Recovery response of soybean to waterlogging during the flowering and early-seed filling stages

Waterlogging (WL) is one of the significant abiotic stresses limiting global crop productivity. In the United States, WL is increasingly becoming problematic in major crop-growing regions due to high rainfall and poor soil drainage. Previous studies examined soybean (Glycine max (L) Merr.) tolerance to WL during early growth stages. However, WL during the reproductive phase can lead to substantial yield reductions due to a cascade of negative physiological responses triggered by hypoxia. Although this is a critical issue, research on the genetic differences in tolerance and recovery of soybeans to WL remains scarce. At full bloom (R2), 17 genotypes were exposed to WL (3–4 cm water depth) for 14 days and allowed to recover. WL caused a 38% reduction in photosynthetic rates (A), driven by a > 35% decline in both stomatal conductance (gs) and transpiration (E), and a 42% reduction in chlorophyll content. Quantum efficiency of photosystem II decreased by 35%, while flavonol levels increased as a protective response. Although gas exchange traits recovered 14 days after WL, chlorophyll and assimilation remained suppressed. During recovery, leaf temperature was positively correlated with seed yield, whereas sustained high flavonol levels were associated with yield penalties. Seed yield decreased by 34%, and seed quality was compromised. Spectral signatures in the shortwave infrared (SWIR) region effectively differentiated the recovery responses. Genotypes S49-F5X, 4795XS, and P46A86X were identified as promising candidates with greater tolerance and recovery under WL. These findings demonstrate the critical importance of recovery traits in enhancing resilience to WL in soybean.