Transcriptome and Co-Expression Network Analyses of Resistant and Susceptible Rice Cultivars in Response to Meloidogyne graminicola

<i>Meloidogyne graminicola</i> represents a significant pathogen of rice, with considerable variability in nematode resistance observed across rice germplasms. However, the gene regulatory networks and molecular mechanisms underlying the differential responses of resistant and susceptible cultivars to <i>M. graminicola</i> infection remain poorly understood. To identify potential sources of resistance, 122 indica cultivars were screened under controlled conditions based on gall formation in infected roots. Notably, Indian indica accession 685 exhibited exceptional resistance, characterized by complete suppression of nematode development within root tissue. To investigate the molecular responses of rice cultivars to <i>M. graminicola</i> infection, RNA sequencing was conducted to analyze gene expression profiles at 5 days post-inoculation (dpi) in resistant cultivar 685, moderately susceptible cultivar 1008, and susceptible cultivar 9311. Subsequent differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) identified key biological pathways, including sugar metabolism, autophagic degradation, and phytohormone signal transduction. Additionally, candidate hub genes were identified and validated through RT-qPCR. This study offers new insights into rice-<i>M. graminicola</i> interactions, highlighting critical molecular factors involved in resistance and susceptibility in host plants.