Skip to main content
SpringerLink
Log in

Molecular authentication of two medicinal plants Ligularia fischeri and Ligularia stenocephala using allele-specific PCR (AS-PCR) strategy

  • Research Article
  • Published:
Genes & Genomics Aims and scope Submit manuscript

Abstract

Ligularia fischeri (Gom-chi) and Ligularia stenocephala (Gon-dal-bi) are popular edible herbs in Korea. L. fischeri is used to treat jaundice, hepatitis, rheumatoid arthritis, and scarlet fever, while L. stenocephala is used to treat anxiety, weakness, and menstrual disorders. The herbal medicinal activities of these two herbs differ, but they are very difficult to distinguish based on their morphologies, especially in their dried forms. In an effort to distinguish these two plant species, we sequenced three barcoding genes in plastids, matK, rbcL, and trnH-psbA. From the analysis of sequence variations, we detected five single nucleotide polymorphisms (SNPs) between two the species. Allele specific (AS)-primers in the SNPs were employed in discrimination of the two species. Of the five AS-primer sets, one primer pair in matK gene showed reproducibly distinguishable PCR amplification between plants of L. fischeri and L. stenocephala. The method is reproducible and efficient, and is the first reported molecular method to discriminate between L. fischeri and L. stenocephala.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Arif IA, Khan HA, Bahkali AH, Al Homaidan AA, Al Farhan AH, Al Sadoon M, Shobrak M (2011) DNA marker technology for wildlife conservation. Saudi J Biol Sci 18:219–225

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chan K (2003) Some aspects of toxic contaminants in herbal medicines. Chemosphere 52:1361–1371

    Article  CAS  PubMed  Google Scholar 

  • Chang WT, Thissen U, Ehlert KA, Koek MM, Jellema RH, Hankemeier T, van der Greef J, Wang M (2006) Effects of growth conditions and processing on Rehmannia glutinosa using fingerprint strategy. Planta Med 72:458–467

    Article  CAS  PubMed  Google Scholar 

  • Choi EM (2007) Ligularia fischeri leaf extract prevents the oxidative stress in DBA/1 J mice with type II collagen-induced arthritis. J Appl Toxicol 27:176–182

    Article  CAS  PubMed  Google Scholar 

  • Drenkard E, Richter BG, Rozen S, Stutius LM, Angell NA, Mindrinos M, Cho RJ, Oefner PJ, Davis RW, Ausubel FM (2000) A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiol 124:1483–1492

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • El Beyrouthy M, Abi-Rizk A (2013) DNA Fingerprinting: the new trend in fighting the adulteration of commercialized and cultivated medicinal plants. Adv Crop Sci Technol 1:4

    Google Scholar 

  • Ganal MW, Altmann T, Roder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12:211–217

    Article  CAS  PubMed  Google Scholar 

  • Ganie SH, Upadhyay P, Das S, Prasad Sharma M (2015) Authentication of medicinal plants by DNA markers. Plant Gene 4:83–99

    Article  CAS  Google Scholar 

  • Ha WY, Shaw PC, Liu J, Yau FCF, Wang J (2002) Authentication of Panax ginseng and Panax quinquefolius using amplified fragment length polymorphism (AFLP) and directed amplification of minisatellite region DNA (DAMD). J Agric Food Chem 50:1871–1875

    Article  CAS  PubMed  Google Scholar 

  • Hamilton M (1999) Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol Ecol 8:521–523

    CAS  PubMed  Google Scholar 

  • Hayashi K, Hashimoto N, Daigen M, Ashikawa I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor Appl Genet 108:1212–1220

    Article  CAS  PubMed  Google Scholar 

  • Hebert PD, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc Biol Sci 270:313–321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA barcode. PLoS ONE 6:e19254

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kress WJ, Erickson DL, Jones FA, Swenson NG, Perez R, Sanjur O, Bermingham E (2009) Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proc Natl Acad Sci USA 106:18621–18626

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kwok S, Chang SY, Sninsky JJ, Wang A (1994) A guide to the design and use of mismatched and degenerate primers. Genome Res 3:S39–S47

    Article  CAS  Google Scholar 

  • Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V (2008) DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci USA 105:2923–2928

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee MY, Doh EJ, Park CH, Kim YH, Kim ES, Ko BS, Oh SE (2006) Development of SCAR marker for discrimination of Artemisia princeps and A. argyi from other Artemisia herbs. Biol Pharm Bull 29:629–633

    Article  CAS  PubMed  Google Scholar 

  • Lee BI, Nugroho A, Bachri MS, Choi J, Lee KR, Choi JS, Kim WB, Lee KT, Lee JD, Park HJ (2010) Anti-ulcerogenic effect and HPLC analysis of the caffeoylquinic acid-rich extract from Ligularia stenocephala. Biol Pharm Bull 33:493–497

    Article  CAS  PubMed  Google Scholar 

  • Levin RA, Wagner WL, Hoch PC, Nepokroeff M, Pires JC, Zimmer EA, Sytsma KJ (2003) Family-level relationships of Onagraceae based on chloroplast rbcL and ndhF data. Am J Bot 90:107–115

    Article  CAS  PubMed  Google Scholar 

  • Li XW, Luo Q, Gan QL (2014) Ligularia zhengyiana sp. nov. (Asteraceae) from the Hubei Province, China. Nord J Bot 32:836–838

    Article  Google Scholar 

  • Liu JQ (2004) Uniformity of karyotypes in Ligularia (Asteraceae: Senecioneae), a highly diversified genus of the eastern Qinghai-Tibet Plateau highlands and adjacent areas. Bot J Linn Soc 144:329–342

    Article  Google Scholar 

  • Liu S, Deng D, Liu J (1993) The origin, evolution and distribution of Ligularia Cass.(Compositae). Acta Phytotaxonomica Sinica 32:514–524

    Google Scholar 

  • Luo B, Liao F, Hu Y, Liu X, He Y, Wu L, Tan H, Luo L, Zhou Y, Mo Q, et al. (2015) Acaricidal activity of extracts from Ligularia virgaurea against the Sarcoptes scabiei mite in vitro. Exp Ther Med 10:247–250

    PubMed  PubMed Central  Google Scholar 

  • Ma XY, Xie CX, Liu C, Song JY, Yao H, Luo K, Zhu YJ, Gao T, Pang XH, Qian J et al (2010) Species identification of medicinal pteridophytes by a DNA barcode marker, the chloroplast psbA-trnH intergenic region. Biol Pharm Bull 33:1919–1924

    Article  CAS  PubMed  Google Scholar 

  • Mishra P, Kumar A, Nagireddy A, Mani DN, Shukla AK, Tiwari R, Sundaresan V (2016) DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant Biotechnol J 14:8–21

    Article  CAS  PubMed  Google Scholar 

  • Newmaster SG, Fazekas AJ, Steeves RA, Janovec J (2008) Testing candidate plant barcode regions in the Myristicaceae. Mol Ecol Resour 8:480–490

    Article  CAS  PubMed  Google Scholar 

  • Newton CR, Graham A, Heptinstall LE, Powell SJ, Summers C, Kalsheker N, Smith JC, Markham AF (1989) Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res 17:2503–2516

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Park HS, Choi HY, Kim GH (2014) Preventive effect of Ligularia fischerion inhibition of nitric oxide in lipopolysaccharide-stimulated RAW 264.7 macrophages depending on cooking method. Biol Res 47:69

    Article  PubMed  PubMed Central  Google Scholar 

  • Semagn K, Bjørnstad Å, Ndjiondjop M (2006) An overview of molecular marker methods for plants. Afr J Biotechnol 5:2540–2568

    CAS  Google Scholar 

  • Shang YF, Kim SM, Song DG, Pan CH, Lee WJ, Um BH (2010) Isolation and identification of antioxidant compounds from Ligularia fischeri. J Food Sci 75:C530–C535

    Article  CAS  PubMed  Google Scholar 

  • Shen J, Ding X, Liu D, Ding G, He J, Li X, Tang F, Chu B (2006) Intersimple sequence repeats (ISSR) molecular fingerprinting markers for authenticating populations of Dendrobium officinale Kimura et Migo. Biol Pharm Bull 29:420–422

    Article  CAS  PubMed  Google Scholar 

  • Tate JA, Simpson BB (2003) Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species. Syst Bot 28:723–737

    Google Scholar 

  • Techen N, Parveen I, Pan Z, Khan IA (2014) DNA barcoding of medicinal plant material for identification. Curr Opin Biotechnol 25:103–110

    Article  CAS  PubMed  Google Scholar 

  • Tori M, Honda K, Nakamizo H, Okamoto Y, Sakaoku M, Takaoka S, Gong X, Shen Y, Kuroda C, Hanai R (2006) Chemical constituents of Ligularia virgaurea and its diversity in southwestern Sichuan of China. Tetrahedron 62:4988–4995

    Article  CAS  Google Scholar 

  • Toyoda K, Yaoita Y, Kikuchi M (2005) Three new dimeric benzofuran derivatives from the roots of Ligularia stenocephala MATSUM. et KOIDZ. Chem Pharm Bull 53:1555–1558

    Article  CAS  PubMed  Google Scholar 

  • Wang CZ, Li P, Ding JY, Jin GQ, Yuan CS (2005) Identification of Fritillaria pallidiflora using diagnostic PCR and PCR-RFLP based on nuclear ribosomal DNA internal transcribed spacer sequences. Planta Med 71:384–386

    Article  CAS  PubMed  Google Scholar 

  • Wang H, Sun H, Kwon WS, Jin H, Yang DC (2010) A PCR-based SNP marker for specific authentication of Korean ginseng (panax ginseng) cultivar “Chunpoong”. Mol Biol Rep 37:1053–1057

    Article  CAS  PubMed  Google Scholar 

  • Wu QH, Wang CM, Cheng SG, Gao K (2004) Bieremoligularolide and eremoligularin, two novel sesquiterpenoids from Ligularia muliensis. Tetrahedron Lett 45:8855–8858

    Article  CAS  Google Scholar 

  • Xu YQ, Wang Y, Li ZZ, Bao ZX, Zhou JF, Huang HW (2006) Characterization of polymorphic microsatellite loci in a traditional Chinese medicinal plant, Gastrodia elata. Mol Ecol Notes 6:316–318

    Article  CAS  Google Scholar 

  • Yang DY, Fushimi H, Cai SQ, Komatsu K (2004) Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and amplification refractory mutation system (ARMS) analyses of medicinally used Rheum species and their application for identification of Rhei Rhizoma. Biol Pharm Bull 27:661–669

    Article  CAS  PubMed  Google Scholar 

  • Yao H, Song JY, Ma XY, Liu C, Li Y, Xu HX, Han JP, Duan LS, Chen SL (2009) Identification of Dendrobium species by a candidate DNA barcode sequence: the chloroplast psbA-trnH intergenic region. Planta Med 75:667–669

    Article  CAS  PubMed  Google Scholar 

  • Yip PY, Chau CF, Mak CY, Kwan HS (2007) DNA methods for identification of Chinese medicinal materials. Chin Med 2:9

    Article  PubMed  PubMed Central  Google Scholar 

  • Yoo JH, Oidovsambuu S, Kim SM, Jeon NR, Yun JH, Kang K, Jho EH, Lee SB, Nho CW (2011) Hepatoprotective effect of Handaeri-gomchi (Ligularia fischeri var. spiciformis Nakai) extract against chronic alcohol-induced liver damage in rats. Food Sci Biotechnol 20:1655–1661

    Article  Google Scholar 

Download references

Acknowledgements

This study was supported by a 2014 Research Grant from Kangwon National University.

Author information

Author notes

    Authors and Affiliations

    1. Gangwon-do Agricultural Research & Extension Services, Chuncheon, 24226, South Korea

      Seong Jin Choi, Yong Bog Kim, Se Won Kim & Hee Sun Noh

    2. Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 24341, South Korea

      Rahul Vasudeo Ramekar & Ju Kyong Lee

    3. Department of Plant Science, Gangneung-Wonju National University, Gangneung, 25457, South Korea

      Nam Il Park

    4. Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, 24341, South Korea

      Ik Young Choi, Seon-Kang Choi & Kyong Cheul Park

    Authors
    1. Seong Jin Choi
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Rahul Vasudeo Ramekar
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Yong Bog Kim
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Se Won Kim
      View author publications

      You can also search for this author in PubMed Google Scholar

    5. Hee Sun Noh
      View author publications

      You can also search for this author in PubMed Google Scholar

    6. Ju Kyong Lee
      View author publications

      You can also search for this author in PubMed Google Scholar

    7. Nam Il Park
      View author publications

      You can also search for this author in PubMed Google Scholar

    8. Ik Young Choi
      View author publications

      You can also search for this author in PubMed Google Scholar

    9. Seon-Kang Choi
      View author publications

      You can also search for this author in PubMed Google Scholar

    10. Kyong Cheul Park
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding author

    Correspondence to Kyong Cheul Park.

    Ethics declarations

    Conflict of interest

    Jin Choi, Rahul Vasudeo Ramekar, Yong Bog Kim, Se Won Kim, Hee Sun Noh, Ju Kyong Lee, Nam Il Park, Ik Young Choi, Seon-Kang Choi and Kyong Cheul Park declare that they do not have conflict of interest.

    Research involving with human and animal studies

    This article does not contain any studies with human subjects or animals performed by any of the authors.

    Additional information

    Seong Jin Choi and Rahul Vasudeo Ramekar have contributed equally to this work.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    Supplementary material 1 (PDF 1539 KB)

    Rights and permissions

    Reprints and permissions

    About this article

    Check for updates. Verify currency and authenticity via CrossMark

    Cite this article

    Choi, S.J., Ramekar, R.V., Kim, Y.B. et al. Molecular authentication of two medicinal plants Ligularia fischeri and Ligularia stenocephala using allele-specific PCR (AS-PCR) strategy. Genes Genom 39, 913–920 (2017). https://doi.org/10.1007/s13258-017-0554-3

    Download citation

    • Received:

    • Accepted:

    • Published:

    • Issue Date:

    • DOI: https://doi.org/10.1007/s13258-017-0554-3

    Keywords

    Search

    Navigation