Multi-Stage Transcriptomics Reveals TF- and lncRNA-Mediated Regulatory Networks Governing Glyphosate Resistance in Cyperus rotundus

Here, we performed multi-stage RNA sequencing of tubers from glyphosate-resistant and -susceptible populations across three developmental stages to investigate the transcriptional dynamics underlying resistance. Differential expression analysis revealed extensive stage-specific transcriptional reprogramming, with the strongest divergence at the III developmental stage.

Integrating constitutive and stage-dependent expression patterns identified 34 high-confidence candidate resistance-associated genes. Co-expression and regulatory network analyses uncovered coordinated transcriptional modules involving WRKY, NAC, ERF, MYB, bHLH, and ARF transcription factors together with multiple long non-coding RNAs. Notably, all allelic copies of <i>ABCC8</i> were consistently up-regulated in glyphosate-resistant plants, validated by RT-qPCR, and occupied a central position in the resistance regulatory network, suggesting multilayered regulation of detoxification.