Study of the genetic diversity of cocoa populations (Theobroma cacao L.) of Martinique (FWI) and potential for processing and the cocoa industry

Adenet, Sandra; Regina, Françoise; Rogers, Dominique; Bharath, Sarah; Argout, Xavier; Rochefort, Katia; Cilas, Christian

doi:10.1007/s10722-020-00953-0

Cited by 5 publications

(18 citation statements)

References 15 publications

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“…The average coverage depth per sample for both SNP datasets was 20.5×, and in 12 cases, depth dropped below 10×, reaching 6× in one of them. Plants with relatively high missing data and low coverage were not removed from the datasets because they accounted for less than 3% of the total, and studies using up to 50% of individual missing data threshold have been reported in cacao genetic studies based on SNP markers ( Adenet et al., 2020 ; Gutiérrez et al., 2021 ).…”

Section: Resultsmentioning

confidence: 99%

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Using ddRADseq to assess the genetic diversity of in-farm and gene bank cacao resources in the Baracoa region, eastern Cuba, for use and conservation purposes

Ramirez-Ramirez,

Mirzaei,

Menéndez-Grenot

et al. 2024

Front. Plant Sci.

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The Baracoa region, eastern Cuba, hosts around 80 % of the country cacao (Theobroma cacao L.) plantations. Cacao plants in farms are diverse in origin and propagation, with grafted and hybrid plants being the more common ones. Less frequent are plants from cuttings, TSH progeny, and traditional Cuban cacao. A national cacao gene bank is also present in Baracoa, with 282 accessions either prospected in Cuba or introduced from other countries. A breeding program associated with the gene bank started in the 1990s based on agro-morphological descriptors. The genetic diversity of cacao resources in Baracoa has been poorly described, except for traditional Cuban cacao, affecting the proper development of the breeding program and the cacao planting policies in the region. To assess the population structure and genetic diversity of cacao resources in Baracoa region, we genotyped plants from both cacao gene bank (CG) and cacao farms (CF) applying a new ddRADseq protocol for cacao. After data processing, two SNPs datasets containing 11,425 and 6,481 high-quality SNPs were generated with 238 CG and 135 CF plants, respectively. SNPs were unevenly distributed along the 10 cacao chromosomes and laid mainly in noncoding regions of the genome. Population structure analysis with these SNP datasets identified seven and four genetic groups in CG and CF samples, respectively. Clustering using UPGMA and principal component analysis mostly agree with population structure results. Amelonado was the predominant cacao ancestry, accounting for 49.22 % (CG) and 57.73 % (CF) of the total. Criollo, Contamana, Iquitos, and Nanay ancestries were detected in both CG and CF samples, while Nacional and Marañon backgrounds were only identified in CG. Genetic differentiation among CG (FST ranging from 0.071 to 0.407) was higher than among CF genetic groups (FST: 0.093–0.282). Genetic diversity parameters showed similar values for CG and CF samples. The CG and CF genetic groups with the lowest genetic diversity parameters had the highest proportion of Amelonado ancestry. These results should contribute to reinforcing the ongoing breeding program and updating the planting policies on cacao farms, with an impact on the social and economic life of the region.

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Section: Resultsmentioning

confidence: 99%

“…(2018) for the identification of 7,009 SNPs carrying cacao ancestry information. Recently, GBS experiments based on genomic digestion with two enzymes were used to perform genetic studies in cacao from French Guiana, Martinique, and Colombia ( Lachenaud et al., 2018 ; Adenet et al., 2020 ; Osorio-Guarin et al., 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Using ddRADseq to assess the genetic diversity of in-farm and gene bank cacao resources in the Baracoa region, eastern Cuba, for use and conservation purposes

Ramirez-Ramirez,

Mirzaei,

Menéndez-Grenot

et al. 2024

Front. Plant Sci.

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“…Extensive research has emphasized the importance of genotype contribution to quality, with a common example being the discrimination of bulk cocoa, such as CCN 51 (bitter, astringent and off‐flavor attributes), from fine types, such as Nacional (fruity and acid) 35,52 . Whereas other works, centered on the recognition of a complex genetic diversity in a territory, have pointed out major contributions from geography on the generation of distinctive aroma and flavor profiles 53 …”

Section: Cocoa Genotypes and Quality Paradigmsmentioning

confidence: 99%

“…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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“…The first classifications of the Theobroma species were made concerning their phenotypic characteristics, evidencing that one of the marked differences between Criollo and the others, was the content of anthocyanins in its seeds [2,4,18]. The first genetic diversity studies of cacao were made using RAPD and RFLP markers [19][20][21][22][23], followed by SSR markers [24][25][26][27][28][29][30][31][32], and SNP markers [33][34][35][36][37][38]. Some of these studies made it possible to identify Criollo as a different genetic group.…”

Section: Introductionmentioning

confidence: 99%

Genetic Purity of Cacao Criollo from Honduras Is Revealed by SSR Molecular Markers

López¹,

Gori²,

Bini³

et al. 2021

Agronomy

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The cultivation of cacao represents an income option and a source of employment for thousands of small producers in Central America. In Honduras, due to the demand for fine flavor cacao to produce high-quality chocolate, the number of hectares planted is increasing. In addition, cacao clones belonging to the genetic group named Criollo are in great demand since their white beans lack of bitterness and excellent aroma are used in the manufacturing of premium chocolate. Unfortunately, the low resistance to pests and diseases and less productive potential of Criollo cacao leads to the replacement with vigorous new cultivars belonging to the other genetic groups or admixture of them. In this study, 89 samples showing phenotypic traits of Criollo cacao from four regions of Honduras (Copán, Santa Bárbara, Intibucá, and Olancho) were selected to study their genetic purity using 16 SSR molecular markers. The results showed that some samples belong to the Criollo group while other accessions have genetic characteristics of “Trinitario” or other admixtures cacao types. These results confirm the genetic purity of Criollo cacao in Honduras, reaffirming the theory that Mesoamerica is a cacao domestication center and also serves to generate interest in the conservation of this genetic wealth both in-situ and ex-situ.

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Study of the genetic diversity of cocoa populations (Theobroma cacao L.) of Martinique (FWI) and potential for processing and the cocoa industry

Cited by 5 publications

References 15 publications

Using ddRADseq to assess the genetic diversity of in-farm and gene bank cacao resources in the Baracoa region, eastern Cuba, for use and conservation purposes

Using ddRADseq to assess the genetic diversity of in-farm and gene bank cacao resources in the Baracoa region, eastern Cuba, for use and conservation purposes

Quality differentiation of cocoa beans: implications for geographical indications

Genetic Purity of Cacao Criollo from Honduras Is Revealed by SSR Molecular Markers

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