Comparative Transcriptomic Analysis of Soybean Recombinant Inbred Lines Differing at the <i>Rmi1</i> Locus for Resistance to <i>Meloidogyne incognita</i> During Early Stages of Nematode Infection

Root-knot nematodes (<i>Meloidogyne</i> spp.) are a continuing threat to soybean production, with <i>M. incognita</i> being the predominant species. The deployment of <i>M. incognita</i>-resistant soybean cultivars is a primary management strategy, but the underlying molecular mechanisms contributing to resistance remain unknown. A single, additive gene for resistance to <i>M. incognita</i>, <i>Rmi1</i>, was previously identified in soybean cultivar Forrest and associated with the emigration of second-stage juveniles from the roots. To better understand the <i>Rmi1</i>-mediated resistance response, we used Forrest-derived F₅ recombinant inbred lines differing for <i>Rmi1</i> to analyze global changes in gene expression in response to <i>M. incognita</i> infection at 2 and 4 days postinoculation. We identified 1,471 differentially expressed (DE) genes in the compatible interaction and 1,037 DE genes in the incompatible interaction. Forty-five percent of DE genes were DE in both interactions, 42% (856) were unique to the compatible interaction, and 13% (261) were unique to the incompatible interaction. Genes uniquely DE in the incompatible interaction included genes involved in cell wall modification, hormone signaling, endomembrane trafficking, and redox reactions, providing new insights into the resistance mechanism of soybean to root-knot nematodes mediated by <i>Rmi1</i>. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.