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Updated: Jul 18, 2026
A PCR-based Genotyping Method to Distinguish Between Wild-type and Ornamental Varieties of Imperata cylindrica
Published on: February 20, 2012
[SNP marker and allele-specific diagnostic PCR for authenticating herbs of Perilla]
Yu-ming Luo1, Wei-ming Zhang, Xiao-yu Ding
1Jiangsu Key Laboratory for Biodiversity and Technology, College of Life Sciences, Nanjing Normal University, Nanjing 210097, China.
Aim:
To authenticate all the varieties of Perilla (single-species genus), to analyze sequences of rDNA ITS regions and single nucleotide polymorphism (SNP) within them and based on these, to design allele-specific diagnostic PCR primers.
Methods:
The rDNA ITS regions of the perilla varieties were sequenced and analyzed by Clustal X 1.8, MEGA 3.0. Allele-specific diagnostic PCR primers that can authenticate all the perilla varieties were designed based on SNPs loci.
Results:
The length of rDNA ITS sequences of perilla varieties ranged from 612 to 615 bp in size, including ITS1 (230 -232 bp), 5.8S (179 bp) and ITS2 (203 -204 bp). The GC content is about 61.5% - 61.9%. There is not only SNPs in non-coding region ITS1 and ITS2 (ncSNP), but also three coding SNPs (cSNP) loci in the conservative region of 5.8S. All the SNPs have only two allele loci polymorphism. The cSNP in 5.8S is related to the morphology variation among the varieties. Allele-specific diagnostic PCR primers have been designed according to SNPs loci to authenticate accurately all the seeds and leaves of Perilla varieties.
Conclusion:
SNPs in rDNA ITS region can be used as an effective molecular markers to authenticate all the varieties of Perilla.
