Perancangan Primer Spesifik Subspesies Berbasis Gen Endoglukanase untuk Deteksi Ralstonia syzygii subsp. syzygii

https://doi.org/10.22146/jpti.32217

Bambang Trianom(1), Triwidodo Arwiyanto(2), Tri Joko(3*)

(1) Balai Karantina Pertanian Bandar Lampung Jln. Soekarno-Hatta km. 7, Bandar Lampung, Lampung 35241
(2) Departemen Hama dan Penyakit Tumbuhan, Fakultas Pertanian, Universitas Gadjah Mada Jln. Flora No. 1, Bulaksumur, Yogyakarta 55281
(3) Departemen Hama dan Penyakit Tumbuhan, Fakultas Pertanian, Universitas Gadjah Mada Jln. Flora No. 1, Bulaksumur, Yogyakarta 55281
(*) Corresponding Author

Abstract


Ralstonia syzygii subsp. syzygii that belong to Ralstonia solanacearum species complex is the cause of Sumateran disease of clove. The disease was reported to cause widespread devastation on clove plantings in Indonesia. One of the control strategies is to reduce the spread of the disease through early detection on clove seedlings. The study aimed to design the specific primers based on endoglucanase (egl) gene of R. syzygii subsp. syzygii as a tool for early diagnosis. The analyses were conducted on development of specific primers design using egl sequences retrieved from GenBank, Polymerase Chain Reaction (PCR), primers sensitivity and specificity test. The pair of primers UGMRss-F (5’-GCTCACCATCGC CAAGGACAGCG-3’) and UGMRss-R (5’-TTCGATCGAACGCCTGGTTGAGC-3’) could amplify R. syzygii subsp. syzygii at ~378 base pairs with 0.8 ng/µl minimum concentration of DNA. The primers was specific to R. syzygii subsp. syzygii but not to other bacterial species even in the same phylotype.

 

Intisari

Ralstonia syzygii subsp. syzygii merupakan bakteri yang termasuk dalam kelompok Ralstonia solanacearum species complex yang menyebabkan penyakit Sumatera pada tanaman cengkih. Penyakit ini menyebabkan kerugian yang sangat besar dan sampai saat ini belum ditemukan cara pengendalian yang efektif. Salah satu  upaya pencegahan penyakit adalah melalui deteksi dini dan mencegah penyebaran penyakit melalui peredaran bibit dari areal yang endemis. Penelitian ini bertujuan untuk merancang primer spesifik berbasis gen endoglukanase (egl) sebagai upaya deteksi dini penyakit Sumatera. Analisis yang dilakukan  meliputi  desain primer spesifik dengan menggunakan data sekuens gen egl dari GenBank, Polymerase Chain Reaction (PCR), uji kepekaan primer dan uji kekhususan primer. Desain primer yang berhasil dirancang terdiri dari UGMRss-F (5’- GCTCACCATCGCCAAGGACAGCG-3’) dan UGMRss-R (5’-TTC GATCGAACGCCTGGTTGAGC-3’) dengan amplikon ~378 pasang basa. Pada konsentrasi DNA 0,8 ng/µl, secara peka R. syzygii subsp. syzygii masih dapat teramplifikasi dengan baik. Primer ini juga hanya dapat mendeteksi R. syzygii subsp. syzygii dan tidak untuk bakteri lain bahkan pada filotipe yang sama.


Keywords


clove; endoglucanase; Ralstonia syzygii subsp. syzygii; specific primer; Sumatera disease

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DOI: https://doi.org/10.22146/jpti.32217

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