Genetic Diversity of Leifsonia xyli Subsp. xyli Causing Ratoon Stunting Diseases of Sugarcane in Indonesia Using Intergenic Spacer Region Sequence Analysis

Leifsonia xyli subsp xyli (Lxx) is the cause of Ratoon Stunting Disease (RSD) on sugarcane and it considers as a quarantine pest in certain regions of Indonesia. RSD is a systemic disease that causes severe cane yield loss. Information about genetic diversity of this bacterial pathogen in Indonesia is limited. While global trading of sugar cane seed may facilitate the spread of Lxx. This research aimed to get information of new distribution area and investigate genetic diversity of Lxx, in several location in Indonesia, including Lampung, Gorontalo, Dompu, Central Java and East Java. A total of 27 cane stalk samples were collected from these areas using a purposive sampling method. The presence and diversity of Lxx were determined using a conventional Polymerase Chain Reaction (PCR) with Cxx1F and Cxx1R primers from the Intergenic Spacer (IGS) region of the ribosomal RNA gene sequence. The findings revealed that only 12 of the 27 samples tested Lxx-positive. Using the Unweighted Pair Group Method with Arithmetic (UPGMA) phylogenetic analysis, it was shown that Lxx from all 12 samples had similar genetic (99-100%) homology with Lxx from China Leifsonia sp. strain HNEa1, except TLH4ST26, which had the highest homology with Lxx found in East Java. The result also suggested that the distribution of the disease was because the source of the sugarcane seeds originated from East Java, which can spread and infect the sugarcane seeds throughout Indonesia.