| dc.description.abstract | Root-knot nematodes (RKNs), Meloidogyne spp., are important plant pathogens that cause significant damage to rice crops in many countries. These cosmopolitant nematodes are distributed worldwide and have a broad host range, including rice, one of Indonesia’s major staple food crops. Several RKN species are known to infect rice, including Meloidogyne graminicola, M. incognita, M. javanica, and M. arenaria. Among these species, M. graminicola is considered the most prevalent and economically important species affecting rice production in various countries. This species has been reported to cause yield losses of up to 87%. According to the Decree of the Head of the Indonesian Quarantine Agency No. 571 of 2025, M. graminicola is classified as a Quarantine Plant Pest A2, indicating that its distribution in Indonesia remains limited to certain areas and has not yet become widespread.
Cilacap Regency is one of the major rice-producing areas in Central Java Province and plays a strategic role in supporting regional food security. Its geographical location, directly bordering West Java Province, makes this regency an important area for the production and distribution of rice commodity between regions. This condition highlights the need for an effective crop health monitoring system capable of detecting production constraints, including Quarantine Plant Pests (QPPs), rapidly and accurately. Root-knot nematodes are often difficult to detect during the early stages of infection because the symptoms they induce are generally nonspecific and may resemble those caused by abiotic stresses or other plant pests. Therefore, accurate detection and identification of RKNs are essential for developing effective and sustainable management strategies. However, scientific information on the occurrence, detection, and identification of RKNs in rice fields in Cilacap Regency remains very limited, and no study has specifically investigated their occurrence and species composition in this region. Species of RKNs exhibit highly similar morphological characteristics, making species-level identification based solely on morphology challenging. Furthermore, multiple Meloidogyne species may occur simultaneously within the roots of a single host plant. Morphological identification is generally performed by examining the perineal pattern of adult females, whereas molecular identification employs Polymerase Chain Reaction (PCR)-based approaches targeting DNA or RNA to improve the accuracy and reliability of species identification.
This study aimed to detect and identify RKNs and other plant-parasitic nematodes associated with lowland rice in Cilacap Regency, Central Java, Indonesia. The study also aimed to determine the dominant species and assess their distribution across the study sites. Species identity was confirmed based on morphological and morphometric characteristics, as well as molecular analysis using the species-specific Mg-F3/Mg-R2 primers. In addition, the genetic relationships of M. graminicola isolates from Cilacap Regency were analyzed in comparison with isolates from other regions or countries. The results of this study are expected to provide information on the identity and distribution of RKN species in rice-growing areas of Cilacap Regency, Central Java. This information
may serve as a reference for updating the list of QPPs and their distribution records, as well as supporting the development of appropriate management strategies and measures to prevent further spread.
Root samples were collected from rice plants at five districts in Cilacap Regency, Central Java, Indonesia. The sampling sites included Matenggeng and Datar villages in Dayeuhluhur District; Wanareja Village in Wanareja District; Jenang and Pahonjean villages in Majenang District; Cimanggu Village in Cimanggu District; and Tritih Lor Village in Jeruklegi District. The sampling locations were selected based on a preliminary survey that indicated the presence of root-knot nematode (Meloidogyne spp.) infestation in rice plants. Five rice plants were selected as samples at each observation site. Root samples were collected from rice plants aged 30–45 days after transplanting (DAT), when symptoms of root-knot nematode infestation become clearly visible. Samples were collected using purposive sampling, in which rice plants were selected based on characteristic symptoms of root-knot nematode infestation, including stunted growth, reduced plant size, yellowing or wilting leaves, and the formation of root galls. Interviews with farmers were conducted to obtain supporting information on the rice varieties cultivated, land management and irrigation history, and cultivation practices implemented at each study site.
Morphological characterization was performed across all life stages (RKNs), including eggs, juveniles, adult females, and adult males obtained from rice root tissues. The morphological and morphometric parameters evaluated included body length, stylet length, body width, tail length, and perineal pattern morphology of adult females. Morphological identification was performed by cutting the perineal pattern of adult females and preparing semi-permanent slides using FAA as the mounting medium. The perineal patterns were examined under a compound microscope and identified using taxonomic identification keys. Due to the high morphological similarity among Meloidogyne species, morphological characteristics alone may not provide sufficient resolution for accurate species-level identification. Therefore, molecular identification was performed using the species-specific primer pair Mg-F3/Mg-R2 to confirm the morphological identification. The PCR products were subsequently sequenced and subjected to phylogenetic analysis to confirm the identity of M. graminicola and determine its phylogenetic relationship with previously reported M. graminicola isolates.
The identification results showed that M. graminicola was detected at all surveyed locations, namely Dayeuhluhur, Wanareja, Majenang, Cimanggu, and Jeruklegi Districts. These findings indicate that M. graminicola has a wide distribution and is the dominant species in rice-growing areas within the surveyed region. In addition to M. graminicola, M. javanica was detected in Majenang District, whereas M. arenaria was detected in Jeruklegi District. The occurrence of M. javanica and M. arenaria in relatively dry fields suggests that environmental conditions may influence the species composition of Meloidogyne. The presence of weeds Cyperus rotundus and Echinochloa colona in the fields may also support the persistence of nematode populations by serving as alternative hosts. In contrast, the detection of M. graminicola in flooded fields in Wanareja and Cimanggu indicates its ability to adapt to rice-growing environments with high water availability. Differences in rice varieties did not show a clear pattern in relation to the occurrence of nematode species.
Species M. graminicola was detected in all rice varieties examined, suggesting that the varieties cultivated in the surveyed areas may have limited resistance to this species. Furthermore, M. graminicola from Majenang was molecularly confirmed using the species-specific Mg-F3/Mg-R2 primers, which produced an approximately 369-bp DNA fragment. Sequence analysis showed 100% homology between the Majenang isolate and a previously reported M. graminicola isolate from China, while phylogenetic analysis indicated a very close genetic relationship between the isolates. Morphological characteristics consistent with M. graminicola were also observed in the roots of the weeds Cyperus rotundus and Echinochloa colona, suggesting that these weeds may serve as alternative hosts and contribute to the persistence of nematode populations in rice fields. In addition, Hirschmaniella oryzae was detected | |
