Genetic Identity, Ancestry and Parentage in Farmer Selections of Cacao from Aceh, Indonesia Revealed by Single Nucleotide Polymorphism (SNP) Markers

• Published in: Tropical plant biology 2014-12, Vol.7 (3-4), p.133-143
• Main Authors: Lukman, Zhang, Dapeng, Susilo, Agung W, Dinarti, Diny, Bailey, Bryan, Mischke, Sue, Meinhardt, Lyndel W
• Format: Article
• Language: English
• Subjects: beans; Biomedical and Life Sciences; breeding; chocolate; clones; cluster analysis; cocoa butter; cocoa powder; farmers; field experimentation; gardens; genetic background; genetic techniques and protocols; germplasm; hybrids; Life Sciences; parentage; Plant Breeding/Biotechnology; Plant Ecology; Plant Genetics and Genomics; Plant Sciences; pods; rain forests; single nucleotide polymorphism; Theobroma cacao; Transgenics
• ISSN: 1935-9756; 1935-9764
• DOI: 10.1007/s12042-014-9144-6

Cacao (Theobroma cacao L.), the source of cocoa powder and cocoa butter used for chocolate, originated in the rainforests of South America. Indonesia is the 3rd largest cocoa producer in the world with an annual cocoa output of 0.84 million tons. The main objective of this study was to examine the genetic background of superior farmer-selected clones from farmers’ fields, in order to provide a scientific basis to support cacao rehabilitation in Aceh, Indonesia. The pilot experiment assessed 136 genotypes, including 80 Aceh farmer selections and 56 reference international clones, using 53 single nucleotide polymorphism (SNP) markers. Principle coordinates analysis revealed that the Aceh farmer selections were largely hybrids between Upper Amazon Forastero and Trinitario. Bayesian clustering analysis further specified the germplasm groups of the ancestral contributors. Of the 80 farmer selections, parentage analysis identified 30 parent-offspring relationships contributed by 16 progenitors. Spatial genetic analysis showed no significant global spatial correlation, but local spatial correlation was detected. These results suggest that only a fraction of cacao germplasm from Upper Amazon has been incorporated into farmers’ fields, despite the use of diversie progenitors in breeding programs and seed gardens. This relatively narrow genetic background was likely due either to limited access to diverse hybrids by local farmers or to the over-emphasis on selecting for yield and morphological appearance, such as pods and bean size. Based on the results, a subset of farmer selections with diverse genetic background are chosen and evaluated in field trials.