Elite cacao clonal cultivars with diverse genetic structure, high production potential, and good organoleptic quality are helping to rebuild the cocoa industry in Brazil

Authors: SOUZA, FREITAS - University Of Santa Cruz - Brazil; SANTOS, SILVA - University Of Santa Cruz - Brazil; FERREIRA, ADRIANA - University Of Santa Cruz - Brazil; SANTOS, LAYSA - University Of Santa Cruz - Brazil; MOTILAL, LAMBERT - University Of The West Indies; CALLE-BELLIDO, JUAN - Mondelez International; Zhang, Dapeng; AHNERT, DARIO - University Of Santa Cruz - Brazil

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/2/2025
Publication Date: 4/4/2025
Citation: Souza, F.L., Santos, S.G., Ferreira, A.C., Santos, L.E., Motilal, L., Calle-Bellido, J., Zhang, D., Ahnert, D. 2025. Elite cacao clonal cultivars with diverse genetic structure, high production potential, and good organoleptic quality are helping to rebuild the cocoa industry in Brazil. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms26073386.
DOI: https://doi.org/10.3390/ijms26073386

Interpretive Summary: Brazil is the leading cocoa producer in the Americas. In Brazil, cacao breeding effort has been focused on developing clonal cultivars, which demonstrate higher productivity compared to traditional biclonal hybrid seedlings. Since the introduction of witches’ broom disease in 1989, several disease-resistant, self-compatible, and productive clones have been selected on local cacao farms in Bahia. Among them include PS 1319, FA 13, and SJ 02. Additionally, CCN 51, introduced from Ecuador, is a significant clone in Brazil. These four clones play a crucial role in revitalizing cacao cultivation in Brazil. The present study aimed to systematically analyze these elite clones concerning their genetic structure, productivity, disease resistance, and organoleptic characteristics of cacao beans. DNA fingerprinting, based on SNP markers, revealed that Clone SJ 02 is predominantly composed of parentage from Contamana (40.7%), Iquitos (34.5%), and Amelonado (23.5%). Clone PS 1319 is primarily composed of Amelonado (67.9%), Criollo (15.7%), and Contamana (15.6%), while FA 13 is mainly composed of Amelonado (53.5%) and Iquitos (44.1%). Regarding productive potential, PS 1319, SJ 02, and FA 13 showed higher productivity than CCN 51. Significant differences were noted among the cultivars for various physico-chemical traits including butter fat, caffeine and theobromine content. Sensorially, SJ 02 outperformed the other cultivars and was comparable to the reference clone BN 34. These findings demonstrated that Brazil’s elite clones, derived from complex crosses, are productive, disease-resistant, and exhibit favorable physico-chemical and organoleptic properties. These elite clones can serve as a valuable source of germplasm for future clonal breeding programs. The resultant information will be used by cacao researchers to improve the efficiency in sustainable conservation and utilization of cacao genetic resources.

Technical Abstract: Brazil is the leading cocoa producer in the Americas. In Brazil, cacao breeding effort has been focused on developing clonal cultivars, which demonstrate higher productivity compared to traditional biclonal hybrid seedlings. Since the introduction of witches’ broom disease in 1989, several disease-resistant, self-compatible, and productive clones have been selected on local cacao farms in Bahia. Amont them include PS 1319, FA 13, and SJ 02. Additionally, CCN 51, introduced from Ecuador, is a significant clone in Brazil. These four clones play a crucial role in revitalizing cacao cultivation in Brazil. The present study aimed to systematically analyze these elite clones concerning their genetic structure, productivity, disease resistance, and organoleptic characteristics of cacao beans. SNP genotyping revealed that Clone SJ 02 is predominantly composed of parentage from Contamana (40.7%), Iquitos (34.5%), and Amelonado (23.5%). Clone PS 1319 is primarily composed of Amelonado (67.9%), Criollo (15.7%), and Contamana (15.6%), while FA 13 is mainly composed of Amelonado (53.5%) and Iquitos (44.1%). Furthermore, SNP analysis showed that the local cultivars from Bahia, Comum and Parazinho, are 100% from the Amelonado group, whereas Maranhão and Pará predominantly contain Amelonado but also include Marañon and other groups. Regarding productive potential, PS 1319, SJ 02, and FA 13 showed higher productivity than CCN 51. Significant differences were noted among the cultivars for various physico-chemical traits including butter fat, caffeine and theobromine content. Sensorially, SJ 02 outperformed the other cultivars and was comparable to the reference clone BN 34. These findings demonstrated that Brazil’s elite clones, derived from complex crosses involving multiple genetic populations, are productive, disease-resistant, and exhibit favorable physico-chemical and organoleptic properties. These elite clones can serve as a valuable source of germplasm for future clonal breeding programs.