Genetic diversity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by microsatellite markers

Abstract

Indonesia is the third largest cocoa-producing country in the world. Knowledge of genetic diversity and parentage of farmer selections is important for effective selection and rational deployment of superior cacao clones in farmers’ fields. We assessed genetic diversity and parentage of 53 farmer selections of cacao in Sulawesi, Indonesia, using 152 international clones as references. Cluster analysis, based on 15 microsatellite markers, showed that these Sulawesi farmer selections are mainly comprised of hybrids derived from Trinitario and two Upper Amazon Forastero groups. Bayesian assignment and likelihood-based parentage analysis further demonstrated that only a small number of germplasm groups, dominantly Trinitario and Parinari, contributed to these farmer selections, in spite of diverse parental clones having been used in the breeding program and seed gardens in Indonesia since the 1950s. The narrow parentage predicts a less durable host resistance to cacao diseases. Limited access of the farmers to diverse planting materials or the strong preference for large pods and large bean size by local farmers, may have affected the selection outcome. Diverse sources of resistance, harbored in different cacao germplasm groups, need to be effectively incorporated to broaden the on-farm diversity and ensure sustainable cacao production in Sulawesi.

A disease and production index (DPI) for selection of cacao (Theobroma cacao) clones highly productive and tolerant to pod rot diseases

“…Cacao is unusual in that there is potential for a superior genotype to be clonally propagated and planted directly in the field without the need for further improvement. In that case, superior clones identified by DPI can be expected to perform as predicted, assuming the conditions of experimentation are properly defined, and have potential for direct release to farmers (Zhang et al , ; Dinarti et al , ). When considering the potential of DPI measures contributing to a breeding programme, other factors not yet tested need to be considered.…”

Variation in Indonesian cocoa farm productivity in relation to management, environmental and edaphic factors

“…For example, the use of side-grafting to rehabilitate old cocoa trees is most widely observed in Sulawesi, whereas in West Papua farmers apply a minimal amount of crop husbandry in terms of, for example, fertiliser addition and pest control. A mixture of hybrid and clonal material is cultivated in Indonesia, with clonal cultivation having expanded in Sulawesi (Dinarti et al, 2015), although clonal cultivation is less prevalent in Sumatra and Java.…”

Incidence Dynamic of Pod Rot Disease of Cocoa Clones in Lampung, Indonesia

“…and frosty pod. However the main founder germplasm groups in Indonesia especially in the Sulawesi farmer selections were three traditional varieties (Trinitario, Amelonado and Criollo) and two wild cocoa germplasm groups (Nanay and Parinari), while wild cocoa from Perunian Amazon (Sca) had little contribution (Dinarti et al, 2015). Amelonado (lower Amazon Forastero) is ancient variety with "melon shaped".…”