Time-course RNA-seq analysis of upland cotton (<i>Gossypium hirsutum</i> L.) responses to Southern root-knot nematode (<i>Meloidogyne incognita</i>) during compatible and incompatible interactions

Abstract

Background: The Southern root-knot nematode (Meloidogyne incognita) poses a substantial threat to cotton (Gossypium hirsutum L.) by causing significant agricultural losses. Host plant resistance is the most plausible approach for minimizing these losses. QTL mapping and early transcriptomic studies have identified candidate genes within the QTL regions on chromosome 11 (qMi-C11) and chromosome 14 (qMi-C14). Although these QTL regions have been fine-mapped and candidate genes identified, expression profiling of Meloidogyne-Gossypium interactions across different stages of infection could further refine the list of candidate genes. This study advances our understanding of the molecular mechanisms underlying the resistance conferred by qMi-C11 and qMi-C14 against Southern root-knot nematode. Results: Using time-course RNA-seq analyses across nematode developmental phases, we uncovered transcriptomic events—both genome-wide and within QTL intervals—underlying defense responses during compatible interactions (with Cocker 201, a susceptible line) and incompatible interactions (with M-120 RNR, a resistant line). Basal defense responses were observed in both compatible and incompatible interactions, with stronger expression in the incompatible interaction. Nematode-responsive genes associated with defense pathways showed distinct dynamics, characterized by repression during compatible interactions and early induction, greater diversity, and heightened upregulation during incompatible interactions. This study uncovers a broad repertoire of disease resistance and putative resistance genes, as well as pathogenesis-related genes, ligands, and receptors, that are differentially expressed in response to nematode parasitism. Mapping of these genes across the cotton genome identified promising candidates, including Gh_A11G3090 (PUB21) and Gh_A11G2836 (RPPL1) within the chromosome 11 QTL region, andGh_D02G0257 (RLP12) and Gh_D02G0259 (RLP12) within the chromosome 14 QTL region. Conclusions: The findings of this study deepen our understanding of host-nematode interactions, identify candidate genes for downstream applications, and contribute to advancements in resistance breeding and sustainable nematode management strategies.