Genetic diversity analysis of cacao (Theobroma cacao L.) germplasm in Samoa using microsatellite markers : a thesis submitted in partial fulfilment of the requirements for the degree of Master of Science in Plant Breeding at Massey University, Palmerston North, New Zealand

Abstract

Cacao (Theobroma cacao L.) is an important tropical crop with significant economic and ecological value. However, its genetic diversity is still insufficiently studied in Samoa. In this study, microsatellite markers were used to assess the genetic diversity of 183 cacao varieties collected from four plantations in Samoa. Six polymorphic SSR loci were used to identify 108 alleles revealing genetic variation in cacao among plantations (expected heterozygosity = 0.49). Both Structure and Neighbor-Net analyses showed that the SIU plantations were mainly Criollo and the SAT plantations were mainly Nanay, while the ALE and SAL plantations were mixtures of several varieties. Four different genetic groups were delineated by cluster analysis (UPGMA) and principal coordinate analysis (PCoA). It was finally determined that the cacao in the Samoa region consists of Amelonado, Trinitario, Nanay, Criollo and LAFI-7. The results of this study revealed the key role of microsatellite markers in analyzing cacao diversity, identified the major Samoa cacao types and provided feasible insights for Samoa molecular marker-assisted cacao breeding. It provides a direction for future improvement of cacao germplasm for biotic and abiotic resistance and the construction of modernized cacao plantations.