Abstract: We established and optimized SRAP-PCR amplification system for Isatis indigotica Fort by the orthogonal design. The order of factors affecting the result of SRAP-PCR were Mg²⁺, dNTPs, primers, template DNA and Taq DNA polymerase. A suitable SRAP-PCR system for Chinese bayberry was that total 25 μL reaction system containing 1.5 mmol·L^-1 Mg²⁺, 0.15 mmol·L^-1 dNTPs, 0.60 μmol·L^-1 primers, 2.0 U Taq DNA polymerase and 26 ng template DNA could be able to amplified the most rich polymorphism and clear bands. This reaction system was experimentally validatied and and primers selected, and should be a suitable system for the genetic diversity analysis of I.indigotica Fort.

Key words: Isatis indigotica Fort, SRAP, optimization, primer selection