Penyakit Busuk Bulir Padi di Kabupaten Purworejo dan Simulasi Analisis Nukleotida Gen 16S rRNA Bakteri Burkholderia glumae

Abstract

Penyakit busuk bulir padi yang disebabkan oleh bakteri Burkholderia glumae adalah penyakit yang baru muncul di banyak negara, termasuk Indonesia. Penyakit ini juga dilaporkan terjadi di beberapa daerah di Jawa Tengah. Saat ini, diagnosis penyakit yang tepat sering memanfaatkan teknik molekuler, yaitu PCR dan sikuensing DNA.Tujuan dari penelitian ini adalah mengetahui hubungan antara teknik budidaya padi terhadap intensitas penyakit bulir padi di Kabupaten Purworejo dan simulasi analisis nukleotida gen 16S rRNA patogennya. Penelitian ini dilakukan melalui pengumpulan data sekunder agro-klimat dan laporan insidensi penyakit, pengamatan lapangan teknik budidaya, perkembangan penyakit selama fase generatif padi di tiga kecamatan di Purworejo. Simulasi analisis nukleotida gen 16S rRNA B. glumae koleksi Laboratorium Bakteriologi Tumbuhan IPB dilakukan menggunakan piranti lunak komputer dan GenBank. Tingkat penyakit busuk bulir padi berupa variabel insidensi dan severitas penyakit, serta AUDPC tampak lebih tinggi pada pertanaman yang menggunakan teknik budidaya lebih konvensional di kecamatan Ngombol dan Purwodadi daripada yang menggunakan PGPR sebagai agen biokontrol di Banyuurip. Tingkat penyakit juga lebih tinggi di musim tanam dengan kelembaban dan curah hujan yang lebih tinggi. Hasil dari simulasi analisis urutan nukleotida gen 16S rRNA dikonfirmasi bahwa patogen penyakit bulir padi adalah Burkholderia glumae melalui program BLAST di situs web GenBank dengan modus proporsi homologi di atas 97.5% dengan beberapa isolat dari negara lain. Konstruksi matriks identitas dengan program BioEdit dan pohon filogenetik dengan Mega X menunjukkan hubungan yang lebih dekat antara isolat B. glumae dan hubungan yang semakin jauh dengan spesies pembanding dari genera yang sama seperti B. gladioli dan B. Cepacia serta genera lain seperti Ralstonia dan Xanthomonas.

Bacterial grain rot disease of rice caused by Burkholderia glumae is a newly emerging disease in many countries, including Indonesia. The disease has also been reported to occur in some areas of Central Java. Currently, the precise diagnosis of disease is often assisted by the use of molecular techniques, such as PCR and DNA sequencing. This study aims to determine the relation between different cultivation techniques used by farmers with disease intensity of rice grown in Purworejo Regency and to simulate analysis of the nucleotide sequence of the bacterial 16S rRNA gene. The research was conducted to collect agro climatic secondary data and reports of disease occurence, field observations on cultivation techniques, development of diseases during the generative phase of rice in three sub-districts in Purworejo. Nucleotide analysis with computer software and GenBank were carried out on the nucleotide sequence of the 16S rRNA gene of the bacterium B. glumae belonging to the Plant Bacteriology Laboratory of IPB. The level of rice grain rot disease in the observed variables of disease incidence and severity and their AUDPCs appeared higher in Ngombol and Purwodadi sub-districts with more conventional cultivation techniques than in Banyuurip subdistricts those using PGPR as biocontrol agents. Disease rates are also higher in the growing season, with higher humidity and rainfall. The simulation results from the analysis of the 16S rRNA gene nucleotide sequence showed that the causative agent was confirmed as Burkholderia glumae through the BLAST program on the GenBank website with modus of homology proportions above 97.5% with several isolates from other countries. Identity matrix construction with BioEdit program and phylogenetic tree with Mega X showed closer relationships between B. glumae isolates and more distant relationships with comparison species from the same genera such as B. gladioli and B. cepacia and from other genera such as Ralstonia and Xanthomonas.