Number of Copies of Endogenous Rice Tungro Bacilliform (RTBV) From Local Rice in Indonesia

The focus of this study was to determine the position and the number of copies of RTBV endogenous fragments integrated into the genomes of local rice varieties. Local rice test consisted of Utri Merah, Pulut Sawijan, Srogel Abang, Bekongan, Blumbungan, and Tachung native 1 (TN1). The analysis showed that the RTBV genome was integrated into the local rice genome on the twelve chromosomes and at all loci. RTBV genome interration was demonstrated through the results of Polymerase Chain Reaction (PCR) analysis with 1200 base pairs (bp) genome length and blast protein analysis results with an alignment of 66.9 % in P194 as Open Reading Frame (ORF) 3 RTBV, 93 % in ORFy, and other various physical genome structures. The number of copies of RTBV endogenous fragments test varieties was very fluctuating and related to gene mutations and protein motifs. All test varieties had gene mutations, but in the Utri Merah, Pulut Sawit, Bekongan and Srogen Abang varieties which had a lower number of fragment copies in compared to the Blumbungan variety and TN1 were able to produce expressions of ile rich protein patterned genes that play a role in plant resistance. In contrast, Blumbungan and TN1 varieties despite having a high number of copies of the endogenous fragment of RTBV, gene expression has no protein ile-rich motifs