Molecular Characterization of Cacao (Theobroma cacao) Germplasm from Jamaica Using Single Nucleotide Polymorphism (SNP) Markers

Lindo, Aliza A.; Robinson, Dwight E.; Tennant, Paula; Meinhardt, Lyndel W.; Zhang, David

doi:10.1007/s12042-018-9203-5

Cited by 15 publications

(16 citation statements)

References 38 publications

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“…Various SNP-based genotyping methods are currently available, enabling high-throughput genotype calling without the need for electrophoresis 34 . Many SNP based genotyping methods – specific for cacao research – have been described in literature, ranging from TaqMan-based assays 12,16,23 , over Maldi TOF MS 6,24,35 , and Fluidigm SNP genotyping 15,36,37 to the competitive allele specific PCR KASPar chemistry 9 . Yet, no standard SNP genotyping method has been proposed for cacao genetic diversity studies.…”

Section: Discussionmentioning

confidence: 99%

“…This shows genotyping efficiency and accuracy is independent of the classification method (manual vs automated), allowing automated calling approaches to streamline and simplify genotype calling. Discrepancies between DMAS-qPCR calls and reference genotype status could be explained by the uncertainty and inaccuracy associated with any experimental method, including DMAS-qPCR, and potential errors that could have slipped in ICGD – we have already identified duplicates in this repository as have others in the same or different collections and in greater amounts 15,40 . The level of inaccuracy associated with DMAS-qPCR can only be tested by applying this method on a sufficiently large sample population, and comparing the calls with results generated using multiple different techniques (e.g.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, they proved to facilitate cacao conservation and domestication, and conjointly assisted in mapping useful genes and selecting breeding parents. In short, the use of genetic markers resulted in a reduction of inbreeding, mislabeling, unwanted progeny, and genetic drift, playing a main role in long-term breeding gains by enhancing efficient and substantiated cacao management 9,11–15 .…”

Section: Introductionmentioning

confidence: 99%

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The development of a novel SNP genotyping assay to differentiate cacao clones

Wever

Everaert

Coppieters

et al. 2019

Sci Rep

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In this study, a double-mismatch allele-specific (DMAS) qPCR SNP genotyping method has been designed, tested and validated specifically for cacao, using 65 well annotated international cacao reference accessions retrieved from the Center for Forestry Research and Technology Transfer (CEFORTT) and the International Cocoa Quarantine Centre (ICQC). In total, 42 DMAS-qPCR SNP genotyping assays have been validated, with a 98.05% overall efficiency in calling the correct genotype. In addition, the test allowed for the identification of 15.38% off-types and two duplicates, highlighting the problem of mislabeling in cacao collections and the need for conclusive genotyping assays. The developed method showed on average a high genetic diversity (H e = 0.416) and information index (I = 0.601), making it applicable to assess intra-population variation. Furthermore, only the 13 most informative markers were needed to achieve maximum differentiation. This simple, effective method provides robust and accurate genotypic data which allows for more efficient resource management (e.g. tackling mislabeling, conserving valuable genetic material, parentage analysis, genetic diversity studies), thus contributing to an increased knowledge on the genetic background of cacao worldwide. Notably, the described method can easily be integrated in other laboratories for a wide range of objectives and organisms.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The development of a novel SNP genotyping assay to differentiate cacao clones

Wever

Everaert

Coppieters

et al. 2019

Sci Rep

View full text Add to dashboard Cite

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“…Por mencionar algunos ejemplos importantes, Ji et al (2013) identificaron un conjunto de SNPs derivados de la caracterización de marcadores de secuencias expresadas (EST; Expressed Tag Sequences) en cacao, cuyo resultado identificó variedades nicaragüenses y hondureños con mayor variabilidad genética. Asimismo, de manera reciente Lindo et al (2018) zación molecular de germoplasma de cacao proveniente de Jamaica utilizando marcadores SNPs. De acuerdo con lo antes mencionado, los resultados de variabilidad alélica polimórfica de las muestras estudiadas en este proyecto abren la posibilidad de seleccionar especímenes con mayor presencia de SNPs para ser reproducidas mediante injertos en invernaderos, o bien, para cultivarse como bancos de germoplasma con fines de conservación in situ o ex situ.…”

Section: Discussionunclassified

Genotipado por secuenciación de variedades tradicionales de Theobroma cacao (Malvaceae) del Estado de Tabasco, México

et al. 2019

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Background: Single nucleotide polymorphisms (SNPs) have been identified in Theobroma cacao through a genotyping-by-sequencing approach. Through this research it is shared for the first time a set of results related to genetic variability and nature of conserved coding regions of reduced nucleotide sequences of mexican native varieties of cocoa.Hypothesis: Obtaining reduced genomes of T. cacao specimens by restriction enzymes (REs) allows the characterization of single nucleotide polymorphisms (SNPs) as well as conserved coding regions (CDs).Species of study and dates: Theobroma cacao L. (Malvaceae)Study site: Theobroma cacao twigs came from traditional agroforestry plots located in the municipalities of Cardenas, Huimanguillo, Comalcalco, Paraiso, Jalpa de Mendez and Cunduacan, Tabasco, as well as Ixtacomitan and Pichucalco, Chiapas, Mexico; and they were collected and grafted among May and June from 2018.Methods: A method of genotyping-by-sequencing for the characterization of biobanks was developed. Filtering of crude sequences, genomic assembly, identification of SNPs, taxonomic molecular characterization and characterization of coding regions as well as minimum evolution of protein transcripts were performed.Results: Theobroma cacao samples showed different SNPs percentages (2 – 11 %) and the molecular evolution analyzes suggested similar maximum compound probabilities respect to their phylogeny. Conserved sequences were observed in the genomes´ coding regions, which suggest heuristic ontological predictions that have been evolutionarily regrouped in five clusters related to transcription processes and secondary metabolism.Conclusions: The GBS method allows to identify SNPs in cocoa. The characterization of reduced genomes determined the structural and transcriptional correlation between the samples and the reference genome of cacao Criollo.

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“…As cocoa genotype evolution, together with hybridization practices and breeding programs, results in special population dynamics, 43,46 molecular methods have been developed in the recognition of the resulting genetic diversity in cocoa producing‐regions. In particular, molecular marker‐based protocols and the use of single nucleotide polymorphism have been well developed for cocoa genotyping 36,53,97–99 . This methodology has been effective in the determination of provenance and geographical delimitation.…”

Section: Authentication and Geographical Differentiation Of Qualitymentioning

confidence: 99%

Quality differentiation of cocoa beans: implications for geographical indications

Hernandez

Granados²

2021

J Sci Food Agric

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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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Molecular Characterization of Cacao (Theobroma cacao) Germplasm from Jamaica Using Single Nucleotide Polymorphism (SNP) Markers

Cited by 15 publications

References 38 publications

The development of a novel SNP genotyping assay to differentiate cacao clones

The development of a novel SNP genotyping assay to differentiate cacao clones

Genotipado por secuenciación de variedades tradicionales de Theobroma cacao (Malvaceae) del Estado de Tabasco, México

Quality differentiation of cocoa beans: implications for geographical indications

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