Elite Cacao Clonal Cultivars with Diverse Genetic Structure, High Potential of Production, and Good Organoleptic Quality Are Helping to Rebuild the Cocoa Industry in Brazil

Freitas, Lívia Souza; Silva, Gonçalo Santos; Santos, Ivanildes Conceição dos; Ferreira, Adriana C. Reis; Santos, Laysa Evelin Silva; Umaharan, Pathmanthan; Motilal, Lambert A.; Calle-Bellido, Juan; Zhang, Dapeng; Corrêa, Ronan Xavier; Ahnert, Dário

doi:10.3390/ijms26073386

Open AccessArticle

Elite Cacao Clonal Cultivars with Diverse Genetic Structure, High Potential of Production, and Good Organoleptic Quality Are Helping to Rebuild the Cocoa Industry in Brazil

by

Lívia Souza Freitas

^1,2

,

Gonçalo Santos Silva

^1,2,*

,

Ivanildes Conceição dos Santos

²,

Adriana C. Reis Ferreira

²,

Laysa Evelin Silva Santos

²,

Pathmanthan Umaharan

³

,

Lambert A. Motilal

³,

Juan Calle-Bellido

⁴,

Dapeng Zhang

⁵

,

Ronan Xavier Corrêa

^1,6,*,†

and

Dário Ahnert

^1,2,†

¹

Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil

²

Centro de Inovação do Cacau, Ilhéus 45662-900, BA, Brazil

³

Cocoa Research Unit, The University of the West Indies, Saint Agustine 311331, Trinidad and Tobago

⁴

Mondelez International, Inc., East Hanover, NJ 07936, USA

⁵

Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA

⁶

Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, BA, Brazil

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Int. J. Mol. Sci. 2025, 26(7), 3386; https://doi.org/10.3390/ijms26073386

Submission received: 9 February 2025 / Revised: 30 March 2025 / Accepted: 2 April 2025 / Published: 4 April 2025

(This article belongs to the Special Issue Plant Biodiversity and Molecular Marker Technology: Discovery and Application of DNA Polymorphisms)

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Abstract

In the Americas’ leading cocoa-producing countries, more productive clonal cultivars than traditional biclonal hybrids have been created. In Brazil, several disease-resistant and self-compatible clones such as PS 1319, FA 13, and SJ 02 have been selected on producer farms. The CCN 51 clone from Ecuador is also significant in Brazil. This study aimed to analyze these clones concerning their genetic structures using single-nucleotide polymorphisms, productive potential, disease resistance, and the physico-chemical and organoleptic characteristics of the beans. Clone SJ 02 has ancestry from Contamana (40.7%), Iquitos (34.5%), and Amelonado (23.5%). PS 1319 is primarily Amelonado (67.9%), with Criollo (15.7%) and Contamana (15.6%). FA 13 mainly consists of Amelonado (53.5%) and Iquitos (44.1%). Local cultivars of Bahia are mostly Amelonado, with 99.8% in Comum and Parazinho, 97.4% in Maranhão, and 95.5% in Pará. PS 1319, SJ 02, and FA 13 clones were significantly more productive than CCN 51 but did not differ in disease resistance levels. Significant differences were noted among the cultivars in physicochemical traits (fat, caffeine, and theobromine content). Sensorially, SJ 02 outperformed the other cultivars and was comparable to the reference clone BN 34. The findings indicate that Brazil’s elite clones, derived from complex crosses involving Amelonado, Contamana, Iquitos, and Criollo groups, are productive, resistant, and exhibit favorable physico-chemical and organoleptic qualities, making them valuable for future clonal breeding programs.

Keywords: molecular breeding; cacao clones; production; cocoa bean quality; organoleptic; genetic ancestry; SNP

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MDPI and ACS Style

Freitas, L.S.; Silva, G.S.; Santos, I.C.d.; Ferreira, A.C.R.; Santos, L.E.S.; Umaharan, P.; Motilal, L.A.; Calle-Bellido, J.; Zhang, D.; Corrêa, R.X.; et al. Elite Cacao Clonal Cultivars with Diverse Genetic Structure, High Potential of Production, and Good Organoleptic Quality Are Helping to Rebuild the Cocoa Industry in Brazil. Int. J. Mol. Sci. 2025, 26, 3386. https://doi.org/10.3390/ijms26073386

AMA Style

Freitas LS, Silva GS, Santos ICd, Ferreira ACR, Santos LES, Umaharan P, Motilal LA, Calle-Bellido J, Zhang D, Corrêa RX, et al. Elite Cacao Clonal Cultivars with Diverse Genetic Structure, High Potential of Production, and Good Organoleptic Quality Are Helping to Rebuild the Cocoa Industry in Brazil. International Journal of Molecular Sciences. 2025; 26(7):3386. https://doi.org/10.3390/ijms26073386

Chicago/Turabian Style

Freitas, Lívia Souza, Gonçalo Santos Silva, Ivanildes Conceição dos Santos, Adriana C. Reis Ferreira, Laysa Evelin Silva Santos, Pathmanthan Umaharan, Lambert A. Motilal, Juan Calle-Bellido, Dapeng Zhang, Ronan Xavier Corrêa, and et al. 2025. "Elite Cacao Clonal Cultivars with Diverse Genetic Structure, High Potential of Production, and Good Organoleptic Quality Are Helping to Rebuild the Cocoa Industry in Brazil" International Journal of Molecular Sciences 26, no. 7: 3386. https://doi.org/10.3390/ijms26073386

APA Style

Freitas, L. S., Silva, G. S., Santos, I. C. d., Ferreira, A. C. R., Santos, L. E. S., Umaharan, P., Motilal, L. A., Calle-Bellido, J., Zhang, D., Corrêa, R. X., & Ahnert, D. (2025). Elite Cacao Clonal Cultivars with Diverse Genetic Structure, High Potential of Production, and Good Organoleptic Quality Are Helping to Rebuild the Cocoa Industry in Brazil. International Journal of Molecular Sciences, 26(7), 3386. https://doi.org/10.3390/ijms26073386

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Elite Cacao Clonal Cultivars with Diverse Genetic Structure, High Potential of Production, and Good Organoleptic Quality Are Helping to Rebuild the Cocoa Industry in Brazil

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