Objective: To develop a rapid, accurate and economical real time fluorescence PCR method with TaqMan probe technology to detect the X chromosome single nucleotide polymorphism (X-SNP).
Methods: TaqMan probes and polymerase chain reaction primers were respectively designed according to the 13 X-SNP. Then, the X-SNP were genotyped after the amplification by real time fluorescence PCR.
Results: All the loci follow the Hardy-Weinberg equilibrium. The polymorphic information content for 13 distinct loci varied between 0.3497 and 0.3750 while the heterozygosity ranged from 0.4537 to 0.5021. A real time fluorescent PCR method based on TaqMan probe was successfully developed and the results were accordant with those analyzed by DNA sequencing of the 13 X-SNP.
Conclusion: The allele specific real time fluorescence PCR based on TaqMan probe is a sensitive, simple technology and suitable for rapid analysis of XSNP. All the loci show highly polymorphic and may be potential in forensic genetics.