Physiological, biochemical, and transcriptomic responses to waterlogging stress in Panicum bisulcatum, an emerging weed in rice fields.

Background: , an annual grass weed of the Panicum genus, is typically found in arid land crop fields, has been observed invaded and become a predominant troublesome weed in rice fields of China in recent years. This study aimed to explore the effect of waterlogging on the control of and to elucidate its physiological, biochemical, and molecular response mechanisms under waterlogging stress.

Results: The results revealed that different water depths showed varied impact on the growth of seedlings. A 2 cm water depth had no significant effect on growth, while a 4 cm water depth completely inhibited plant height and aboveground biomass accumulation. Under waterlogging stress, the activities of key anaerobic respiration enzymes (alcohol dehydrogenase [ADH], pyruvate decarboxylase [PDC], and lactate dehydrogenase [LDH]), malondialdehyde (MDA) content, and antioxidant enzyme activities (superoxide dismutase [SOD], peroxidase [POD], and catalase [CAT]) were significantly increased. Comparative transcriptomic analysis at two waterlogging time points identified 11,986 and 1295 differentially expressed genes (DEGs) at 1 day and 7 days, respectively. These DEGs were significantly enriched in signal transduction, carbohydrate metabolism, and translation pathways. Notably, 18 genes associated with anaerobic respiration, ethylene biosynthesis, and gibberellin synthesis were upregulated after one day of waterlogging stress. Following the identification of as the most stable reference gene for normalization, quantitative real-time PCR analysis revealed significant upregulation of key pathway-related genes in under waterlogging stress, including , , , , , and . These findings are consistent with the enhanced waterlogging tolerance observed following exogenous gibberellin treatment.

Conclusion: This study provides valuable information for unrevealing the adaptive mechanisms of under waterlogging conditions and helps developing strategies for the management of in rice fields.

Supplementary Information: The online version contains supplementary material available at 10.1186/s12870-025-06874-3.