Revealing the soybean seed waterlogging tolerance molecular mechanism through integrated transcriptome and proteome analysis

Waterlogging stress is one of the factors restricting soybean agricultural production. However, there are few studies on waterlogging tolerance in soybean seeds at germination stage. In this study, the physiological responses of soybean seeds under waterlogging stress at different durations (0, 12, 24, 36, 48 hours) were investigated. In the sensitive material (SX19-787), germination rate, root length, seedling length, fresh weight and vigor index were significantly lower than the control after 36 h waterlogging treatment, while the tolerant material (CN-5) still maintained high germination vigor. To elucidate the waterlogging tolerance mechanism, proteome, transcriptome sequencing and physiological–biochemical tests were employed. A total of 32 DEPs and 2281 DEGs were specifically expressed in CN-5. Seven DEPs and 11,067 DEGs were co-expressed in CN-5 and SX19-787. Combined proteome and transcriptome sequencing analysis showed that GRP-2, PER53, and PME31 proteins which regulate cell wall metabolism and RPL protein were hub proteins, DHAR3, GSTF9, CAMTA5, ACO3 and SDH were hub genes, indicating that they played a key role in waterlogging tolerance in soybean seeds at germination stage. The tolerant material (CN-5) showed higher PME and GST enzyme activity and lower PDC enzyme activity. The adaptive strategies for waterlogging tolerance in soybean seeds at germination stage may be: enhancing cell wall homeostasis, enhancing the tricarboxylic acid cycle and reducing ethanol fermentation to provide energy, enhancing antioxidant activity, and regulating ribosome metabolism. Overall, these findings provide in-depth insights into the waterlogging tolerance in soybean seeds at germination stage, and provide a theoretical basis for the breeding and identification of waterlogging-tolerant soybean varieties. • Transcriptome, proteome sequencing and physiological-biochemical methods were used to reveal the regulation mechanism of waterlogging tolerance in soybean seeds at germination. • The waterlogging tolerance in soybean seeds at germination stage is a complex process. • DHAR3, GSTF9, CAMTA5, ACO3, and SDH genes/ proteins may be the key genes/proteins regulating soybean seed waterlogging tolerance.n stage.