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All Journal Jurnal Bioteknologi & Biosains Indonesia (JBBI)
Devit Purwoko
The Center for Biotechnology, National Research and Innovation Agency (BRIN)
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Immunology & microbiology

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SSR MARKERS CHARACTERIZATION FOR TEMU IRENG (Curcuma aeruginosa Roxb.) GENERATED FROM EST OF Curcuma longa Devit Purwoko; Siti Zulaeha; Teuku Tajuddin; Hayat Khairiyah; Reynaldi Zulfikar Fauzi; . Priyanti
Jurnal Bioteknologi & Biosains Indonesia (JBBI) Vol. 8 No. 2 (2021): December 2021
Publisher : Balai Bioteknologi, Badan Pengkajian dan Penerapan Teknologi (BPPT)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (555.554 KB) | DOI: 10.29122/jbbi.v8i2.4763

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.
Co-Authors . Priyanti Hayat Khairiyah Reynaldi Zulfikar Fauzi Siti Zulaeha Teuku Tajuddin