Molecular characterization of Vietnamese cocoa genotypes (Theobroma cacao L.) using microsatellite markers

Everaert, Helena; Rottiers, Hayley; Pham, Phuoc Hong Duc; Ha, Lam Thi Viet; Nguyễn, Thành Tiên; Tran, Phuong Diem; Wever, Jocelyn De; Maebe, Kevin; Smagghe, Guy; Dewettinck, Koen; Messens, Kathy

doi:10.1007/s11295-017-1180-6

Cited by 9 publications

(7 citation statements)

References 32 publications

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“…The 143 samples had few matching duplicates (nine groups with two members each) and these were usually within a province rather than across provinces. This internal duplicate matching was lower than that recorded for cacao collected in Belize (Motilal et al, 2010) and for farm selections in Dominica (Gopaulchan et al, 2019), Dominican Republic (Boza et al, 2013), Hawaii (Nagai et al, 2009), Nicaragua (Trognitz et al, 2011, the Huallaga and Ucayali valleys in Peru (Zhang et al, 2006a), Puerto Rico (Cosme et al, 2016) but higher than that reported in one farm in Jamaica (Lindo et al, 2018), Vietnam (Everaert et al, 2017) or for the ICS and TRD accessions in Trinidad (Johnson et al, 2009). Furthermore, an absence of duplicates was reported for 164 trees in Bolivia (Zhang et al, 2012), 93 trees in Tumaco, Colombia (Yacenia Morillo et al, 2014), for 53 trees in Sulawesi, Indonesia (Dinarti et al, 2015), for 220 trees in the Juanjui province of the Huallaga valley, Peru (Zhang et al, 2011), and for 109 trees in Uganda (Gopaulchan et al, 2019).…”

Section: Discussionmentioning

confidence: 60%

Genetic diversity and population structure of fine aroma cacao (Theobroma cacao L.) from north Peru revealed by single nucleotide polymorphism (SNP) markers

et al. 2022

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Cacao (Theobroma cacao L.) is the basis of the lucrative confectionery industry with “fine or flavour” cocoa attracting higher prices due to desired sensory and quality profiles. The Amazonas Region (north Peru) has a designation of origin, Fine Aroma Cacao, based on sensory quality, productivity and morphological descriptors but its genetic structure and ancestry is underexplored. We genotyped 143 Fine Aroma Cacao trees from northern Peru (Bagua, Condorcanqui, Jaén, Mariscal Cáceres, and Utcubamba; mainly Amazonas Region), using 192 single nucleotide polymorphic markers. Identity, group, principal coordinate, phylogenetic and ancestry analyses were conducted. There were nine pairs of matched trees giving 134 unique samples. The only match within 1,838 reference cacao profiles was to a putative CCN 51 by a Condorcanqui sample. The “Peru Uniques” group was closest to Nacional and Amelonado-Nacional genetic clusters based on FST analysis. The provinces of Bagua and Utcubamba were genetically identical (Dest = 0.001; P = 0.285) but differed from Condorcanqui (Dest = 0.016–0.026; P = 0.001–0.006). Sixty-five (49%) and 39 (29%) of the Peru Uniques were mixed from three and four genetic clusters, respectively. There was a common and strong Nacional background with 104 individuals having at least 30% Nacional ancestry. The fine aroma of cacao from Northern Peru is likely due to the prevalent Nacional background with some contribution from Criollo. A core set of 53 trees was identified. These findings are used to support the continuance of the fine or flavour industry in Peru.

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Section: Discussionmentioning

confidence: 60%

Genetic diversity and population structure of fine aroma cacao (Theobroma cacao L.) from north Peru revealed by single nucleotide polymorphism (SNP) markers

et al. 2022

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“…Ten internationals standard SSR primers (Table 2) commonly used for DNA sequencing of cocoa genotype [18] were chosen for this study. These SSR primers were purchased from the Integrated DNA Technologies (IDT, Coralville, Iowa).…”

Section: Ssr Markersmentioning

confidence: 99%

Agronomic Traits and Genetic Fidelity of Four Cocoa Clones Derived from Somatic Embryogenesis Culture

et al. 2022

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Morphological and genetic characterization of MCBC1, PBC230, KKM22 and KKM4 cocoa clones derived from staminode and immature zygotic embryo culture were compared with those conventionally grafted. Somatic embryogenesis culture successfully produced true-to-type progenies of elite cocoa clones of MCBC1, PBC230, KKM22 and KKM4 (from staminode culture). Phenotype variations (p < 0.05) were observed only in KKM4 clone from immature zygotic embryo culture which exhibited lower quantities in the fresh pod weight, number of flat beans per pod, seed length, seed width and individual seed weight. The genetic stability of the cultured clones was tested using fragment analysis with 12 SSR primers to validate these results. Eleven of these SSR primers detected mutations only in the allelic profiles of KKM4 clone from immature zygotic embryo. These results validated those variations in KKM4 clones of immature zygotic embryo culture were due to interactions between genotypic and explant types. Unfortunately, these variations were negative attributes to cocoa productivity. Thus, it is suggested that successful production of true-to-type KKM4 cocoa clone should consider other means of propagation including modification of the culture conditions. HIGHLIGHTS It is crucial to evaluate and confirm the quality of the immature zygotic and staminode regenerated cocoa plant before using the culture technique for commercial production The quality can be detected in both phenotype and genotype by comparing the regenerated cocoa plant with those regenerated from the conventional asexual propagation method of grafting Phenotype and genotype differences were only observed in KKM4 clone regenerated from immature zygotic embryo culture and thus validated that this clone exhibited variation KKM4 clone from immature zygotic embryo culture which has lower quantities in the fresh pod weight, number of flat beans per pod, seed length, seed width and individual seed weight confirmed the negative effect of using immature zygotic embryo explant for KKM4 clone propagation. It is suggested to modify the culture technique GRAPHICAL ABSTRACT

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“…For genetic analysis, one young and healthy leaf from each somatic embryogenesis culture and grafted donor trees were collected from the MCB Research Station for the analysis of somaclonal variation. DNA was extracted from each treatment using a slightly modified CTAB-SDS method from Everaert et al [16] and Johnsiul and Awang [17]. Freshly extracted DNA (5 μl) was then electrophoresed on 1% Agarose gel, stained with ethidium bromide, and visualised under ultraviolet transilluminator for the quality and yield assessments.…”

Section: Field Performancementioning

confidence: 99%

“…From these, mTcCIR7, mTcCIR40 and mTcCIR22 primers were labeled with 6-FAM (blue dye) whereas mTcCIR18 and mTcCIR33 primers were labeled with HEX (green dye) (Table 1). The thermal cycling protocol for the amplification was based on a modified method described by Everaert et al [16]. All the PCR amplification was carried out in a GeneAmp® PCR System 9700 (Applied Biosystems, Inc.).…”

Section: Field Performancementioning

confidence: 99%

Agronomic Performance and Genetic Fidelity of the Selected Elite Cocoa Clones Derived from Somatic Embryogenesis Culture

Entuni

Nori

Edward

et al. 2021

Curr. Appl. Sci. Technol.

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This study was conducted to compare the agronomic performance of four elite cocoa clones (MCBC1, KKM22, KKM4 and PBC230) regenerated from staminode and immature zygotic embryo culture with conventional grafted cocoa clones. From the results, it was found that the KKM4 clone propagated from immature zygotic embryo culture exhibited variations in the fresh pod weight (339.6 g), fresh individual seed weight (4.13 g) and number of flat beans per pod (4 beans) compared with the rest of the regenerated clones. The genetic stability of the somatic embryogenesis cultured clones and the donor clones was then tested using fragment analysis with five SSR primers, i.e. mTcCIR7, mTcCIR18, mTcCIR22, mTcCIR33 and mTcCIR40. Four of these primers identified variations in the allele size and allele addition in KKM4 clone from immature zygotic embryo. Molecular analysis validated that the difference in agronomic performance of the KKM4 clone from immature zygotic embryo culture was due to genetic mutation created during the immature zygotic embryo culture process.

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Molecular characterization of Vietnamese cocoa genotypes (Theobroma cacao L.) using microsatellite markers

Cited by 9 publications

References 32 publications

Genetic diversity and population structure of fine aroma cacao (Theobroma cacao L.) from north Peru revealed by single nucleotide polymorphism (SNP) markers

Genetic diversity and population structure of fine aroma cacao (Theobroma cacao L.) from north Peru revealed by single nucleotide polymorphism (SNP) markers

Agronomic Traits and Genetic Fidelity of Four Cocoa Clones Derived from Somatic Embryogenesis Culture

Agronomic Performance and Genetic Fidelity of the Selected Elite Cocoa Clones Derived from Somatic Embryogenesis Culture

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