Post-waterlogging recovery and adventitious-root plasticity explain contrasting yield retention of field-grown cotton and soybean under transient waterlogging

Context Transient waterlogging during reproductive growth threatens yield formation in field crops, but final yield loss depends on both flooding-period injury and post-waterlogging recovery. Cotton and soybean may differ in waterlogging tolerance, yet direct comparative evidence under a unified waterlogging regime remains limited, particularly for separating flooding-period damage from post-waterlogging recovery. We hypothesized that waterlogging tolerance is more strongly linked to recovery efficiency after waterlogging relief than to growth suppression during flooding alone. Methods A three-year field experiment evaluated 10-d waterlogging at two reproductive timings, with the complete two-timing comparison conducted in 2024 and 2025. Yield, yield components, biomass dynamics, root function, photosynthetic traits, phytohormones and selected molecular responses were measured. A biphasic growth model was used to separate flooding-induced inhibition from recovery-phase compensation, and integrated damage, recovery, quiescence, escape and compensation indices were constructed. Results Waterlogging reduced yield in both crops, but losses were consistently greater in cotton. Under early waterlogging, cotton yield declined by 40.4%–45.4%, compared with 29.5%–30.3% in soybean; under late waterlogging, the corresponding reductions were 31.7%–35.7% and 20.6%–24.7%, respectively. Yield loss was mainly associated with boll density in cotton and pod density in soybean. Biomass suppression during flooding was broadly similar between crops, whereas recovery differed markedly after waterlogging relief. Soybean entered compensatory growth earlier and showed a stronger relative growth-rate increase, maintained higher root activity and xylem bleeding sap, accumulated less hydrogen peroxide (H₂O₂) and malondialdehyde (MDA), and recovered photosynthesis more rapidly than cotton. Soybean also formed functionally active adventitious roots, which showed higher activity and lower oxidative injury than primary roots. Integrated analysis showed that soybean had a 9.4%–11.0% lower damage index and a 23.0%–24.5% higher recovery index than cotton. Path analysis indicated that quiescence and compensation were associated with yield retention in both crops, whereas soybean gained an additional advantage from adventitious root-mediated escape. Conclusions The higher yield retention of the tested soybean cultivar than the tested cotton cultivar was associated mainly with stronger recovery efficiency after waterlogging relief, rather than with smaller flooding-period growth suppression alone. These findings support a recovery-centered framework for evaluating crop waterlogging tolerance: effective quiescence represents functional conservation during flooding, compensation represents recovery-driven growth reconstruction, and adventitious-root-mediated escape can strengthen the transition from injury buffering to post-stress recovery. Root functional integrity, photosynthetic restoration, compensatory growth and reproductive sink retention should therefore be considered key targets for breeding and agronomic regulation in waterlogging-prone field-crop systems.