Objective The purpose of this research was to evaluate differences in seed germination characteristics, morphological indexes, and root cell structure in ‘Huaduo1’ under different concentrations of NaCl and to evaluate the gene expression differences of salt stress related genes in ‘Huaduo1’.

Method Using ‘Huaduo1’ as the research material, the differences in seed germination time, germination potential, germination rate, and germination index under various concentrations of NaCl (0, 50, 100, 150, 200, and 250 mmol/L) were analyzed. The differences in total root number, seedling length, root length, seedling fresh weight, water content, and root-to-head ratio of ‘Huaduo1’ at seedling forming stage under various concentrations of NaCl were summarized and compared. Root tip cell morphology of ‘Huaduo1’ was observed by the WE-CLSM and semi-thin section analysis. Genomic resequencing, bioinformatics analysis, and qRT-PCR analysis were conducted to analyze and quantify the expression of the salt stress genes in ‘Huaduo1’ related to its parents.

Result The seed germination rate and germination index of ‘Huaduo1’ decreased with increased NaCl concentration, while the relative salt damage rate and average germination time increased. ‘Huaduo1’ showed a strong salt tolerance with the relative salt damage rate reached 35% under 250 mmol/L NaCl treatment. After 8 to 20 days of NaCl treatment, the total root number of ‘Huaduo1’ seedlings decreased with increased NaCl concentration. Meanwhile, the seedling length, root length, fresh weight and water content of seedlings under NaCl stress showed a decreasing trend, and the root-to-head ratio showed an increasing trend. NaCl stress inhibited the growth of the ‘Huaduo1’ seedlings, resulting in smaller cell volume, cell shrinkage, and loose cell arrangement in the root tip elongation zone. Moreover, the cells of the epidermis and outer cortex layer in the root tip elongation zone were thickened, the number of cell layers in the mesocortex increased, the diameter of the middle column decreased, and the number of xylem ductal differentiation increased under salt stress. Totally 85 salt stress-related genes of ‘Huaduo1’ showed variance in the CDS region compared with its two parents, including 53 salt sensitivity related genes and 32 salt stress tolerance related genes. The qRT-PCR results showed that the expressions of four salt sensitivity genes (LOC_Os03g16900, LOC_Os06g48510, LOC_Os02g34810, and LOC_Os04g32920) and two salt tolerance genes (LOC_Os03g20090 and LOC_Os11g26790) were significantly increased compared with the control.

Conclusion The study can be used to evaluate the salt tolerance of tetraploid rice germplasm, reveal the regulation mechanism of salt tolerance in tetraploid rice, and provide a theoretical basis of the salt-tolerant germplasm selection in polyploidy rice.