Abstract Using the genomic DNA extracted from Yane geese, the orthogonal design was used to optimize ISSR-PCR amplification system in five levels of five factors(Taq DNA polymerase, Mg2+,DNA template, dNTPs and primer)， respectively. Based on the preliminary experiment, the density within factors of ISSR-PCR was further optimized. The purpose of this experiment was to determine the reaction condition of ISSR-PCR fleetly and accurately, which was basis for the study on genetic diversity, map construction and gene localization of Yane geese. The results showed that a better amplification of ISSR was obtained with the reaction system containing 0.20umol/L primer, 0.28mmol/L dNTPs, 40ng templet DNA of Yane geese, 1.5mmol/L Mg2+,1.0U Taq DNA polymerase in the total volume of 25uL. Based on the orthogonal design experiment, the prime reaction condition of ISSR-PCR can be established through the density within factors of ISSR-PCR further optimized.
