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Background Soil salinization is a threat to food security. China is rich in saline land resources for potential and current utilization. The cultivation and promotion of salt-tolerant rice varieties can greatly improve the utilization of this saline land. The super hybrid rice Chaoyouqianhao (CY1000) is one of the most salt-tolerant rice varieties and is widely used, but the molecular mechanism underlying its salt tolerance is not clear. Results In this study, the characteristics of CY1000 and its parents were evaluated in the field and laboratory. The results showed that aboveground parts of CY1000 were barely influenced by salt stress, while the roots were less affected than those of its parents. A comparative transcriptomic strategy was used to analyze the differences in the response to salt stress among the male and female parents of CY1000 at the seedling stage and the model indica rice 93–11. We found that the salt tolerance of CY1000 was mainly inherited from its male parent R900, and its female parent GX24S showed hardly any salt tolerance. To adapt to salt stress, CY1000 and R900 upregulated the expression of genes associated with soluble component synthesis and cell wall synthesis and other related genes and downregulated the expression of most genes related to growth material acquisition and consumption. In CY1000 and R900, the expression of genes encoding some novel key proteins in the ubiquitination pathway was significantly upregulated. After treatment with MG-132, the salt tolerance of CY1000 and R900 was significantly decreased and was almost the same as that of the wild type after salt stress treatment, indicating that ubiquitination played an important role in the salt tolerance mechanism of CY1000. At the same time, we found that some transcription factors were also involved in the salt stress response, with some transcription factors responding only in hybrid CY1000, suggesting that salt tolerance heterosis might be regulated by transcription factors in rice. Conclusion Our results revealed that the ubiquitination pathway is important for salt tolerance in rice, and several novel candidate genes were identified to reveal a novel salt tolerance regulation network. Additionally, our work will help clarify the mechanism of heterosis in rice. Further exploration of the molecular mechanism underlying the salt tolerance of CY1000 can provide a theoretical basis for breeding new salt-tolerant rice varieties.

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Long-term soil salinization easily contributes to soil hardness, soil nutrient imbalance, and soil microbial diversity reduction, resulting in low rice yields in the salinized fields, and microbial remediation is one of the important measures to improve salinized soil. To verify the effect of biofertilizer based on halotolerant microorganisms on promoting rice growth and alleviating saline stress, this study discussed the effects of biofertilizer on soil microbial diversity and community structure and analyzed the correlation between the formation of microbial community structure and soil nutrient factors in the salinized field. The result, in comparison with applying inorganic fertilizer (referred to as CK), showed that notably increased soil available nitrogen, available phosphorus, available potassium, and rice paddy yield (p < 0.05) and significantly decreased soil electrical conductivity (p < 0.05) were achieved via biofertilizer (referred to as G2). Additionally, the application of biofertilizer contributes to the increase in soil microbial diversity and reorganization of microbial community structure, and through the analysis of linear discriminant analysis effect size, a notable difference in relative abundance was found in 13 genera, 6 families, and 3 orders between the control group and experimental groups (p < 0.05), and by linear discriminant analysis, Desulfomonas was further identified as the differentiated indicator. The redundancy analysis showed that available phosphorus and cation exchange capacity were the key environmental factors that affected microbial community structure and composition. Through bacterial functional prediction, increased rhizosphere soil bacterial metabolism, enzyme activity, membrane transport, and other potential functions were achieved by applying biofertilizer. Therefore, the application of biofertilizer could significantly alleviate rice growth stress and increase nutrient supply capacity in saline soil. These findings provide theoretical support for soil microbial improvement technology in the salinized field.