Morphological characterization and RNA sequencing reveal adaptive strategies of <i>Coix lacryma</i> - <i>jobi</i> L. under waterlogging stress during the jointing stage

Flooded plants exhibited significant morphological changes, with key growth parameters decreasing by 14.4-21.8%. A pronounced adaptive response was a 76.6% increase in adventitious root formation. RNA-Seq revealed 207 DEGs (133 upregulated, 74 downregulated). Enrichment analyses indicated these DEGs were predominantly involved in photosynthetic processes, carbohydrate dynamics, and signaling pathways. qRT-PCR confirmed consistent expression patterns for six candidate genes associated with photosynthesis and carbohydrate metabolism. These findings demonstrate that <i>Coix lacryma</i>-<i>jobi</i> L. activates coordinated molecular responses, including photosynthetic efficiency adjustment and metabolic pathway remodeling, to enhance waterlogging tolerance. This work identifies critical genetic components governing waterlogging adaptation, providing molecular markers for developing stress-tolerant cultivars through targeted breeding.