Response mechanism of Cynodon dactylon to flooding stress based on integrating metabonomics and transcriptomics analysis

Cynodon dactylon, a perennial herbaceous of Poaceae, possessing unique abilities in flooding tolerance and clonal propagation. However, evidences on molecular response mechanism from field are missing. Here, the differential responses of above-ground (stolon) and below-ground (root) organs of C. dactylon under flooding and non-flooding (CK) conditions were compared at the transcriptional and metabolomic levels. Under flooding stress, significant enrichment of differentially expressed genes (DEGs) related to dehydration responses, including cell water homeostasis and ion transmembrane transport were observed in both roots and stolons. The stolons were more sensitive to flooding, while enrichment in energy metabolism in roots were higher, such as the glycolytic process and glycogen biosynthetic process. The DEGs of photosynthesis in stolons were significantly down-regulated compared to roots. Under flooding stress, oxidative phosphorylation (OXPHOS) is inactivated, and the terminal oxidase of the mitochondrial electron transport chain (mtETC), cytochrome c oxidase (COX), is inhibited. Consequently, the expression of pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) involved in fermentative metabolism is upregulated. The combined analysis indicated that phenylalanine, tyrosine, and tryptophan biosynthetic pathways in roots were significantly enriched in the flooding group. In contrast, there was a significant increase in phenylalanine biosynthesis in stolons, and the metabolite phenol exhibited up-regulated expression. In summary, phenylalanine metabolism and phenylalanine biosynthesis are the major responses to flooding stress, indicating the crucial role of these pathways in the flood tolerance of C. dactylon. These findings provide valuable evidence for understanding plant regulatory mechanisms underlying flooding tolerance.