Detection and molecular characteristics of Meloidogyne graminicola on rice in Java Indonesia based on ribosomal DNA gene

Rice root-knot nematode, Meloidogyne graminicola, is widely distributed globally, including in Indonesia. However, information on molecular detection of M. graminicola was limited, especially in Java, as one of the rice-producing areas in Indonesia. This study aimed to detect and investigate the molecular characteristics of M. graminicola in Java, Indonesia. Population samples were collected purposively from three locations in West Java, Central Java, and East Java provinces. Species identification was performed using specific primers Mg-F3/Mg-R2. All samples were sequenced and subjected to phylogenetic analyses, genetic distances, and nucleotide sequence analysis across populations. The results confirmed that all samples from Java provinces were M. graminicola and several isolates were closely related to the isolate from the Philippines. The multiple sequence alignment displayed high single-nucleotide polymorphisms on the first 100 bp, then tended to be identical on the next 200 bp, and varied on the last 78 bp. This research highlighted that the M. graminicola population was detected on samples from the west-to-east region of Java, Indonesia. A rigorous study on the molecular characteristics of M. graminicola in rice grown in Java is crucial because this nematode poses a serious threat to the production of rice, a staple food in Indonesia.