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Genetic diversity and parentage of cacao (Theobroma cacao L.) populations from Ghana using single nucleotide polymorphism (SNP) markers

Published online by Cambridge University Press:  16 October 2024

Kwabena Asare Bediako Open the ORCID record for Kwabena Asare Bediako [Opens in a new window] ,
Francis Kwame Padi Open the ORCID record for Francis Kwame Padi [Opens in a new window] ,
Ebenezer Obeng-Bio  and
Atta Ofori
Kwabena Asare Bediako*
Affiliation:
Cocoa Research Institute of Ghana, New Tafo-Akim, Ghana
Francis Kwame Padi
Affiliation:
Cocoa Research Institute of Ghana, New Tafo-Akim, Ghana
Ebenezer Obeng-Bio
Affiliation:
Cocoa Research Institute of Ghana, New Tafo-Akim, Ghana
Atta Ofori
Affiliation:
Cocoa Research Institute of Ghana, New Tafo-Akim, Ghana
*
Corresponding author: Kwabena Asare Bediako; Email: [email protected]
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Abstract

Ortet selection remains an integral component of cacao breeding programme to develop improved clones and expand the gene pool of available germplasm. This study assessed the population structure of 168 cacao clones developed recently from selected ortets in on-station and on-farm progeny trials in Ghana using 45 SNP markers. Selection of ortets was primarily based on high bean yield, high yield efficiency, adaptability to marginal growing conditions, and low incidence of black pod and cocoa swollen shoot virus diseases. Additionally, 58 SNPs were employed to verify the parentage of 752 bi-clonal seedlings supplied to farmers for commercial plantations. Pairwise multilocus matching based on 45 SNPs showed that the 168 clones were all distinct. Overall, the clones had moderate genetic diversity (He = 0.349 ± 0.022) and shared ancestry with Marañón, Guiana, Contamana, Iquitos, Amelonado, Trinitario, Nanay and Purús based on Bayesian clustering, principal coordinates, and parentage analyses. Parentage analysis of bi-clonal seedlings assigned parent-offspring trios (>80% confidence level) to 65.2% of the farmers' varieties based on breeder's active clone collection. The results of the parentage analysis suggested the existence of mislabelled clones in the seed gardens, necessitating the need for correct clone identification or rogueing. Taken together, this study presents a new group of cacao genetic resources with potential to broaden the gene pool of cacao in cacao improvement programmes. Further, the study conveys evidence of the need for countries with established seed garden systems to constantly monitor the genetic purity of seedlings produced from the seed gardens.

Keywords

clonesDNA fingerprintinggenetic structureortetsseed gardensTheobroma cacao
Type
Research Article
Information
Plant Genetic Resources , Volume 23 , Issue 1 , February 2025 , pp. 40 - 47
Copyright
Copyright © The Author(s), 2024. Published by Cambridge University Press on behalf of National Institute of Agricultural Botany

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