SSR MARKERS CHARACTERIZATION FOR TEMU IRENG (Curcuma aeruginosa Roxb.) GENERATED FROM EST OF Curcuma longa

Main Article Content

Devit Purwoko
Siti Zulaeha
Teuku Tajuddin
Hayat Khairiyah
Reynaldi Zulfikar Fauzi
. Priyanti

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.


Temu ireng (Curcuma aeruginosa) digunakan sebagai bahan baku obat herbal tradisional di Indonesia. Expressed Sequence Tags (EST) dari C. longa digunakan karena sampai saat ini belum adanya data genome dari C. aeruginosa. Penelitian ini bertujuan untuk mengetahui keragaman karakteristik SSR dan mengembangkan primer untuk prastudi keragaman genetik C. aeruginosa. EST dilakukan prapemrosesan dan dianalisis motif SSR. Primer didesain menggunakan motif SSR selain mononukleotida (? 20 bp) dan dianalisis berdasarkan ontologi gen. Hasil yang diperoleh dari 12.678 EST yang digunakan dihasilkan 3.005 contig dan 548 motif perfect SSR dengan frekuensi motif 1/15,27 kb sekuen. AGG trinukleotida merupakan yang paling banyak terdistribusi (37,40%). Sebanyak 380 primer didesain dan 10 primer divalidasi melalui PCR pada 3 klon C. aeruginosa asal Ponorogo, Cikarang, dan Kebumen. Jumlah alel yang terdeteksi sekitar 2 sampai 3 per lokus. Marka mikrosatelit polimorfik yang dihasilkan dari penelitian ini dapat digunakan untuk analisis keragaman genetik C. aeruginosa di Indonesia.

Article Details

How to Cite
Purwoko, D., Zulaeha, S., Tajuddin, T., Khairiyah, H., Fauzi, R. Z., & Priyanti, . (2020). SSR MARKERS CHARACTERIZATION FOR TEMU IRENG (Curcuma aeruginosa Roxb.) GENERATED FROM EST OF Curcuma longa. Jurnal Bioteknologi &Amp; Biosains Indonesia (JBBI), 8(2), 160–173. https://doi.org/10.29122/jbbi.v8i2.4763
Section
Research Articles
Author Biography

Devit Purwoko, The Center for Biotechnology, National Research and Innovation Agency (BRIN)

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JBBI Editor: http://ejurnal.bppt.go.id/Devit Purwoko

Google Scholar: https://scholar.google.com/Devit Purwoko

Research Gate: https://www.researchgate.net/Devit Purwoko

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