Abstract: 【Objective】The purpose of the study was to investigate the salt tolerance of salt-tolerant rice Changmaogu at seedling stage and to analyze its whole genome sequencing data,in order to clarify the salt-tolerant physiological mechanism of Changmaogu and to provide reference for the excavation of high-quality salt-tolerant rice varieties and the improvement of saline-alkali land.【Method】Pokkali (salt-tolerant control),IR29 (salt-sensitive control) and the prescreened salt-tolerant rice Changmaogu were selected as the research objects.Five salt concentrations (0,80,100,120and 150 mmol/L) were set as treatments.At seedling stage,9 phenotypic indexes and 13 physiological indexes of three rice materials were observed,and the salt-tolerant physiological mechanism of Changmaogu was investigated based on whole genome sequencing data.【Result】Under salt stress,the phenotypic indexes of Changmaogu were least affected by the change of salt concentration.The activity of antioxidant enzymes was stronger,the content of other active substances and osmotic regulatory substances was higher,the damage of cell membrane caused by salt stress was smaller,and it had relatively good tolerance to salt stress.Correlation analysis results showed that the biomass accumulation of Changmaogu seedlings was extremely significantly positively correlated with seedling height,root length,number of root tips,root surface area and root volume (P<0.01,the same below),and extremely significantly negatively correlated with the con-tents of malonaldehyde(MDA) and hydrogen peroxide(H₂O₂).And the six physiological indexes of the activities of superoxide dismutase(SOD),peroxidase(POD),catalase(CAT),ascorbate peroxidase(APX) and the contents of soluble pro-tein and glutathione(GSH) were extremely significantly positively correlated with each other.By comparing the protein sequences of 30 known salt-tolerant genes in rice with those of Changmaogu,it was found that the similarity and homology of 28 salt-tolerance genes in Changmaogu reached 98%or above,while the similarity of OsP5CS and OsBADH1genes were 96%and 90%respectively.For OsP5CS gene,Changmaogu contained 30 amino acids more than the reference protein sequence.For OsBADH1 gene,Changmaogu was 17 amino acids less than the reference protein sequence,and there were four amino acid sites of difference at the same time,suggesting that the differences might be related to salt tolerance.【Conclusion】Changmaogu has excellent salt tolerance under salt stress,and the protein sequences of two salttolerant genes are different from those of the reference genes.