Mechanistic elucidation of cyanamide's selective herbicidal activity via integrated transcriptome-metabolome analysis: Implications for cleaner alfalfa production.

Redroot pigweed (Amaranthus retroflexus L.) is one of the common weeds in alfalfa (Medicago sativa L.) field, compromising yield and forage quality. Cyanamide (CA), a phytogenic herbicide, effectively suppresses redroot pigweed without harming alfalfa, yet its molecular mechanisms remain elusive. This study employed an integrated transcriptomic and metabolomic approach to analyze leaves of redroot pigweed and alfalfa treated with and without CA spraying. This multi-angled investigation elucidates the mechanisms underlying CA's effects on the growth of both plant species. Integrated transcriptomic and metabolomic analyses revealed that CA upregulates genes linked to indole-3-acetic acid (IAA) biosynthesis (MPK9, MPK3, MPK6, WRKY33) and key enzymes (tryptophan aminotransferase, acetaldehyde amine dehydratase, indoleacetic acid dehydrogenase) in alfalfa, enhancing stress tolerance. Conversely, CA downregulates genes (Cluster-14830.0, Cluster-17212.0, Cluster-21179.2, Cluster-26728.0) and enzymes (branched-chain amino acid aminotransferase, acetolactate synthase, dihydroxy-acid dehydratase) in redroot pigweed, disrupting valine, leucine, and isoleucine biosynthesis and inducing leaf wilting. These findings elucidate CA's dual role in alfalfa defense and weed suppression, supporting its use as a sustainable bioherbicide.