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[Objectives]To investigate the effect of low temperature treatment on cotton leaves at the two-leaf stage.[Methods]Two cotton varieties（CN01 and SJB016（low temperature-tolerant）） were used as the trial materials. They were treated at 25（CK） and 12 ℃（low temperature） for 0,3,6,12,24,48 and 72 h, respectively. Then, the changes in the contents of MDA,SS and Pro in the cotton leaves were analyzed. Based on the analysis results, RNA-seq verification was performed.[Results]Two cotton varieties（CN01 and SJB016（ low temperature-tolerant）） were used as the trial materials. They were treated at 25（CK） and 12 ℃（low temperature） for 0,3,6,12,24,48 and 72 h, respectively. Then, the changes in the contents of MDA,SS and Pro in the cotton leaves were analyzed. Based on the analysis results, RNA-seq verification was performed.[Conclusions] These genes may play an important role in improving the cold resistance of cotton. [ABSTRACT FROM AUTHOR]