Transcriptomic profiling reveals Agave Lechuguilla extract as a multi-target pre-emergent bioherbicide candidate against Chenopodium album

The widespread application of synthetic herbicides, particularly glyphosate, has resulted in the emergence of resistant weed species, prompting the need for new, eco-friendly alternatives, such as bioherbicides. This study explores the bioherbicidal potential of an Agave lechuguilla (AGE) extract on the seeds of the resilient weed Chenopodium album and compares its effects to those of glyphosate. Through mRNA-seq-guided transcriptomic analysis, over 1.03 billion quality reads were generated, and 6,240 differentially expressed genes (DEGs) were identified across all comparisons. Specifically, the AGE treatment induced 3,246 DEGs, while glyphosate affected 5,234 genes. AGE treatments significantly reduced germination rates and triggered transcriptional changes linked to oxidative stress, hormonal imbalance, and drought stress responses. This study provides transcriptome-level evidence of differential stress modulation and developmental gene expression in Chenopodium album seeds, highlighting the distinct biochemical impacts of a plant-derived vs. synthetic herbicide. Protein-protein interaction networks revealed that AGE-modulated 15 hub genes were primarily associated with energy production and stress responses, while in glyphosate, the focus was on developmental processes. Validation of 10 selected key DEGs using RT-qPCR confirmed the transcriptomic findings and underscored the multi-target action of AGE. The findings highlight the potential of AGE as a pre-emergence bioherbicide, suggesting a sustainable alternative to chemical herbicides by utilizing its multi-target mode of action. This research enhances the understanding of the action mechanisms of plant-based herbicides. It may contribute to integrating these alternatives into weed management strategies for sustainable and regenerative agriculture.