Development of Insertions and deletions (InDel) Markers for the Differentiation of Cnidium officinale Makino and Ligusticum chuanxiong Hort

Background: In Korea, the medicinal herb Cnidii Rhizoma is manufactured using Cnidium officinale Makino and Ligusticum chuanxiong Hort., with the former being the primary ingredient. C. officinale and L. chuanxiong have similar external appearances, and because their roots are dried for use as medicinal materials, it is difficult to distinguish between them. Therefore, there is a need to develop easy-to-use molecular markers to facilitate the classification of Cnidii Rhizoma varieties and the identification of medicinal materials.BR/Methods and Results: DNA was extracted from C. officinale and L. chuanxiong and analyzed using an Illumina HiSeq 2500 platform. After de novo assembly, the loci showing polymorphisms between C. officinale and L. chuanxiong were identified. Primers were designed for polymorphic loci, and genotyping was performed. Finally, three nuclear genome-based insertion and deletion (InDel) markers, CoInDel-01, CoInDel-02, and CoInDel-03, were developed. These markers produced a single band at 230, 369, and 245 bp, respectively, in C. officinale, whereas two bands were observed in L. chuanxiong at 230 and 264 bp, 304 and 369 bp, and 197 and 245 bp, respectively.BR/Conclusion: The three InDel markers developed in this study will be useful for differentiating between C. officinale and L. chuanxiong