Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions

Argout, Xavier; Fouet, Olivier; Wincker, Patrick; Gramacho, Karina Peres; Legavre, Thierry; Sabau, Xavier; Risterucci, Ange Marie; Silva, Corinne Da; Cascardo, Júlio Cézar De Mattos; Allègre, Mathilde; Kuhn, David N.; Verica, Joseph A.; Courtois, B.; Loor, Gaston; Babin, Régis; Sounigo, Olivier; Ducamp, Michel; Guiltinan, Mark J.; Ruiz, Manuel; Alemanno, Laurence; Machado, Rubens E. G.; Phillips, Wilberth; Schnell, R. J.; Gilmour, Martin; Rosenquist, Eric; Butler, David; Maximova, Siela N.; Lanaud, Claire

doi:10.1186/1471-2164-9-512

Cited by 129 publications

(93 citation statements)

References 48 publications

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“…These libraries of the International Oil Palm Genome Projects (OPGP) Consortium were sequenced by the Genoscope-CEA (Evry, France) using the 454 Roche/GS-FLX Pyrosequencing technology (1/2 run per library). Each read library was analyzed using the ESTtik tool (Expressed Sequence Tag treatment and investigation kit) (Argout et al 2008) especially modified for the analysis of 454 sequence data. The 454 reads obtained from the eight pulp libraries were assembled using the TGICL (Pertea et al 2003) assembler.…”

Section: Intra-gene Snp Detection and Mapping Of Chosen Key Genesmentioning

confidence: 99%

Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (H.B.K.) Cortés and oil palm (Elaeis guineensis Jacq.)

Montoya¹,

Lopes

Flori

et al. 2013

Tree Genetics & Genomes

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Section: Intra-gene Snp Detection and Mapping Of Chosen Key Genesmentioning

confidence: 99%

Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (H.B.K.) Cortés and oil palm (Elaeis guineensis Jacq.)

Montoya¹,

Lopes

Flori

et al. 2013

Tree Genetics & Genomes

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“…DNA concentration was determined with a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE). Based on the level of polymorphism and on their distribution across the ten chromosomes in cacao, 54 SNP markers were selected from 1560 candidate SNPs that had been developed using cDNA sequences from a wide range of cacao tissues (Argout et al, 2008). SNP genotyping was performed at the Human Genetics Division Genotyping Core facility, Washington University, St. Louis, using MALDI-TOF mass spectrometry (Sequenom, Inc., San Diego, CA).…”

Section: Sample Preparation and Snp Genotypingmentioning

confidence: 99%

Verification of genetic identity of introduced cacao germplasm in Ghana using single nucleotide polymorphism (SNP) markers

Takrama¹,

Kun²,

Meinhardt³

et al. 2014

Afr. J. Biotechnol.

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Accurate identification of individual genotypes is important for cacao (Theobroma cacao L.) breeding, germplasm conservation and seed propagation. The development of single nucleotide polymorphism (SNP) markers in cacao offers an effective way to use a high-throughput genotyping system for cacao genotype verification. In the present study, high-throughput genotyping with SNP markers was used to fingerprint 160 cacao trees in the germplasm collection at the Cocoa Research Institute of Ghana (CRIG). These accessions had been originally introduced from international germplasm collections. The multilocus SNP profiles, generated by the Sequenom Mass Spectrometry platform, were compared with the SNP profiles of reference trees maintained in the international cacao collections. The comparison unambiguously identified mislabeled trees. For materials introduced as hybrid seeds without an available reference genotype, parentage analysis and model-based assignment were applied to verify their recorded parentage and genetic background. Our study shows that a small set of polymorphic SNP markers can provide a robust and accurate result for cacao genotype identification. This protocol can be applied for large-scale genotyping of cacao as well as for many other crops.

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“…Even with the introduction of resistant varieties, Cacao production in South America reflects the severity of this pathogen, as the yields in most of the infected regions have not returned to pre-outbreak levels. Several functional genomics studies of the cacao-Moniliophthora perniciosa plant-pathogen interaction have been developed (Gesteira et al 2007;Argout et al 2008, CEPLAC projects granted by FAPESB and CNPq). These programs allowed the identification of ESTs involved in resistance of cacao to WBD.…”

Section: Introductionmentioning

confidence: 99%

“…A large number of SNPs has been also identified in EST collections (Argout et al 2008, Lima et al 2009). In 2009, Lima and collaborators reported the detection and analysis of 71 SNPs in ESTs from the cacao-M. perniciosa interaction using in silico analysis, but these SNPs have not been validated.…”

Section: Introductionmentioning

confidence: 99%

DEVELOPMENT OF SNP MARKERS PRESENT IN EXPRESSED GENES OF THE PLANT-PATHOGEN INTERACTION: Theobroma cacao - Moniliophtora perniciosa

Lemos¹,

Gramacho²,

Pires³

et al. 2017

Agrotropica

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We report the detection, validation and analysis of SNPs in the plant-pathogen interaction between cacao and Moniliophthora perniciosa ESTs using resequencing. This analysis in 73 EST sequences allowed the identification of 185 SNPs, 57% of them corresponding to transversion, 29% to transition and 14% to indels. The ESTs containing SNPs were classified into 14 main functional categories. After validation, 91 SNPs were confirmed, categorized and the parameters of nucleotide diversity and haplotype were calculated. Haplotype-based gene diversity and polymorphic information content (PIC) ranged from 0.559 to 0.56 and 0.115 to 0.12; respectively. Also, it was the advantage when considering haplotypes structure for each locus in place of single SNPs. Most of the gene fragments had a major haplotype combined to a series of low frequency haplotypes. Thus, the re-sequencing approach proved to be a valuable resource to identify useful SNPs for wide genetic applications. Furthermore, the cacao genome sequence availability allow a positional selection of DNA fragments to be re-sequenced enhancing the usefulness of the discovered SNPs. These results indicate the potential use of SNPs markers to identify allelic status of cacao resistance genes through marker-assisted selection to support the development of promising genotypes with high resistance to witch's broom disease.Key words: Cacao, ESTs, plant-pathogen interaction, resistante genes, single nucleotide polymorphism.Desenvolvimento de marcadores SNPs presentes em genes expressos da interação planta-patógeno: Theobroma cacao -Moniliophtora perniciosa. Foi reportado aqui a detecção, validação e análise de SNPs em ESTs da interação planta-patógeno entre cacau e Moniliophthora perniciosa, utilizando re-sequenciamento. Esta análise em 73 sequencias ESTs permitiu a identificação de 185 SNPs, 57% deles correspondendo a transversão, 29% a transição e 14% a inserções e deleções. As ESTs contendo SNPs foram classificadas em 14 principais categorias funcionais. Através da validação, 91 SNPs foram confirmados, categorizados e os parâmetros de diversidade de nucleotídeos e haplótipos foram calculados. A diversidade genética baseada em haplótipos e o conteúdo informativo polimórfico (PIC) variaram de 0,559 a 0,56 e 0,115 a 0,12, respectivamente. Além disso, foi apontado a vantagem de considerar estrutura de haplótipos para cada locus no lugar de um único SNPs. A maioria dos fragmentos de genes apresentou um haplótipo principal acompanhado por uma série de haplótipos de baixa frequência. Assim, a abordagem de re-sequenciamento provou ser eficiente para identificar SNPs úteis de ampla aplicação genética. Além disso, a disponibilidade da sequência genômica de Cacau permite uma seleção posicional de fragmentos de DNA a serem resequenciados, aumentando a utilidade dos SNPs descobertos. Estes resultados indicam a potencialidade do uso dos marcadores SNPs para identificação do estado alélico dos genes de resistência do cacau, através de seleção assistida por marcadores, para apoiar o desenv...

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Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions

Cited by 129 publications

References 48 publications

Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (H.B.K.) Cortés and oil palm (Elaeis guineensis Jacq.)

Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (H.B.K.) Cortés and oil palm (Elaeis guineensis Jacq.)

Verification of genetic identity of introduced cacao germplasm in Ghana using single nucleotide polymorphism (SNP) markers

DEVELOPMENT OF SNP MARKERS PRESENT IN EXPRESSED GENES OF THE PLANT-PATHOGEN INTERACTION: Theobroma cacao - Moniliophtora perniciosa

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