Abstract: 【Objective】 The objective of the study is to research the change of genomic DNA methylation under different types of salt and to compare the variation of DNA methylation between leaves and roots, which can help us make it clear about the relation between DNA methylation and the salt tolerance in cotton.【Method】In the study, salt-tolerant variety Zhong9806 and salt-sensitive variety ZhongS9612 were used as experimental materials, which were treated with NaCl and Na2CO3 at concentration of 0.4%, respectively. DNA extracted from control materials and the treatment materials were used for double digestions, ligation reactions, pre-amplification reactions and selective amplification reactions, then MSAP technology (Methylation sensitive amplified polymorphism) was used to explore the change of DNA methylation between the control and treatment materials in cotton seedlings. The differentially methylated DNA fragments were isolated from the polyacrylamide gel, sequenced and BLAST analysis in NCBI library. Real time-PCR technology was used to test the expression quantity of polymorphic fragments in cotton seedlings.【Result】The results of salt stress indicated that the effects of different salt stresses on the growth of cotton seedlings were different. Neutral salt NaCl at 0.4% concentration had a relatively small effect on cotton seedling，and the morphological characters of different tissues changed a little, but 0.4% alkaline salt Na2CO3 had a bigger harm, resulted in the cotyledon soft, and the basal part of stem and roots of cotton seedlings black. MSAP analysis showed that after NaCl treatment, the genomic DNA methylation level of leaves of Zhong9806 and ZhongS9612 were 23.5% and 27.7%, in which full methylated ratio was 20.3% and 22.9%, respectively. The methylation level of roots of Zhong9806 and ZhongS9612 was 24.7% and 27.1%, in which full methylated ratio was 19.6% and 21.6%, respectively. After Na2CO3 treatment, the methylation level of leaves of Zhong9806 and ZhongS9612 were 28.9% and 28.1%, in which full methylated ratio was 24.3% and 24.5%, respectively. The methylation level of roots of Zhong9806 and ZhongS9612 was 25.7% and 27.6%, in which full methylated ratio was 21.5% and 24.0%, respectively. Genomic DNA methylation levels were different between leaves and roots. With the salt type changed from neutral salt to alkaline salt, the genomic DNA methylation levels went up rapidly and reached the maximum in the Na2CO3 treatment. From the result of DNA methylation status analysis, we could learn that the methylated band ratio (% polymorphic bands) in leaves of Zhong9806 was 40.00% and 50.00%, respectively, and demethylated band ratio (% polymorphic bands) was 54.12% and 46.67%, respectively. The methylated band ratio (% polymorphic bands) in roots of Zhong9806 was 35.53% and 43.59%, respectively, and demethylated band ratio (% polymorphic bands) was 56.58% and 51.28%, respectively. But the methylated band ratio (% polymorphic bands) and the demethylated band ratio (% polymorphic bands) in leaves and roots of ZhongS9612 changed a little after stress. In total, 6 fragments were obtained from the gel, which were amplified and analyzed with BLAST method. The result indicated that the 6 sequences were homologous to 6 different genes, widely distributed in coding region and non-coding region, involving different metabolic reactions. The analysis of qRT-PCR showed that these genes were differentially expressed between control and treatment.【Conclusion】The response of cotton varieties with different salt-tolerances to the stress of different salt is different. The DNA methylation level of Zhong 9806, a salt-tolerant variety, declined under salt stress, which could induce the expression of genes related to salt-tolerance, but Zhong S9612, a salt-sensitive variety, lack relevant genes to make the damage increase, reaching the most after the Na2CO3 treatment. A big difference exists in the DNA methylation level between the control and treatment，and the pattern of DNA methylation has tissue specificity. From the analysis of polymorphic fragments, homogenous genes involve many metabolic pathways, through the synergistic effect of three pathways to deal with the stress.

Key words: cotton , DNA methylation , MSAP , salt , qRT-PCR