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Methylation study of Theobroma cacao L. clones raised under alternative temperature conditions.

ABSTRACT: Methylation differences between SIC 5 cocoa seedlings germinated in a common environment before growth for 74 days under semic controlled environmental conditions set to mimic the Malaysian or Brazilian temperature environment. Genomic DNA sonicated and the methylated fraction enriched using a 5-methylcytosine antibody before whole genome amplification and hybridisation to the array.

ORGANISM(S): Theobroma cacao

PROVIDER: GSE31500 | GEO | 2011/08/19

SECONDARY ACCESSION(S): PRJNA145751

REPOSITORIES: GEO

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Methylation study of Theobroma cacao L. clones raised under alternative temperature conditions.

Project description:Methylation differences between SIC 5 cocoa seedlings germinated in a common environment before growth for 74 days under semic controlled environmental conditions set to mimic the Malaysian or Brazilian temperature environment. Genomic DNA sonicated and the methylated fraction enriched using a 5-methylcytosine antibody before whole genome amplification and hybridisation to the array. Two-condition experiment, Methyl enriched gDNA Malaysian vs. Brazilian leaf samples. 7 Biological replicates independently grown and harvested. Environmental (temperature) effect

2011-08-18 | E-GEOD-31500 | biostudies-arrayexpress

Project description:Malaysian cocoa genome database

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Transcriptomic analysis of cocoa (Theobroma cacao L.) response to water deficit.

Project description:Cocoa is a crop of cultural, nutritional and social importance in Latin America. Cocoa production is mainly supported by smallholders and is central for the food security of these farmer families. Despite being part of their everyday diet and an important source of antioxidants and other healthy bioactive compounds, cocoa cropping is also a solid source of stable incomes supporting the livelihood of farmer families. Water deficit stress is one of the main limiting factors affecting crop yields. The ability of plants to tolerate or recover from the effects associated with this abiotic stress is of immense importance in terms of improvement in the context of climate change. Despite the emergence of functional genomics and phenotyping tools to approach these responses, many of these mechanisms are still little understood for many tropical food crops such as cocoa. For a transcriptomic analysis were selected 2 cocoa genotypes, from a hydric stress assay established in a greenhouse. 5-month-old plants of T. cacao of the genotypes EET 8 and TSH565 were tested for water deficit trial. A divided plot experimental design was applied: the hydric state of the 2 genotypes was evaluated with two levels: field capacity and water deficit by irrigation suspension during a period that generates severe stress (Leaf Water Potential of -3.0 Mpa). The irrigation suspension lasted 52 days.

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Project description:Brazilian cocoa microbiome

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Theobroma cacao

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Characterization of the proteome of Theobroma cacao beans by nanoUHPLC-ESI MS/MS

Project description:Cocoa seed storage proteins play an important role in flavour development as aroma precursors are formed from their degradation during fermentation. Major proteins in the beans of Theobroma cacao are the storage proteins belonging to the vicilin and albumin fraction. Although both these classes of proteins have been fully characterized, there is still limited information on the expression and abundance of other proteins present in cocoa beans. This work is the first attempt to characterize the whole cocoa bean proteome by nanoUHPLC-ESI MS/MS analysis using tryptic digests of cocoa bean protein extracts. The results of this analysis show that a total of 906 proteins could be identified using a species-specific Theobroma cacao database. The majority of the identified proteins were involved with metabolism and energy. However, a significant number of the identified proteins were linked to protein synthesis and processing. Several proteins were also involved with plant response to stress conditions and defence. Albumin and vicilin storage proteins showed the highest intensity values among all detected proteins, although only seven entries were identified as storage proteins. A comparison of MS/MS data searches carried out against larger non-specific databases confirmed that using a species-specific database can increase the number of identified proteins, and at the same time reduce the number of false positives. The results of this work will be useful in developing tools which can allow the comparison of the proteomic profile of cocoa beans from different genotypes and geographic origins.

2018-01-04 | PXD005586 | Pride

Comparison between saprotrophic and biotrophic-like mycelia of cacao WBD causal agent Moniliophthora perniciosa II

Project description:Moniliophthora perniciosa is the causal agent of cacao Witche´s broom disease. This disease has been causing extensive damages to Brazilian cacao plantation, especially in Southern Bahia. Using glass slides microarrays, we analyzed the expression profile of 3872 whole genome shotgun reads from M. perniciosa genome, comparing two stages of development (Biotrophic-like mycelia and saprotrophic mycelia). Keywords: Moniliophthora perniciosa, Witches Broom Disease, Pathogenesis, Cacao

2008-06-13 | GSE9627 | GEO

Comparison between saprotrophic and biotrophic-like mycelia of cacao WBD causal agent Moniliophthora perniciosa I

2008-06-13 | GSE9626 | GEO

Comparison between saprotrophic and biotrophic-like mycelia of cacao WBD causal agent Moniliophthora perniciosa II

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2010-06-25 | E-GEOD-9627 | biostudies-arrayexpress

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