Development and Application of InDel Markers for Authentication of the Korean Herbs Zanthoxylum schinifolium and Zanthoxylum piperitum

Abstract

Zanthoxylum schinifolium and Zanthoxylum piperitum are the sources of the well-known traditional Korean herbal medicines “sancho” (prickly ash) and “chopi” (Korean pepper), respectively. Sancho and chopi are often indiscriminately mixed due to the similar appearance of the herbal materials when used as spices and herbal medicines. Moreover, commercial sancho and chopi products often contain adulterants, which is insufficient to ensure food efficacy and safety. In this study, we developed hypervariable insertion/deletion (InDel) markers to distinguish between sancho and chopi products by comparing the complete chloroplast genome sequences of four Zanthoxylum species deposited in the National Center for Biotechnology Information (NCBI) GenBank. Comparative analyses of the nucleotide diversity (Pi) of these Zanthoxylum genomes revealed four hypervariable divergent sites (trnH-psbA, psbZ-trnG, trnfM-rps14, and trnF-ndhK) with Pi > 0.025 among 520 windows. Of these four regions, including two genic and two intergenic regions, only psbZ-trnG yielded accurate PCR amplification results between commercial sancho and chopi products from the Korean herbal medicine market. We therefore selected psbZ-trnG, an InDel-variable locus with high discriminatory powers, as a candidate DNA barcode locus. This InDel marker could be used as a valuable, simple, and efficient tool for identifying these medicinal herbs, thereby increasing the safety of these spices and herbal materials in the food market.

Comparative analysis of jujube and sour jujube gave insight into their difference in genetic diversity and suitable habitat

“…To expedite species identification, a novel PCR-based Indel marker identification method has gained prominence. This method enables direct identification through the analysis of gel profiles of PCR-amplified fragments and is progressively finding applications in crop and medicinal plant discrimination ( Guo et al, 2019 ; Jain et al, 2019 ; Kim et al, 2019 ; Fang et al, 2021 ).…”

Emerging biotechnology applications in natural product and synthetic pharmaceutical analyses

“…Kim et al. 6 accurately distinguished Zanthoxylum schinifolium and Zanthoxylum piperitum by the InDel analysis of psbZ-trnG . Simple sequence repeat (SSR) can be used to mark 2–6 bases of tandem repeats in genetic information, and this method could accurately distinguish multiple cultivars of plum varieties 34 .…”

Elucidation of Japanese pepper (Zanthoxylum piperitum De Candolle) domestication using RAD-Seq

“…However, three important studies have examined the DNA sequences of Zanthoxylum piperitum growing in Korea. One is the complete sequencing of the chloroplast genome 12 , and the others involved the development of markers to identify Zanthoxylum piperitum 13 , 14 . Many other studies have used the genetic information for Zanthoxylum piperitum as a reference for comparison 15 – 20 , 22 , 23 .…”