand the demographic history, genetic diversity and population structure plays a pivotal role in cacao breeding programs. Here, we report the use of a modified genotyping-by-sequencing (GBS) approach for large-scale single nucleotide polymorphism (SNP) discovery and allele ancestry mapping. We identified 12,357 bi-allelic SNPs after filtering, of which, 7,009 variants were ancestry informative. The GBS approach proved to be rapid, cost-effective, and highly informative for ancestry assignment in this species.
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Affiliation(s)
- Jaime A. Osorio-Guarín
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Corey R. Quackenbush
- School of Biological Sciences, Washington State University, Pullman, WA, United States of America
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA, United States of America
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42
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Vázquez-Ovando A, Escalona-Buendía H, Ovando-Medina I, Salvador-Figueroa M. Association Between SSR Molecular Markers and Chemical and Sensory Traits of Cacao Samples Using Multiple Regression Analysis. Biochem Genet 2018; 57:301-322. [PMID: 30284127 DOI: 10.1007/s10528-018-9891-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 09/25/2018] [Indexed: 11/26/2022]
Abstract
The sensory properties of cacao beans are linked to the chemical composition of the seeds, and both characteristics are the partial results of its allelic composition. Therefore, it is useful to search for molecular markers associated with these traits. We perform multiple regression analysis to associate previously generated data of alleles generated with 12 SSR (of cultivated cacao trees) with data obtained from chemical and sensory characterization (of beans) of plants grown in the southern region from Mexico. When the association was significant, the mathematical models for predictive purposes were proposed. All phenotypic traits evaluated showed equations with setting values R2 > 0.5. All chemical characters tested have a significant association with at least two alleles (P < 0.05). In addition, the fat content was associated with six molecular markers (mTcCIR03209, mTcCIR12188, mTcCIR19286, mTcCIR07150, mTcCIR19310). The most common allele was mTcCIR12188, which was associated with the contents of eicosanoic acid, moisture, fat and total polyphenols content. The mTcCIR28362 allele is associated with sensory characters bitterness, musty odor, and roasted odor. These alleles could be useful as molecular markers of chemical and sensory characteristics of cacao samples.
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Affiliation(s)
- Alfredo Vázquez-Ovando
- Instituto de Biociencias, Universidad Autónoma de Chiapas. Boulevard Príncipe Akishino sin número, Colonia Solidaridad 2000, C.P. 30798, Tapachula, Chiapas, Mexico
| | - Héctor Escalona-Buendía
- Departamento de Biotecnología, Universidad Autónoma Metropolitana, Unidad Iztapalapa, 09340, Ciudad de México, Mexico
| | - Isidro Ovando-Medina
- Instituto de Biociencias, Universidad Autónoma de Chiapas. Boulevard Príncipe Akishino sin número, Colonia Solidaridad 2000, C.P. 30798, Tapachula, Chiapas, Mexico
| | - Miguel Salvador-Figueroa
- Instituto de Biociencias, Universidad Autónoma de Chiapas. Boulevard Príncipe Akishino sin número, Colonia Solidaridad 2000, C.P. 30798, Tapachula, Chiapas, Mexico.
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do Nascimento JL, de Almeida AAF, Barroso JP, Mangabeira PAO, Ahnert D, Sousa AGR, Silva JVS, Baligar VC. Physiological, ultrastructural, biochemical and molecular responses of young cocoa plants to the toxicity of Cr (III) in soil. Ecotoxicol Environ Saf 2018; 159:272-283. [PMID: 29753828 DOI: 10.1016/j.ecoenv.2018.04.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 04/18/2018] [Accepted: 04/26/2018] [Indexed: 06/08/2023]
Abstract
The objective of this study was to evaluate Cr toxicity in young plants of the CCN 51 Theobroma cacao genotype at different concentrations of Cr3+ in the soil (0, 100, 200, 400 and 600 mg kg-1) through physiological, ultrastructural, antioxidant and molecular changes. Doses of 400 and 600 mg Cr3+ kg-1 soil severely affected foliar gas exchange, promoted by damages in photosynthetic machinery evidenced by the decrease in CO2 fixation. Decreased expression of psbA and psbO genes, changes in enzymatic activity and lipid peroxidation also affected leaf gas exchange. A hormesis effect was observed at 100 mg Cr3+ kg-1 soil for the photosynthetic activity. As a metal exclusion response, the roots of the cocoa plants immobilized, on average, 75% of the total Cr absorbed. Ultrastructural changes in leaf mesophyll and roots, with destruction of mitochondria, plasmolysis and formation of vesicles, were related to the oxidative stress promoted by excess ROS. The activity of the antioxidant enzymes SOD, APX, GPX and CAT and the amino acid proline coincided with the greater expression of the sod cyt gene demonstrating synchronicity in the elimination of ROS. It was concluded, therefore, that the tolerance of the cocoa plants to the toxicity of Cr3+ depends on the concentration and time of exposure to the metal. Higher doses of Cr3+ in the soil promoted irreversible damage to the photosynthetic machinery and the cellular ultrastructure, interfering in the enzymatic and non-enzymatic systems related to oxidative stress and gene expression. However, the low mobility of the metal to the leaf is presented as a strategy of tolerance to Cr3+.
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Affiliation(s)
- Junea Leandro do Nascimento
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900 Ilhéus, BA, Brazil
| | - Alex-Alan Furtado de Almeida
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900 Ilhéus, BA, Brazil.
| | - Joedson P Barroso
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900 Ilhéus, BA, Brazil
| | - Pedro A O Mangabeira
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900 Ilhéus, BA, Brazil
| | - Dário Ahnert
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900 Ilhéus, BA, Brazil
| | - Artur G R Sousa
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900 Ilhéus, BA, Brazil
| | - José Vitor S Silva
- State University of Santa Cruz, Department of Biological Sciences, Rodovia Jorge Amado, km 16, 45662-900 Ilhéus, BA, Brazil
| | - Virupax C Baligar
- USDA-ARS-Beltsville Agricultural Research Center, Beltsville, MD, USA
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44
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Gallego AM, Rojas LF, Parra O, Rodriguez HA, Mazo Rivas JC, Urrea AI, Atehortúa L, Fister AS, Guiltinan MJ, Maximova SN, Pabón-Mora N. Transcriptomic analyses of cacao cell suspensions in light and dark provide target genes for controlled flavonoid production. Sci Rep 2018; 8:13575. [PMID: 30206304 PMCID: PMC6134037 DOI: 10.1038/s41598-018-31965-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/03/2018] [Indexed: 12/16/2022] Open
Abstract
Catechins, including catechin (C) and epicatechin (E), are the main type of flavonoids in cacao seeds. They play important roles in plant defense and have been associated with human health benefits. Although flavonoid biosynthesis has been extensively studied using in vitro and in vivo models, the regulatory mechanisms controlling their accumulation under light/dark conditions remain poorly understood. To identify differences in flavonoid biosynthesis (particularly catechins) under different light treatments, we used cacao cell suspensions exposed to white-blue light and darkness during 14 days. RNA-Seq was applied to evaluate differential gene expression. Our results indicate that light can effectively regulate flavonoid profiles, inducing a faster accumulation of phenolic compounds and shifting E/C ratios, in particular as a response to switching from white to blue light. The results demonstrated that HY5, MYB12, ANR and LAR were differentially regulated under light/dark conditions and could be targeted by overexpression aiming to improve catechin synthesis in cell cultures. In conclusion, our RNA-Seq analysis of cacao cells cultured under different light conditions provides a platform to dissect key aspects into the genetic regulatory network of flavonoids. These light-responsive candidate genes can be used further to modulate the flavonoid production in in vitro systems with value-added characteristics.
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Affiliation(s)
- Adriana M Gallego
- Universidad de Antioquia, Grupo de Biotecnología, Medellín, Colombia
| | - Luisa F Rojas
- Universidad de Antioquia, Grupo de Biotecnología-Escuela de Microbiología, Medellín, Colombia
| | - Oriana Parra
- Universidad de Antioquia, Grupo de Biotecnología, Medellín, Colombia
| | - Héctor A Rodriguez
- Corporación para Investigaciones Biológicas and Departamento de Ciencias Agronómicas, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, UNALMED-CIB, Medellín, Colombia
| | | | - Aura Inés Urrea
- Universidad de Antioquia, Grupo de Biotecnología, Medellín, Colombia
| | - Lucía Atehortúa
- Universidad de Antioquia, Grupo de Biotecnología, Medellín, Colombia
| | - Andrew S Fister
- Department of Plant Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Mark J Guiltinan
- Department of Plant Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Siela N Maximova
- Department of Plant Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States.
| | - Natalia Pabón-Mora
- Universidad de Antioquia, Instituto de Biología, Grupo Evo-Devo en Plantas, Medellín, Colombia.
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Wickramasuriya AM, Dunwell JM. Cacao biotechnology: current status and future prospects. Plant Biotechnol J 2018; 16:4-17. [PMID: 28985014 PMCID: PMC5785363 DOI: 10.1111/pbi.12848] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 05/03/2023]
Abstract
Theobroma cacao-The Food of the Gods, provides the raw material for the multibillion dollar chocolate industry and is also the main source of income for about 6 million smallholders around the world. Additionally, cocoa beans have a number of other nonfood uses in the pharmaceutical and cosmetic industries. Specifically, the potential health benefits of cocoa have received increasing attention as it is rich in polyphenols, particularly flavonoids. At present, the demand for cocoa and cocoa-based products in Asia is growing particularly rapidly and chocolate manufacturers are increasing investment in this region. However, in many Asian countries, cocoa production is hampered due to many reasons including technological, political and socio-economic issues. This review provides an overview of the present status of global cocoa production and recent advances in biotechnological applications for cacao improvement, with special emphasis on genetics/genomics, in vitro embryogenesis and genetic transformation. In addition, in order to obtain an insight into the latest innovations in the commercial sector, a survey was conducted on granted patents relating to T. cacao biotechnology.
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Affiliation(s)
| | - Jim M. Dunwell
- School of Agriculture, Policy and DevelopmentUniversity of ReadingReadingUK
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Silva Monteiro de Almeida D, Oliveira Jordão do Amaral D, Del-Bem LE, Bronze dos Santos E, Santana Silva RJ, Peres Gramacho K, Vincentz M, Micheli F. Genome-wide identification and characterization of cacao WRKY transcription factors and analysis of their expression in response to witches' broom disease. PLoS One 2017; 12:e0187346. [PMID: 29084273 PMCID: PMC5662177 DOI: 10.1371/journal.pone.0187346] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/18/2017] [Indexed: 12/01/2022] Open
Abstract
Transcriptional regulation, led by transcription factors (TFs) such as those of the WRKY family, is a mechanism used by the organism to enhance or repress gene expression in response to stimuli. Here, we report on the genome-wide analysis of the Theobroma cacao WRKY TF family and also investigate the expression of WRKY genes in cacao infected by the fungus Moniliophthora perniciosa. In the cacao genome, 61 non-redundant WRKY sequences were found and classified in three groups (I to III) according to the WRKY and zinc-finger motif types. The 61 putative WRKY sequences were distributed on the 10 cacao chromosomes and 24 of them came from duplication events. The sequences were phylogenetically organized according to the general WRKY groups. The phylogenetic analysis revealed that subgroups IIa and IIb are sister groups and share a common ancestor, as well as subgroups IId and IIe. The most divergent groups according to the plant origin were IIc and III. According to the phylogenetic analysis, 7 TcWRKY genes were selected and analyzed by RT-qPCR in susceptible and resistant cacao plants infected (or not) with M. perniciosa. Some TcWRKY genes presented interesting responses to M. perniciosa such as Tc01_p014750/Tc06_p013130/AtWRKY28, Tc09_p001530/Tc06_p004420/AtWRKY40, Tc04_p016130/AtWRKY54 and Tc10_p016570/ AtWRKY70. Our results can help to select appropriate candidate genes for further characterization in cacao or in other Theobroma species.
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Affiliation(s)
- Dayanne Silva Monteiro de Almeida
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, Ilhéus-BA, Brazil
| | - Daniel Oliveira Jordão do Amaral
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, Ilhéus-BA, Brazil
| | - Luiz-Eduardo Del-Bem
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brasil
| | - Emily Bronze dos Santos
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, Ilhéus-BA, Brazil
| | - Raner José Santana Silva
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, Ilhéus-BA, Brazil
| | | | - Michel Vincentz
- Centro de Biologia Molecular e Engenharia Genética, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brasil
| | - Fabienne Micheli
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, Ilhéus-BA, Brazil
- CIRAD, UMR AGAP, Montpellier, France
- * E-mail:
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47
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Lanaud C, Fouet O, Legavre T, Lopes U, Sounigo O, Eyango MC, Mermaz B, Da Silva MR, Loor Solorzano RG, Argout X, Gyapay G, Ebaiarrey HE, Colonges K, Sanier C, Rivallan R, Mastin G, Cryer N, Boccara M, Verdeil JL, Efombagn Mousseni IB, Peres Gramacho K, Clément D. Deciphering the Theobroma cacao self-incompatibility system: from genomics to diagnostic markers for self-compatibility. J Exp Bot 2017; 68:4775-4790. [PMID: 29048566 PMCID: PMC5853246 DOI: 10.1093/jxb/erx293] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/31/2017] [Indexed: 05/26/2023]
Abstract
Cocoa self-compatibility is an important yield factor and has been described as being controlled by a late gameto-sporophytic system expressed only at the level of the embryo sac. It results in gametic non-fusion and involves several loci. In this work, we identified two loci, located on chromosomes 1 and 4 (CH1 and CH4), involved in cocoa self-incompatibility by two different processes. Both loci are responsible for gametic selection, but only one (the CH4 locus) is involved in the main fruit drop. The CH1 locus acts prior to the gamete fusion step and independently of the CH4 locus. Using fine-mapping and genome-wide association studies, we focused analyses on restricted regions and identified candidate genes. Some of them showed a differential expression between incompatible and compatible reactions. Immunolocalization experiments provided evidence of CH1 candidate genes expressed in ovule and style tissues. Highly polymorphic simple sequence repeat (SSR) diagnostic markers were designed in the CH4 region that had been identified by fine-mapping. They are characterized by a strong linkage disequilibrium with incompatibility alleles, thus allowing the development of efficient diagnostic markers predicting self-compatibility and fruit setting according to the presence of specific alleles or genotypes. SSR alleles specific to self-compatible Amelonado and Criollo varieties were also identified, thus allowing screening for self-compatible plants in cocoa populations.
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Affiliation(s)
- Claire Lanaud
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Avenue Agropolis TA, Montpellier Cedex, France
| | - Olivier Fouet
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Avenue Agropolis TA, Montpellier Cedex, France
| | - Thierry Legavre
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Avenue Agropolis TA, Montpellier Cedex, France
| | - Uilson Lopes
- Centro de Pesquisas do Cacau (CEPEC), CEPLAC, Rod. Ilhéus-Itabuna, Ilhéus, BA, Brazil
| | - Olivier Sounigo
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UR Bioagresseurs, Elig-Essono, Yaoundé, Cameroun
- Institut de Recherche Agricole pour le Developpement (IRAD), Yaoundé, Cameroun
| | - Marie Claire Eyango
- Institut de Recherche Agricole pour le Developpement (IRAD), Yaoundé, Cameroun
| | - Benoit Mermaz
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Avenue Agropolis TA, Montpellier Cedex, France
| | - Marcos Ramos Da Silva
- Centro de Pesquisas do Cacau (CEPEC), CEPLAC, Rod. Ilhéus-Itabuna, Ilhéus, BA, Brazil
| | - Rey Gaston Loor Solorzano
- Instituto Nacional de Investigaciones Agropecuarias (INIAP), EET-Pichilingue. CP 24 Km 5 vía Quevedo El Empalme, Quevedo, Los Ríos, Ecuador
| | - Xavier Argout
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Avenue Agropolis TA, Montpellier Cedex, France
| | - Gabor Gyapay
- Commissariat à l’Energie Antomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | | | - Kelly Colonges
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Avenue Agropolis TA, Montpellier Cedex, France
| | - Christine Sanier
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Avenue Agropolis TA, Montpellier Cedex, France
| | - Ronan Rivallan
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Avenue Agropolis TA, Montpellier Cedex, France
| | - Géraldine Mastin
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Avenue Agropolis TA, Montpellier Cedex, France
| | - Nicholas Cryer
- Mondelez UK R&D Limited, Bournville Place, Bournville Lane, Birmingham, UK
| | - Michel Boccara
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Avenue Agropolis TA, Montpellier Cedex, France
| | - Jean-Luc Verdeil
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Avenue Agropolis TA, Montpellier Cedex, France
| | | | - Karina Peres Gramacho
- Centro de Pesquisas do Cacau (CEPEC), CEPLAC, Rod. Ilhéus-Itabuna, Ilhéus, BA, Brazil
| | - Didier Clément
- Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), UMR AGAP, Avenue Agropolis TA, Montpellier Cedex, France
- Centro de Pesquisas do Cacau (CEPEC), CEPLAC, Rod. Ilhéus-Itabuna, Ilhéus, BA, Brazil
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48
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Scotton DC, Azevedo MDS, Sestari I, Da Silva JS, Souza LA, Peres LEP, Leal GA, Figueira A. Expression of the Theobroma cacao Bax-inhibitor-1 gene in tomato reduces infection by the hemibiotrophic pathogen Moniliophthora perniciosa. Mol Plant Pathol 2017; 18:1101-1112. [PMID: 27454588 PMCID: PMC6638249 DOI: 10.1111/mpp.12463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 05/26/2023]
Abstract
Programmed cell death (PCD) plays a key role in plant responses to pathogens, determining the success of infection depending on the pathogen lifestyle and on which participant of the interaction triggers cell death. The hemibiotrophic basidiomycete Moniliophthora perniciosa is the causal agent of witches' broom disease of Theobroma cacao L. (cacao), a serious constraint for production in South America and the Caribbean. It has been hypothesized that M. perniciosa pathogenesis involves PCD, initially as a plant defence mechanism, which is diverted by the fungus to induce necrosis during the dikaryotic phase of the mycelia. Here, we evaluated whether the expression of a cacao anti-apoptotic gene would affect the incidence and severity of M. perniciosa infection using the 'Micro-Tom' (MT) tomato as a model. The cacao Bax-inhibitor-1 (TcBI-1) gene, encoding a putative basal attenuator of PCD, was constitutively expressed in MT to evaluate function. Transformants expressing TcBI-1, when treated with tunicamycin, an inducer of endoplasmic reticulum stress, showed a decrease in cell peroxidation. When the same transformants were inoculated with the necrotrophic fungal pathogens Sclerotinia sclerotiorum, Sclerotium rolfsii and Botrytis cinerea, a significant reduction in infection severity was observed, confirming TcBI-1 function. After inoculation with M. perniciosa, TcBI-1 transformant lines showed a significant reduction in disease incidence compared with MT. The overexpression of TcBI-1 appears to affect the ability of germinating spores to penetrate susceptible tissues, restoring part of the non-host resistance in MT against the S-biotype of M. perniciosa.
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Affiliation(s)
- Danielle Camargo Scotton
- Centro de Energia Nuclear na Agricultura, Universidade de São PauloPiracicabaSP13400‐970Brazil
- Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São PauloPiracicabaSP13418‐900Brazil
| | - Mariana Da Silva Azevedo
- Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São PauloPiracicabaSP13418‐900Brazil
| | - Ivan Sestari
- Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São PauloPiracicabaSP13418‐900Brazil
| | - Jamille Santos Da Silva
- Centro de Energia Nuclear na Agricultura, Universidade de São PauloPiracicabaSP13400‐970Brazil
- Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São PauloPiracicabaSP13418‐900Brazil
| | - Lucas Anjos Souza
- Centro de Energia Nuclear na Agricultura, Universidade de São PauloPiracicabaSP13400‐970Brazil
- Present address:
Instituto Federal GoianoCampus Rio Verde, Rio VerdeGO 75901-970Brazil
| | | | - Gildemberg Amorim Leal
- Centro de Estudos Agrários, Universidade Federal de AlagoasBR 104, Km 85 Norte, Rio LargoAL57100‐00Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São PauloPiracicabaSP13400‐970Brazil
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49
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Almeida DSM, Gramacho KP, Cardoso THS, Micheli F, Alvim FC, Pirovani CP. Cacao Phylloplane: The First Battlefield against Moniliophthora perniciosa, Which Causes Witches' Broom Disease. Phytopathology 2017; 107:864-871. [PMID: 28430024 DOI: 10.1094/phyto-06-16-0226-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The phylloplane is the first contact surface between Theobroma cacao and the fungus Moniliophthora perniciosa, which causes witches' broom disease (WBD). We evaluated the index of short glandular trichomes (SGT) in the cacao phylloplane and the effect of irrigation on the disease index of cacao genotypes with or without resistance to WBD, and identified proteins present in the phylloplane. The resistant genotype CCN51 and susceptible Catongo presented a mean index of 1,600 and 700 SGT cm-2, respectively. The disease index in plants under drip irrigation was reduced by approximately 30% compared with plants under sprinkler irrigation prior to inoculation. Leaf water wash (LWW) of the cacao inhibited the germination of spores by up to 98%. Proteins from the LWW of CCN51 were analyzed by two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis followed by tandem mass spectrometry. The gel showed 71 spots and identified a total of 42 proteins (28 from the plant and 14 from bacteria). Proteins related to defense and synthesis of defense metabolites and involved in nucleic acid metabolism were identified. The results support the hypothesis that the proteins and water-soluble compounds secreted to the cacao phylloplane participate in the defense against pathogens. They also suggest that SGT can contribute to the resistance of cacao.
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Affiliation(s)
- D S M Almeida
- First, third, fifth, and sixth authors: Proteomics Laboratory, Center of Biotechnology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Rodovia Ilhéus-Itabuna km 16, 45652-900, Brazil; second author: Molecular Plant Pathology Laboratory, CEPLAC, Ilhéus, BA, Brazil; and fourth author: CIRAD-BIOS, UMR AGAP, Montpellier, France
| | - K P Gramacho
- First, third, fifth, and sixth authors: Proteomics Laboratory, Center of Biotechnology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Rodovia Ilhéus-Itabuna km 16, 45652-900, Brazil; second author: Molecular Plant Pathology Laboratory, CEPLAC, Ilhéus, BA, Brazil; and fourth author: CIRAD-BIOS, UMR AGAP, Montpellier, France
| | - T H S Cardoso
- First, third, fifth, and sixth authors: Proteomics Laboratory, Center of Biotechnology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Rodovia Ilhéus-Itabuna km 16, 45652-900, Brazil; second author: Molecular Plant Pathology Laboratory, CEPLAC, Ilhéus, BA, Brazil; and fourth author: CIRAD-BIOS, UMR AGAP, Montpellier, France
| | - F Micheli
- First, third, fifth, and sixth authors: Proteomics Laboratory, Center of Biotechnology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Rodovia Ilhéus-Itabuna km 16, 45652-900, Brazil; second author: Molecular Plant Pathology Laboratory, CEPLAC, Ilhéus, BA, Brazil; and fourth author: CIRAD-BIOS, UMR AGAP, Montpellier, France
| | - F C Alvim
- First, third, fifth, and sixth authors: Proteomics Laboratory, Center of Biotechnology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Rodovia Ilhéus-Itabuna km 16, 45652-900, Brazil; second author: Molecular Plant Pathology Laboratory, CEPLAC, Ilhéus, BA, Brazil; and fourth author: CIRAD-BIOS, UMR AGAP, Montpellier, France
| | - C P Pirovani
- First, third, fifth, and sixth authors: Proteomics Laboratory, Center of Biotechnology and Genetics, Department of Biological Sciences, State University of Santa Cruz, Rodovia Ilhéus-Itabuna km 16, 45652-900, Brazil; second author: Molecular Plant Pathology Laboratory, CEPLAC, Ilhéus, BA, Brazil; and fourth author: CIRAD-BIOS, UMR AGAP, Montpellier, France
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50
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Abstract
Selecting parents and evaluating progenies is a very important step in breeding programs and involves approaches such as understanding the initial stages of growth and characterizing the variability among genotypes for different parameters, such as physiological, growth, biomass partitioning and nutrient translocation to the aerial part. In these cases, facilitating tools can be used to understand the involved gene dynamics, such as diallel crosses and genetic and phenotypic correlations. Our main hypothesis is that the contrasting phenotypes of these parental genotypes of cocoa used are due to genetic factors, and progenies derived from crosses of these parental genotypes are useful for breeding programs related to plant architecture, physiological parameters and translocation of mineral nutrients. We aimed to evaluate the combining abilities in progenies of cacao (Theobroma cacao L) originating from contrasting parents for canopy vigor. Emphasis was given to the evaluation of morphological and physiological parameters and the phenotypic and genotypic correlations to understand the dynamics of the action of the genes involved, as well as in expression profile from genes of gibberellins biosynthesis pathway in the parents. Fifteen F1 progenies were obtained from crosses of six clones (IMC 67, P4B, PUCALA, SCA 6, SCA 24 and SJ 02) that were evaluated in a randomized complete block design with four replicates of 12 plants per progeny, in a balanced half table diallel scheme. It is possible to identify and select plants and progenies of low, medium and high height, as there is expressive genetic variability for the evaluated parameters, some of these on higher additive effects, others on larger nonadditive effects and others under a balance of these effects. Most physiological parameters evaluated show that for selection of plants with the desired performance, no complex breeding methods would be necessary due to the high and medium heritability observed. Strong genetic components were observed from many of the correlations, which indicate the possibility to formulate selection indices for multi-traits, such as dwarfism or semidwarfism, tolerance to increase of leaf sodium concentrations and maintenance of the photosynthetic apparatus integrity under these conditions. Additionally, plants with higher carbon fixation, better water use, higher carboxylation efficiency and greater magnesium accumulation in leaves can be selected.
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Affiliation(s)
- Allan Silva Pereira
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Campus Soane Nazaré de Andrade, Rod. Jorge Amado, Ilhéus, BA, Brasil
| | - Alex-Alan Furtado de Almeida
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Campus Soane Nazaré de Andrade, Rod. Jorge Amado, Ilhéus, BA, Brasil
- * E-mail:
| | - Márcia Christina da Silva Branco
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Campus Soane Nazaré de Andrade, Rod. Jorge Amado, Ilhéus, BA, Brasil
| | - Marcio Gilberto Cardoso Costa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Campus Soane Nazaré de Andrade, Rod. Jorge Amado, Ilhéus, BA, Brasil
| | - Dario Ahnert
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Campus Soane Nazaré de Andrade, Rod. Jorge Amado, Ilhéus, BA, Brasil
- Centro de Pesquisas do Cacau, Comissão Executiva do Plano da Lavoura Cacaueira (CEPEC/CEPLAC). Rod. Jorge Amado, Ilhéus, BA, Brasil
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