The Yangtze River basin is the main producing area of rapeseeds in China, which is wet and rainy all the year round, and the rapeseed-rice rotation system is implemented in the producing area, resulting in frequent waterlogging. To explore the effects of waterlogging at seedling stage on phenotypic traits, physiological characteristics, photosynthesis, relative gene transcriptional levels, and the regulation of exogenous hormone inhibitors on rapeseed damage under waterlogging, a pot experiment was conducted, and the strong waterlogging tolerant line YZ12, medium waterlogging tolerant line YZ45, and weak waterlogging tolerant line YZ59 were used as the experimental materials. The results indicated that flooding stress severely inhibited the growth of rapeseed, and root activity could be used as an indicator to measure the impact of flooding stress on rapeseed growth. The observation of root cell ultrastructure showed that flooding stress led to plasmolysis and organelle fragmentation of rape root cells. The organelle of strong and medium waterlogging resistant rape was less damaged, and it could maintain a more normal cell morphology under flooding stress. The relative transcriptional levels of cytoskeletal genes Bnamicrotubule1.A3, Bnatubulin-α2.C3, Bnatubulin-β7.C6, and Bnalamin-like.A2 in rape roots were significantly decreased under flooding stress, which were 0.2-0.5 times that of the control (CK) samples. The relative expressional levels of BnaPDH.C9, BnaLDH.A1, and BnaADH.A7 associated to anaerobic respiration were significantly increased, which was 3-6 times higher than that of CK, and higher expression levels were observed in medium and strong waterlogging tolerant rapeseed seedlings than in weak waterlogging tolerant line YZ59. During waterlogging, the activities of POD and SOD increased first and then decreased, while the activity of CAT and the content of MDA increased. Among them, the enzyme activities of YZ12 line such as POD, SOD, CAT were relatively high, and the increase of MDA was small. The photosynthetic efficiency and chlorophyll content of rapeseed leaves were seriously affected by flooding stress. The chlorophyll content, photosynthetic rate, stomatal conductance and transpiration rate of rapeseed decreased significantly, and the intercellular CO2 concentration increased significantly, and the change range of the weak waterlogging tolerant line YZ59 was larger than that of the other two lines. Under flooding stress, ET and ABA contents of rapeseed increased significantly. Among the three lines, YZ12 had higher ET content, while YZ59 had higher ABA content. The relative transcriptional levels of ET related genes BnaACO1.C8, BnaERF73.C6 were significantly up-regulated in the strong waterlogging tolerant line YZ12, while the relative transcriptional level of ABA-related gene BnaZEP.A7 was up-regulated in the weak waterlogging tolerant line YZ59. Exogenous application of hormone inhibitors could improve the damage of flooding stress to rapeseed, but the effects of different exogenous hormone inhibitors varied significantly. In conclusion, there were differences in physiological metabolism, photosynthesis, hormone, and gene transcriptional levels in response to flooding stress at seedling stage in B. napus with different waterlogging tolerance. B. napus responsed to flooding stress by regulating the relative transcription levels of genes related to cytoskeleton, anaerobic respiration, hormone metabolism, causing changes in antioxidant enzyme activity, hormone levels, photosynthetic efficiency, root ultrastructure and root vitality.
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