SSR MARKERS CHARACTERIZATION FOR TEMU IRENG (Curcuma aeruginosa Roxb.) GENERATED FROM EST OF Curcuma longa
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Abstract
Temu ireng (Curcuma aeruginosa) is used as a traditional herb medicine in Indonesia. Expressed Sequence Tags (EST) of C. longa was used because there were no genome data of C. aeruginosa. This study aimed to recognize the diversity of SSR characteristic and to develop a primer for C. aeruginosa genetic diversity. The EST was preprocessed and analyzed fogg7r the SSR motif. Primers were designed using SSR motifs excluding mononucleotide (? 20 bp) and analyzed based on gene ontology. The result showed that out of 12.675 EST used there were 3.005 contig and 548 perfect SSR motif with the motif frequency of 1/15,27 kb sequences achieved. AGG trinucleotide was mostly distributed (37,40%). There were 380 primers designed and 10 primers validated by PCR on three C. aeruginosa clones from Ponorogo, Cikarang, and Kebumen. The number of alleles detected was about 2 to 3 per locus. The polymorphic microsatellite markers produced from this study could be used for the analysis of genetic diversity of C. aeruginosa in Indonesia.
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