We established a cDNA-AFLP （amplified fragment length polymorphism） system for Populus euphratica, after optimizing several key factors. The results show that optimized CTAB method is suitable for the extraction of ideal RNA from P euphratica; the double-stranded cDNA （ds-cDNA） is completely digested by the combination of EcoRI and MseI for 4.5 h; the reducible result can be obtained when the preamplification products were diluted 10-fold for selective amplification templates. The amplification products resulting from this reaction system were determined by silver staining and the fragments were clear and stable. Detected by RT-PCR, the optimized differential display cDNA-AFLP technique can accurately reflect the true differences of gene expressions among plants. In addition, 42 pairs of primer arrays, producing repeatable and prolific bands, were successfully selected by this improved method. This investigation establishes a cDNA-AFLP system for P. euphratica, which forms a basis for further study on stress-response genes in P. euphratica.
