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

Authors: KHANAL, SAMEER - University Of Georgia; KUMAR, PAWAN - Bayer Cropscience; DA SILVA, MYCHELE - Virginia Tech; SINGH, RIPPY - University Of Georgia; SUASUNNA, NELSON - Embrapa; NICHOLS, ROBERT - Cotton, Inc; Davis, Richard; CHEE, PENG - University Of Georgia

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/10/2025
Publication Date: 2/24/2025
Citation: Khanal, S., Kumar, P., Da Silva, M., Singh, R., Suasunna, N., Nichols, R.L., Davis, R.F., Chee, P.W. 2025. Time-course RNA-seq analysis of upland cotton (Gossypium hirsutum L.) responses to southern root-knot nematode (Meloidogyne incognita) during compatible and incompatible interactions. BMC Genomics. 26, 183. https://doi.org/10.1186/s12864-025-11339-w.
DOI: https://doi.org/10.1186/s12864-025-11339-w

Interpretive Summary: The southern root-knot nematode causes significant yield losses in cotton. This study investigates the molecular basis of resistance that is conferred by two sections of DNA (quantitative trait loci, or QTLs) against this nematode. By using advanced molecular techniques at multiple times during nematode development, we uncover genetic activity within the two QTLs during nematode infection and development, which sheds light on plant defense responses during compatible (nematode susceptible) and incompatible (nematode resistant) interactions. Plant defense responses were observed in both compatible and incompatible interactions, with a stronger expression in the resistant genotype. Nematode-responsive genes associated with plant defense pathways displayed distinct patterns: they were repressed during compatible interactions, whereas they exhibited earlier gene activity, greater diversity, and heightened activity during incompatible interactions. The mapping of these genes across the cotton genome identifies specific genes as potential candidates to be root-knot nematode resistance genes. These findings expand our understanding of host-nematode interactions and contribute to advancements in resistance breeding and sustainable nematode management strategies.

Technical Abstract: The southern root-knot nematode (Meloidogyne incognita) causes significant yield losses in cotton (Gossypium hirsutum L.). This study investigates the molecular basis of resistance conferred by the qMi-C11 and qMi-C14 quantitative trait loci (QTLs) against this nematode. Through time-course RNA-seq analyses across nematode developmental phases, we uncover the intricate transcriptomic events within QTL intervals, shedding light on defense responses during compatible (Cocker 201, a susceptible line) and incompatible (M-120 RNR, a resistant line) interactions. Basal defense responses were observed in both compatible and incompatible interactions, with a stronger manifestation in the resistant genotype. Nematode-responsive genes associated with defense pathways displayed distinct dynamics, being repressed during compatible interactions while exhibiting early induction, greater diversity, and heightened up-regulation during incompatible interactions. This study reveals an extensive repertoire of disease resistance and putative resistance genes, along with pathogenesis-related genes, ligands, and receptors, all differentially expressed in response to nematode parasitism. The mapping of these genes across the cotton genome identifies potential candidates, including Gh_A11G3090 (PUB21) and Gh_A11G2836 (RPPL1) in the chromosome 11 QTL region, as well as Gh_D02G0259 (RLP12) in the chromosome 14 QTL region. These findings expand our understanding of host-nematode interactions and contribute to advancements in resistance breeding and sustainable nematode management strategies.