Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L.

Allègre, Mathilde; Argout, Xavier; Boccara, Michel; Fouet, Olivier; Roguet, Yolande; Berard, Aurélie; Thévenin, Jean-Marc; Chauveau, Aurélie; Rivallan, Ronan; Clément, Didier; Courtois, B.; Gramacho, Karina Peres; Boland‐Augé, Anne; Tahi, Mathias Gnion; Umaharan, Pathmanathan; Brunel, Dominique; Lanaud, Claire

doi:10.1093/dnares/dsr039

Cited by 47 publications

(53 citation statements)

References 63 publications

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“…During natural selection, transitions mutations are better tolerated than transversions because they generate synonymous mutations in protein-coding sequences [64].…”

Section: Resultsmentioning

confidence: 99%

De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

et al. 2014

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Hevea brasiliensis (Willd. Ex Adr. Juss.) Muell.-Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection.Citation: Mantello CC, Cardoso-Silva CB, da Silva CC, de Souza LM, Scaloppi Junior EJ, et al. (2014) De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways. PLoS ONE 9(7): e102665.

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“…During natural selection, transitions mutations are better tolerated than transversions because they generate synonymous mutations in protein-coding sequences [64].…”

Section: Resultsmentioning

confidence: 99%

De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

et al. 2014

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“…Besides EST-SSR, there are other alternative data mining techniques such as expressed sequence tag-single nucleotide polymorphism (EST-SNP) in maize (Batley et al, 2003), barley (Varshney et al, 2007), melon (Deleu et al, 2009), citrus (Jiang et al, 2010), and cocoa (Allegre et al, 2011), expressed sequence tag-rapid amplified polymorphic DNA (EST-RAPD) in oil palm (Balakrishnan & Vadivel, 2012), and expressed sequence tag-sequence tagged site (EST-STS) in wheat (Leonard et al, 2008;Naji et al, 2008). All the aforementioned techniques are useful for functional genetic diversity estimation of GenBank collections and valuable for use in marker-assisted programmes.…”

Section: Data Mining Of Vmpest-ssrmentioning

confidence: 99%

Discovering Fragrance Biosynthesis Genes from Vanda Mimi Palmer Using the Expressed Sequence Tag (EST) Approach

Teh¹,

Abdullah²,

Namasivayam³

et al. 2012

Data Mining Applications in Engineering and Medicine

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“…A SNP‐based linkage map for cacao was initially developed by Allegre et al . (). This genetic linkage map contains a set of 1262 markers spanning in a length of 734 cM, and of these markers, 681 are EST‐based SNPs.…”

Section: Introductionmentioning

confidence: 97%

Cacao biotechnology: current status and future prospects

Wickramasuriya

Dunwell

2017

Plant Biotechnology Journal

105

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Summary 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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Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L.

Cited by 47 publications

References 63 publications

De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

De Novo Assembly and Transcriptome Analysis of the Rubber Tree (Hevea brasiliensis) and SNP Markers Development for Rubber Biosynthesis Pathways

Discovering Fragrance Biosynthesis Genes from Vanda Mimi Palmer Using the Expressed Sequence Tag (EST) Approach

Cacao biotechnology: current status and future prospects

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