Genetic Diversity of Meloidogyne graminicola on Rice in Java Indonesia Based on Ribosomal DNA Gene

Abstract Rice root-knot nematode, Meloidogyne graminicola is widely distributed globally, including in Indonesia, where it may influence genetic diversity among local populations. Understanding this genetic diversity is essential for developing effective management strategies for this nematode. This study aimed to investigate the genetic diversity of M. graminicola in Java, Indonesia. Population samples were collected from West Java, Central Java, and East Java. Species identification was performed using specific primers Mg-F3/Mg-R2. All samples were sequenced and analysed for phylogenetic analyses, genetic distances, haploid diversity, and population structure. The results confirmed that all samples from Java were M. graminicola and were closely related an isolate from the Philippines. The haploid diversity (Hd) of the M. graminicola population in Java was high (Hd = 1) and the nucleotide diversity (π = 0.06357). The Fst index indicated that there was no significant genetic difference among populations in Java, categorizing the overall genetic diversity as low (Fst = -0.08370). The haplotype network analysis further revealed that the Java populations did not form a single haplogroup, suggesting that each isolate in Java possessed a unique haplotype. This research highlighted that while M. graminicola populations in Java display high genetic diversity within individual population, this could potentially impact the virulence levels of these nematodes. The insights on genetic diversity of M. graminicola in Java could inform better management practices for controlling this pest.