Shuyan Li, Qiling Yan, Jianhua Tong, Yong Li, Lianyang Bai, Qiong Peng
Allelopathic rice is increasingly recognised as a promising strategy for sustainable weed management. Resistance to the herbicide quinclorac is widespread in barnyardgrass, but it remains unclear whether allelopathic rice exerts the same defence against herbicide-susceptible and -resistant barnyardgrass. We conducted integrated transcriptomic, metabolomic, and metagenomic analyses to investigate the responses of allelopathic rice to quinclorac-susceptible (S) and -resistant barnyardgrass (R) lines. Distinct chemical strategies were identified in allelopathic rice: Terpenoids (e.g., carnosic acid, phytocassane B, and ipomeatetrahydrofuran) mainly suppressed S, while amino acids (e.g., pipecolic acid, L-glutamate, and L-histidine) were key against R. Correspondingly, terpenoid biosynthesis and nitrogen metabolism were the most enriched pathways under S and R stress, respectively. Additionally, terpenoid accumulation correlated positively with salicylic acid (SA) and jasmonic acid (JA) concentrations in roots under S. Both terpenoids and amino acids formed the stable ecological networks with rhizosheath microbiota. Functional metagenomic analysis further showed that ABC transporter and quorum sensing pathways were upregulated under S, whereas nitrogen fixation predominated under R. Notably, amino acids formed a nitrogen-related ecological network with nitrogen-metabolising microbiota, contributing to improved plant-available soil nitrogen and total nitrogen content in rice plants. Bioassays showed that exogenous pipecolic acid (≥ 40 μM) and L-histidine (80 μM) inhibited barnyardgrass seedling growth without affecting allelopathic and non-allelopathic rice. These findings demonstrate that allelopathic rice employs divergent chemical-microbial defence strategies against S and R barnyardgrass, highlight the dual role of amino acids, and provide a basis for precision weed management, particularly for herbicide-resistant weeds in paddy fields.