Molecular insights into genetic diversity and population dynamics of Paris polyphylla Smith in the Eastern Himalaya, India: a threatened anticancer medicinal herb of broad-spectrum therapeutic importance

, , , , ,

Research Articles | Published:

Print ISSN : 0970-4078.
Online ISSN : 2229-4473.
Pub Email:
Doi: 10.1007/s42535-022-00396-1
First Page: 1104
Last Page: 1117
Views: 142

Keywords: Paris polyphylla , Anticancer phytochemicals, Genetical diversity, ISSR, SCoT markers, Gene flow


Paris polyphylla is a threatened medicinal herb endowed with prized anticancer phytochemicals, namely, diosgenin, pennogenin and polyphyllin belonging to the class of steroidal saponins. In the present study, an attempt has been made to provide an insight into the population structure of P. polyphylla in the Eastern Himalayas, India using the molecular-based approach for effective conservation and sustainable utilization. Using Intersimple Sequence Repeat (ISSR) and Start Codon Targeted Polymorphism (SCoT) markers, forty-six accessions of P. polyphylla collected from eleven natural population sites were assessed which revealed 82.89% and 77.37% polymorphism, respectively. The recorded gene flow value (Nm) amongst the population was found low (0.31). The molecular variance analysis (AMOVA) revealed high genetic variance (81.17%) among the population than within the population (18.83%). Eleven natural population groups investigated from the Arunachal Himalayan region of India were found divided into two major clusters (I and II): Cluster I comprises fourteen accessions which are further divided into two subclusters and showed genetical closeness to each other while cluster II comprises thirty-two accessions which are further divided into three subclusters. The Mantel test revealed that the ISSR and SCoT techniques had a similar polymorphism distribution pattern, with a correlation coefficient (r) of 0.89, indicating that both techniques were effective in determining genetic diversity. While ISSR markers showed higher polymorphism, SCoT markers were also found reliable and informative technique for assessing genetic diversity and relationships among P. polyphylla populations, according to our findings. The present studies have confirmed ISSR and SCoT based markers as an efficient, reliable, quick and inexpensive tools for determining the genetic diversity of P. polyphylla. The present findings are expected to help researchers in the selection of superior chemotype and genotype of P. polyphylla which possess higher content of bioactive anticancer phytochemicals (diosgenin, pennogenin & polyphyllin) of pharmaceutical importance for conservation, genetic improvement and utilization as a viable source of anticancer drug development.

                Paris polyphylla
              , Anticancer phytochemicals, Genetical diversity, ISSR, SCoT markers, Gene flow

*Pdf Download Buy Printed Copy

(*Only SPR Members can download pdf file; #Open Access;)


Abdein MA, Abd El-Moneim D, Taha SS, Al-Juhani WS, Mohamed SE (2018) Molecular characterization and genetic relationships among some tomato genotypes as revealed by ISSR and SCoT markers. Egypt J Genet Cytol 47(1)

Al Salameen F, Habibi N, Kumar V, Al Amad S, Dashti J et al (2018) Genetic diversity and population structure of Haloxylon salicornicum moq Kuwait by ISSR Markers. Plos One 13(11):e0207369.

Ali F, Nadeem MA, Habyarimana E, Yılmaz A, Nawaz MA et al (2020) Molecular characterization of genetic diversity and similarity centers of safflower accessions with ISSR markers. Braz J Bot 43(1):109–121.

Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36(1):181–186.

Baruah J, Gogoi B, Das K, Ahmed NM, Sarmah DK et al (2017) Genetic diversity study amongst Cymbopogon species from NE-India using RAPD and ISSR markers. Ind Crops Prod 95:235–243.

Bhattacharyya P, Kumaria S (2015) Molecular characterization of Dendrobium nobile Lindl., an endangered medicinal orchid, based on randomly amplified polymorphic DNA. Plant Syst Evol 301(1):201–210.

Bhattacharyya P, Staden JV (2018) Molecular insights into genetic diversity and population dynamics of five medicinal Eulophia species: a threatened orchid taxa of Africa. Physiol Mol Biol Plant 24(4):631–641.

Bhattacharyya P, Kumaria S, Kumar S, Tandon P (2013) Start Codon Targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species. Gene 529(1):21–26.

Bhattacharyya P, Kumar V, Staden JV (2017) Assessment of genetic stability amongst micropropagated Ansellia africana, a vulnerable medicinal orchid species of Africa using SCoT markers. S Afr J Bot 108:294–302.

Bourhim T, Chakhchar A, Lamaoui M, El Kharrassi Y, Alaoui A et al (2021) Morphological characterization and assessment of genetic diversity of natural Moroccan populations of Capparis spinosa. Acta Physiol Plant 43:1–10.

Caughley G (1994) Directions in conservation biology. J Anim Ecol.

Chai X, Dong R, Liu W, Wang Y, Liu Z et al (2017) Optimizing sample size to assess the genetic diversity in common vetch (Vicia sativa L.) populations using start codon targeted (SCoT) markers. Molecules 22(4):567.

Collard BC, Mackill DJ (2009) Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol Biol Rep 27:86–93.

Dehestani A, Tabar SK (2007) A rapid efficient method for DNA isolation from plants with high levels of secondary metabolites. Asian J Plant Sci 6(6):977–981

Devi MB, Yaikhom V, Singh D (2019) Evaluation of genetic variability in wild population of chironomids of Manipur using SCoT marker. J Entomol Zool 7(1):1192–1195

El-Fiki A, Fahmy E, Doma AA, Helmy O, Adly M et al (2021) The genetic variation assessment of in vitro irradiated tomato (Lycopersicon esculentum Mill) by SCoT and ISSR markers. J Microbiol Biotechnol Food Sci 10(4):557–565.

Etminan A, Pour-Aboughadareh A, Noori A, Ahmadi-Rad A, Shooshtari L et al (2018) Genetic relationships and diversity among wild Salvia accessions revealed by ISSR and SCoT markers. Biotechnol Biotechnol Equip 32(3):610–617.

Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50

Ghafoor A, Sharif A, Ahmad Z, Zahid MA, Rabbani MA (2001) Genetic diversity in blackgram (Vigna mungo L. Hepper). F Crop Res 69(2):183–190

Govaerts R (2020) World checklist of Melanthiaceae. Facilitated by the Royal Botanic Gardens, Kew. Retrieved 22 August 2020

Gupta V, Jatav PK, Haq SU, Verma KS, Kaul VK et al (2019) Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various capsicum accessions: insight from their amplification, cross-transferability and genetic diversity. J Genet 98(2):1–12.

Gupta DD, Mishra S, Verma SS, Shekher A, Rai V et al (2021) Evaluation of antioxidant, anti-inflammatory and anticancer activities of diosgenin enriched Paris polyphylla rhizome extract of Indian Himalayan landraces. J Ethnopharmacol 270:113842.

Hajibarat Z, Saidi A, Hajibarat Z, Talebi R et al (2015) Characterization of genetic diversity in chickpea using SSR markers, start codon targeted polymorphism (SCoT) and conserved DNA-derived polymorphism (CDDP). Physiol Mol Biol Plants 21(3):365–373.

Holsinger KE, Vitt P (1997) The Future of Conservation Biology: What’s a Geneticist to Do?. In: Pickett STA, Ostfeld RS, Shachak M, Likens GE (eds) The Ecological Basis of Conservation. Springer, Boston, 202–216

Huang Y, Li X, Yang Z, Yang C, Yang J et al (2016) Analysis of complete chloroplast genome sequences improves phylogenetic resolution in Paris (Melanthiaceae). Front Plant Sci 7:1–12.

Jacquemyn H, Brys R, Honnay O, Hermy M, Roldan-Ruiz I (2006) Sexual reproduction, clonal diversity and genetic differentiation in patchily distributed populations of the temperate forest herb Paris quadrifolia (Trilliaceae). Oecologia 147(3):434–444.

Ji Y, Fritsch PW, Li H, Xiao T, Zhou Z (2006) Phylogeny and classification of Paris (Melanthiaceae) inferred from DNA sequence data. Ann Bot 98:245–256.

Juibary PL, Seyedmehdi FS, Sheidai M, Noormohammadi Z, Koohdar F (2021) Genetic structure analysis and genetic finger printing of sweet orange cultivars (Citrus sinensis (L.) Osbeck) by using SCoT molecular markers. Genet Resour Crop Evol.

Jun HE, Bai-Yun YA, Shao-Feng CH, Lian-Ming GA, Hong WA (2007) Assessment of genetic diversity of Paris polyphylla (Trilliaceae) by ISSR Markers. Plant Divers 29(04):388

Liu T, Ji Y (2012) Molecular authentication of the medicinal plant Paris polyphylla Smith var. yunnanensis (Melanthiaceae) and its related species by polymerase chain reaction fragment length polymorphism (PCR-RFLP). J Med Plant Res 6(7):1181–1186.

Li Z, Xin B, Yang H, Liu C, Tian M (2014) SCoT genetic diversity of plants in Paris. Guangxi Zhiwu/Guihaia 34(3):315–368.

Liu T, Li X, Xie S, Wang L, Yang S (2016) RNA-seq analysis of Paris polyphylla var. yunnanensis roots identified candidate genes for saponin synthesis. Plant Divers 38(3):163–170.

Mao R, Xia P, He Z, Liu Y, Liu F et al (2017) Identification of seeds based on molecular markers and secondary metabolites in Senna obtusifolia and Senna occidentalis. Bot Stud 58:43.

Pakseresht F, Talebi R, Karami E (2013) Comparative assessment of ISSR, DAMD and SCoT markers for evaluation of genetic diversity and conservation of landrace chickpea (Cicer arietinum L.) genotypes collected from north-west of Iran. Physiol Mol Biol Plants 19(4):563–574.

Paul A, Gajurel PR, Das AK (2015) Threats and conservation of Paris polyphylla an endangered, highly exploited medicinal plant in the Indian Himalayan Region. Biodiversitas 16(2):295–302.

Pei YF, Wu LH, Zhang QZ, Wang YZ (2019) Geographical traceability of cultivated Paris polyphylla var. yunnanensis using ATR-FTMIR spectroscopy with three mathematical algorithms. Anal Methods 11:113–122.

Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238.

POWO. Plants of the World Online ( Kew Science, Royal Botanic Gardens, Kew.

Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98(1):107–112.

Qi J, Zheng N, Zhang B, Sun P, Hu S et al (2013) Mining genes involved in the stratification of Paris polyphylla seeds using high-throughput embryo transcriptome sequencing. BMC Genom 14(1):1–14.

Rohlf FJ (1997) NTSYS-pc version. 2.02i numerical taxonomy and multivariate analysis system. Applied Biostatistics Inc., Exeter Software, Setauket, New York.

Safari H, Zebarjadi A, Kahrizi D, Jafari AA (2019) The study of inter-specific relationships of Bromus genus based on SCoT and ISSR molecular markers. Mol Biol Rep 46(5):5209–5223.

Sharma A, Kalita P, Tag H (2015) Distribution and phytomedicinal aspects of Paris polyphylla Smith from the Eastern Himalayan region: a review. Tang [Humanitas Medicine 5: 15.1–15.12.

Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ, Senior ML, Mitchell SE, Kresovich S, Ziegle J (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPs and pedigree. Theor Appl Genet 95:163–173.

Sneath PHA, Sokal RR (1973) Numerical taxonomy: the principles and practice of numerical classification. W.H. Freeman & Company, San Francisco, USA.

Song Y, Xu J, Chen N, Li M (2017) The complete chloroplast genome of traditional Chinese medical plants Paris polyphylla var. yunnanensis. Mitochondrial DNA Part A 28(2):159–160.

Surendran K, Nair RA, Pillai PP (2020) Molecular markers and their application in the identification of elite germplasm. In: Plant metabolites: methods, applications and prospects. Springer, Singapore 57–70

Tabasi M, Sheidai M, Hassani D, Koohdar F (2020) DNA fingerprinting and genetic diversity analysis with SCoT markers of Persian walnut populations (Juglans regia L.) in Iran. Genet Resour Crop Evol 67(6):1437–1447.

Tang M, Wang L, Weng Z (2008) AFLP analysis on genetic diversity and differentation of Paris thibetica. J Sich Univ Natl Sci Ed 45(2):402

Tariq M, Paul S, Bhatt ID, Chandrasekar K, Pande V, Nandi SK (2016) Paris polyphylla Smith: an important high value himalayan medicinal herb. Int J Adv Res 4:850–857.

Tariq M, Nandi SK, Bhatt ID, Bhavsar D, Roy A, Pande V (2021) Phytosociological and niche distribution study of Paris polyphylla Smith, an important medicinal herb of Indian Himalayan region. Trop Ecol 62(2):163–173.

Tikendra L, Potshangbam AM, Amom T, Dey A, Nongdam P (2021) Understanding the genetic diversity and population structure of Dendrobium chrysotoxum Lindl.-An endangered medicinal orchid and implication for its conservation. S Afr J Bot 138:364–376.

Wang L, Yang Y, Zhao Y, Yang S, Udikeri S et al (2016) De Novo characterization of the root transcriptome and development of EST-SSR markers in Paris polyphylla Smith var. yunnanensis, an endangered medical plant. J Agric Sci Technol 18:437–452.

Wu YG, Guo QS, He JC, Lin YF, Luo LJ et al (2010) Genetic diversity analysis among and within populations of Pogostemon cablin from China with ISSR and SRAP markers. Biochem Syst Ecol 38(1):63–72.

Xiong F, Zhong R, Han Z, Jiang J, He L et al (2011) Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Mol Biol Rep 38(5):3487–3494.

Yang Z, Yang C, Ji Y (2019) Paris variabilis (Melanthiaceae), a new species from southwestern China. Phytotaxa 401:190–198.

Yeh FC, Yang RC, Boyle T (1999) Popgene Version 1.31: Microsoft window-based freeware for population genetics analysis. University of Alberta, Edmonton, Canada.

Zarei A, Erfani-Moghadam J (2021) SCoT markers provide insight into the genetic diversity, population structure and phylogenetic relationships among three Pistacia species of Iran. Genet Resour Crop Evol.

Zhao X, Zou G, Zhao J, Hu L, Lan Y et al (2020) Genetic relationships and diversity among populations of Paris polyphylla assessed using SCoT and SRAP markers. Physiol Mol Biol Plants 26:1281–1293.

Zheng JY, Wang H, Chen XX, Wang P, Gao P et al (2012) Microsatellite markers for assessing genetic diversity of the medicinal plant Paris polyphylla var. chinensis (Trilliaceae). Genet Mol Res 11(3):1975–1980

Zietkiewicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeats (SSR)-anchored polymerase chain reaction amplification. Genomics 20(2):176–183.



The authors are thankful to Mr Sanjay Moyong for helping in the preparation of the Paris distribution map. The authors are also thankful to Mr Bipul Ch. Kalita, Mr Abhijit Paul, Mr Atek Nangkar, Ms Momang Taram and Ms Rubu Rinyo for providing valuable information on the current distribution status of the P. polyphylla population in the Eastern Himalaya. The vital logistic support extended by the Director of NIT Arunachal Pradesh, Jote, and Vice-Chancellor of Rajiv Gandhi University, Rono Hills, Doimukh, Arunachal Pradesh are deeply acknowledged.

Author Information

Das Gupta Debmalya
Department of Biotechnology, National Institute of Technology (NIT)-Arunachal Pradesh, Papum Pare, India
Paul Dipayan
Department of Biotechnology, National Institute of Technology (NIT)-Arunachal Pradesh, Papum Pare, India

Das Sanjib Kumar
Department of Biotechnology, National Institute of Technology (NIT)-Arunachal Pradesh, Papum Pare, India
Mahanta Saurov
National Institute of Electronics and Information Technology, Guwahati, India
Tag Hui
Plant Systematics and Ethnobotanical Research Laboratory, Department of Botany, Rajiv Gandhi University, Doimukh, India
Hui Pallabi Kalita
Department of Biotechnology, National Institute of Technology (NIT)-Arunachal Pradesh, Papum Pare, India