In this paper,we have sequenced the whole-genome of the Miscanthus(M.sinensis No.02381、M.sacchariflorus No.04005)chloroplast and developed 12 pairs of In Del markers.The orthogonal design was employed to optimize the cp In Del-PCR system,the best combination of the five key factors in this system,such as template DNA,d NTPs,Mg2 +,primers,Taq DNA polymerase were obtained.A list of 43 Miscanthus and 2 sugarcane materials were used to amplify by 12 pairs of In Del markers and 538 bands were amplified totally.1...