Rice (Oryza sativa L.) is one of the most widely grown crops in the world, and is a staple food for more than half of the global total population. Root-knot nematodes (RKNs), Meloidogyne spp., and especially M. graminicola, seem to be significant rice pests, which makes them the most economically important plant-parasitic nematode in this crop. RKNs develop a feeding site in galls by causing host cells to differentiate into hypertrophied, multinucleate, metabolically active cells known as giant cells. This grazing framework gives the nematode a constant food source, permitting it to develop into a fecund female and complete its life cycle inside the host root. M. graminicola effector proteins involved in nematode parasitism, including pioneer genes, were functionally characterized in earlier studies. Molecular modelling and docking studies were performed on Meloidogyne graminicola protein targets, such as β-1,4-endoglucanase, pectate lyase, phospholipase B-like protein, and G protein-coupled receptor kinase, to understand the binding affinity of Beta-D-Galacturonic Acid, 2,6,10,15,19,23-hexamethyltetracosane, (2S)-2-amino-3-phenylpropanoic acid, and 4-O-Beta-D-Galactopyranosyl-Alpha-D-Glucopyranose against ligand molecules of rice. This study discovered important molecular aspects of plant–nematode interaction and candidate effector proteins that were regulated by M. graminicola-infected rice plants. To the best of our knowledge, this is the first study to describe M. graminicola’s molecular adaptation to host parasitism.

Rice root-knot nematode Meloidogyne graminicola is a destructive plant parasitic nematode that significantly affects rice production worldwide. Endophytic bacteria confer resistance against nematodes through the production of various bioactive molecules. In the present study, the bioactive molecules produced by Bacillus cereus were evaluated against the potential protein targets of M. graminicola, such as Metalloendopeptidase, MgGPP, MgM0237, MgPDI1, MgPDI2, MgPEL1 and Mg-vap1 (venom allergenlike protein) by employing molecular docking techniques. The study revealed that all the bioactive molecules had a significant impact on the protein targets of M. graminicola. Among the 12 biomolecules, Picoxystrobin and 3-Deoxy-d-mannonic acid had a dominant effect on various protein targets through molecular docking approaches, and these biomolecules from B. cereus can be explored as the novel nematostatic molecules against M. graminicola.

The survey results revealed that Meloidogyne incognita was most prevalent in major cultivated regions. By using the morphometric analysis and molecular methods, M. incognita was identified. The ITS rDNA (Internal Transcribed Spacer region specific ribosomal DNA) was used for identification besides posterior cuticular pattern (PCP) of adult females and morphological characters of males and second stage juveniles also used for species level identification.

Understanding the management of the rice root-knot nematode Meloidogyne graminicola is an essential component of rice. The study aimed to investigate the extent to which the nematicidal actions of 2,1,3- benzothiadiazole, fluopyram, fluensulfone and carbofuran against the rice root-knot nematode, M. graminicola could be determined using in vitro, in vivo and in silico studies. Among the tested compounds, fluopyram demonstrated the highest juvenile mortality rate (91.26%) and binding affinity (-8.3 kcal/mol) to the seven selected target proteins of M. graminicola, driven by significant hydrophobic, alkyl and H-bonding interactions. Comparative binding affinities were recorded for fluensulfone (-6.9 kcal/mol), carbofuran (-6.4 kcal/mol), 2,1,3-benzothiadiazole (-5.0 kcal/mol) and untreated control. These findings have significant implications for agricultural practices, particularly in developing integrated pest management (IPM) strategies. The high efficacy of fluopyram, as evidenced by its biochemical ligand-target protein interactions, suggests its potential as a key component in IPM programs. By integrating nematicidal treatments with other control measures such as crop rotation, resistant rice varieties and biological control agents, sustainable management of M. graminicola can be achieved by reducing dependency on chemical pesticides. Furthermore, this study underscores the importance of using molecular insights to design targeted pest management solutions, paving the way for environmentally responsible and economically viable approaches to nematode control in rice cultivation.