Transcriptome and physiological analyses reveal that two different response mechanisms mediate rice-barnyardgrass co-cultivation

Understanding the interference mechanisms between rice (Oryza sativa) and barnyardgrass (BYG) is critical for developing sustainable weed management strategies and improving crop performance. In this work, we revealed the physiological, biochemical, and transcriptomic insights into the different levels of exploitative interference exerted by two ecotypes of BYG (Echinochloa crus-galli var. mitis (Pursh) Petermann (ECG) and Echinochloa colona (L.) Link (ECO) on rice. The physiological and biochemical assessments demonstrated notable changes in several indicators, the grain yield, shoot biomass, and plant height showed that rice was subjected to different degrees of stress when growing in co-cultivation with the two Echinochloa species. This external stress is also manifested in a decrease in the number of rice roots, root length, and leaf photosynthetic rate. The altered levels of antioxidant enzymes (CAT, POD, SOD) and malondialdehyde (MDA) indicate rice stress adaptation under the two different Echinochloa species, which implies a compensatory strategy to enhance belowground competitiveness. Comparative transcriptome profiling of rice roots co-cultivated with Echinochloa species revealed significant enrichment in phenylpropanoid biosynthesis and plant hormone signal transduction pathways. Concurrently, gene changes in endogenous levels of hormones (ABA, JA, and ethylene) further supported their central roles in mediating plant-plant interactions. Collectively, these results suggest that phenylpropanoids and plant hormone signal transduction orchestrate key transcriptional and biochemical responses in rice that facilitate a form of beneficial coexistence with Echinochloa spp. This study provides novel insights into rice-weed interactions, with implications for breeding rice varieties with improved competitive or cooperative traits and for developing ecologically based weed management strategies.