Quinoa is a biennial herbaceous dicotyledonous plant in the Amaranthaceae family, with edible grains and seedlings. Flooding stress is an important factor affecting plant distribution and growth and development, and research on plant flooding tolerance is the key to improving crop flooding tolerance to cope with increasingly severe climate extremes. In order to study the effects of flooding stress on metabolites and genes in quinoa grains, this study flooded quinoa using the nesting method during the filling period, and samples were taken at 7 and 14 days of flooding and 14 days of reoxygenation; metabolomics and transcriptomics measurements were then made. After flooding treatment, the activities of superoxide dismutase and peroxidase in quinoa grains increased. Metabolomics and transcriptomics revealed that flavonoid biosynthesis and linoleic acid metabolism pathways play important roles in quinoa's response to flooding stress. The expression pattern of differentially expressed genes was also analyzed and verified using real-time fluorescence quantitative polymerase chain reaction, which was found to be consistent with the RNA sequencing results, confirming the accuracy of the sequencing results. This study provides a preliminary understanding of the molecular response mechanism of quinoa grain to flooding stress and provides basic data and theoretical support for the subsequent mining of candidate gene functions. © 2025 Society of Chemical Industry.

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