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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Publications at this Location » Publication #286834

Title: Genetic identity, ancestry and parentage in farmer selections of cacao from Aceh, Indonesia revealed by single nucleotide polymorphism (SNP) markers

item LUKMAN - Indonesian Agency For Agricultural Research And Development
item Zhang, Dapeng
item SUSILO, AGUNG - Indonesian Coffee And Cocoa Research Institute
item DINARTI, DINY - Bogor Agricultural University
item Bailey, Bryan
item Mischke, Barbara
item Meinhardt, Lyndel

Submitted to: Tropical Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/30/2014
Publication Date: 11/13/2014
Citation: Lukman, Zhang, D., Susilo, A., Dinarti, D., Bailey, B.A., Mischke, B.S., Meinhardt, L.W. 2014. Genetic identity, ancestry and parentage in farmer selections of cacao from Aceh, Indonesia revealed by single nucleotide polymorphism (SNP) markers. Tropical Plant Biology. 7:133-143.

Interpretive Summary: Cacao is an important tropical crop because it is the source of cocoa butter and powder for the confectionery industry. An understanding of the genetic variability of cacao in farmers’ fields is important for breeding new cacao varieties and for rehabilitation and rejuvenation of old unproductive trees. Indonesia is the 3rd largest cacao producer in the world, however yields are low due to the lack of suitable varieties. Little is known about the ancestry and parentage of cacao varieties selected by farmer from Aceh, Indonesia where cacao production is expanding. This study looked at 80 superior farmer selections of cacao and compared them to reference varieties from South America. Even though disease resistant cacao materials are available to the farmers as the result of governmental programs, the findings from this study show most of the farmer selections lacked these genetic components due to local preferences for large seed and pod size. This local preference reduces the impact of disease resistance breeding programs and leads to a narrow range of variability in farmers’ fields. The study shows that local farmers’ selection preferences must be taken into account for cacao improvement programs. This information will be used by plant breeders, scientists and extension people to improve cacao production around the world.

Technical Abstract: Cacao (Theobroma cacao L.) is the source of cocoa powder and butter used for chocolate and this species originated in the rainforests of South America. Indonesia is the 3rd largest cacao producer in the world with an annual cacao output of 0.55 million tons. Knowledge of on-farm genetic diversity is important for cacao rehabilitation and rejuvenation. DNA fingerprinting was undertaken to assess population structure, ancestry and parentage in farmer selections from six regions in Aceh, Indonesia. The main objective of this study was to examine the genetic background of the superior farmer selected clones from farmers’ fields, in order to provide scientific basis to backstop cacao rehabilitation in Aceh. The pilot experiment assessed a total of 140 genotypes, including 80 Aceh farmer selections and 60 reference clones, using single nucleotide polymorphism (SNP) markers. Principle coordinate 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 main ancestral contributors. Out of the 80 farmer selections, parentage analysis identified 30 parent-offspring relationships contributed by 16 progenitors, which were used in various seeds gardens in Indonesia. Spatial genetic analysis showed that there was no significant global spatial correlation, but local spatial correlation was detected in five out of the six regions. These results suggest that cacao germplasm from the Upper Amazon has been commonly incorporated into farmers’ fields in Aceh. However, the progenitors with significant impact were mainly from two populations. This relatively narrow genetic background was likely due to limited access to diverse hybrids by local farmers or due to the over-emphasis on selecting for yield and morphological appearance, such as pods and bean size, whereas disease-resistance was not given sufficient weight. This finding is in congruence with the known varietal preference of Aceh farmers. Based on the results, a subset of farmer selections with diverse genetic background will be chosen and evaluated in field trials. The combined information of agronomic performance and molecular characterization then will be used to select the best clones for propagation and dissemination. The elite farmer selections provide a good basis for rapid identification of productive trees for rehabilitation and rejuvenzation of cacao farms in Aceh.