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Information about the genetic diversity of Red wood is needed to improve the quality and quantity of the plant. This information can be provided by analyzing plant DNA using molecular markers which are polymorphic and generate clear and thick bands. The objective of the study was to obtain primers that could generate clear and polymorphically bands from Red wood DNA. The evaluated Red wood was from Alor, Sika, Lembata, Rote, and Timur Tengah Selatan (TTS) provenances. As many as 54 primers screened to polymorphism assay. Those primers consisted of RAPD, SSR, and chloroplast.The SSR primers were developed from Pterocarpus indicus (six primers) and Prosopis alba (12 primers). Chloroplast primers were divided into two types, four Rubisco Large Sub-unit genes (rbcL) and 12 MaturaseK genes (matK). SSR primers of P. alba were not able to amplify Red wood DNA, whereas those of P. indicus could amplify the DNA. Three of each chloroplast primers successfully amplified the DNA, yet, each primer could only amplify one to four of 12 evaluated samples. rbcL 2 generated the highest number of sample, and samples from Lembata were amplified the most. Moreover, 16 RAPD primers were able to generate DNA.

Selection of Dominant and Co-dominant Markers for Red Wood (Pterocarpus indicus Willd) Polymorphism from Five Provenances in East Nusa Tenggara