Molecular identification of bacteria causing grain rot disease on rice

Abstract

Bacterial grain rot disease on rice plantation is a new disease in Indonesia. The disease become a big threat for formers in Indonesia because it causes high losses and no effective means of control has yet been found. This study was aimed to identify the causal agent of grain rot disease by PCR technique using specific B. glumae primers (1418S and 1418A) in 17 bacterial isolates obtained from several regions and rice varieties. Stages of the used method include extraction and amplification of DNA and continued with secuencing. The secencing result were processed using the BLAST program and compared with NCBI data for phylogenetic analysis. All isolates tested were morphological and physiological testing before. The amplification result showed that all 17 isolates tested produced DNA band in the size of ± 571 bp. These results indicated that all test isolates were classified as B.glumae. 4 of the isolates that had their DNA bases sequenced were then confirmed in the BLAST program from NCBI with results that showed that B.glumae isolates were found to have values homology 98-99% with Burkholderia glumae LMG 2196 = ATCC 33617 in Genebank.