Coconut palm is known as “tree of life” because it has important rules in many aspects in people’s life and full of benefits. Indonesia has been known as the coconut center of origin. Therefore there will be a high diversity of coconut in this nation. The objectives of this study are to determine the diversity of coconut germplasm that is part of coconut collection at Indonesian Plam Crops Reserach Institute (IPCRI). This research conducted at Mapanget Experimental Garden, IPCRI and Laboratory of Plant Breeding and Genetics, Faculty of Agriculture, Universitas Gadjah Mada (UGM) by survey method. Plant materials used in this research consists of eight dwarf coconut accessions and two tall coconut accessions. Molecular analysis using SSR markers performed to all of the samples. The results showed that the highest heterozygosity found in the Bali Tall (BAT) population, while the lowest was in the population of Bali Yellow Dwarf (BYD). Shannon diversity index analysis showed that individual heterogeneity values in each population were low. The closest similarity relationship found between the Sweet Green Dwarf (SGD) and BAT population. The widest genetic distance was observed between the population of BYD and Nias Yellow Dwarf (NYD). The genetic similarity coefficients of 122 individual coconut palms from 10 populations observed on the pattern of DNA bands amplified using 10 SSR markers ranged from 0.19 to 1. Individuals from 10 observed coconut populations were divided into six main groups (A, B, C, D, E, and F) on the genetic similarity coefficient of 0.25.

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