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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 #287399
Title: Genetic identity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by molecular markers

Author
item DINARTI, DINY - Bogor Agricultural University
item SUSILO, AGUNG - Indonesian Coffee And Cocoa Research Institute
item Meinhardt, Lyndel
item JI, KUN - South China Agricultural University
item MOTILAL, LAMBERT - University Of The West Indies
item Mischke, Barbara
item Zhang, Dapeng

Submitted to: Journal of Breeding Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/19/2015
Publication Date: 12/19/2015
Citation: Dinarti, D., Susilo, A.W., Meinhardt, L.W., Ji, K., Motilal, L., Mischke, B.S., Zhang, D. 2015. Genetic identity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by molecular markers. Journal of Breeding Science. 65:438-446.

Interpretive Summary: Theobroma 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. Indonesia is the 3rd largest cacao producer in the world; however little is known about the genetic diversity and parentage of cacao varieties from Sulawesi, which is the main cacao production region in Indonesia. This study looked at 53 superior farmer selections of cacao and compared them to reference varieties from South America using two different types of molecular markers. The results showed the efficacy of the single nucleotide polymorphic (SNP) markers and that the on-farm diversity in Sulawesi is largely based on hybrids between two cacao germplasm groups. This limited parental base also showed that the cacao in Sulawesi has a narrow range of host resistances to cacao diseases and pests. New sources of resistances harbored in other germplasm groups need to be introduced and integrated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi. This information will be used by plant breeders, scientists and extension people to improve cacao production in Indonesia and around the world.

Technical Abstract: Indonesia is the 3rd largest cocoa producing countries in the world and 71% of its production is from Sulawesi Island. Knowledge about the genetic background of farmer selections is highly important for effective identification and rational deployment of superior cacao clones in farmers’ fields. Moreover, quality control for clone propagation is essential to ensure the accuracy and reliability of planting materials. Using single nucleotide polymorphism and microsatellite markers, we assessed genetic identity and parentage of 58 Sulawesi farmer selections, including 210 cacao trees.SNP fingerprints detected six intra-clone errors and four synonymous sets. Multivariate coordination analysis based on SSR data showed that these farmer selections are mainly comprised of hybrids mainly derived from three cacao germplasm groups, including Trinitario and two Upper Amazon Forastero groups. The Sulawesi farmer varieties had an average number of alleles at 8.7 per locus whereas the reference international clones had 11.6 per locus. Bayesian clustering analysis further assigned the population memberships, in average, as 51.0% Trinitario, 27.5% Parinari, 12.6% Nanay, 4.2% Morona & Scavina and 4.7% Iquitos Mixed Calabacillo in the 58 farmer selections. Parentage analysis identified 15 international clones as probable parents for 18 farmer selections. The outcomes of this study demonstrated the efficacy of using SNP markers for cacao clone identity verification. The results also confirmed that the current on-farm diversity in Sulawesi is largely based on hybrids between Trinitario and Upper Amazon Forastero germplasm groups, which explain their superior adaptability and yield. However the result also shows that the number of germplasm groups and parental clones contributing to these farmer selections is small, implying a narrow range of host resistances to cacao diseases and pests. New sources of resistances harbored in other germplasm groups need to be introduced and integrated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi. The present study thus provide important baseline information for selecting promising clones from farmers’ fields and ensure genotype conformity in clone propagation, both of which are essential for the on-going program of cacao rehabilitation and intensification in Sulawesi.