Abstract： Inter-Simple Sequence Repeat ( ISSR) is a good molecular marker for revealing genetic diversity. In our study, the systems of DNA extracting and ISSR-PCR reaction were constructed using eggplant(Solanum melongena L) leaves. The results indicated the DNA quality was improved by modified CTAB protocol and applied to ISSR-PCR system. The amylase, polyphenol and pigment of the eggplant leaves were wiped off completely. Orthogonal design was used to optimize ISSR amplification system on eggplant in four factors(Taq, dNTP, primers, template) three levels respectively. Using eggplant genome DNA as template, Optimal PCR(20μL) mix for eggplant contained: 2. 0μL 10 ×stock buffer (25mM Mg2+), 375μmol/ L of each dNTP, 0.4μmol/ L primer , 1 unit of DNA polymerase and 4ng DNA template. The study construct a base for the research of genetic diversity of eggplant.
