[Objective] The aim was to identify genetic variation in Citrus sinensis （sweet orange） germplasm from Hunan Province according to the Start Codon Targeted （SCoT） Polymorphism. [Method] The reaction system for SCoT amplification from sweet orange was first optimized, and then the SCoT fragments were amplified from 24 sweet orange cultivars collected in Hunan Province and sequenced for genetic variation analysis. [Result] The optimum reaction system for SCoT markers amplification was 2.0 μl containing 80 ng of template DNA, 0.3 mmol/L dNTPs, 0.2 μmol/L primer, 1.6 mmol/L Mg2＋, 1.6 U of Taq DNA polymerase and 10×PCR buffer. By using this reaction system, the PCR products from the sweet orange cultivars produced clear and reproducible bands at 100-2 000 bp through electrophoresis. The SCoT fragments of the 24 sweet orange cultivars were 1 090-1 091 bp, with the homology of 99.84% and nucleotide deletion and substitution. After being sequenced, the SCoT polymorphisms could distinguish 12 sweet orange cultivars. In addition, the BLAST result showed that part of the SCoT fragments coding region shared high homology with ribosomal protein S3 N superfamily. [Conclusion] This study will provide a theoretical basis for breeding sweet orange cultivars.
