Genetic Diversity of Halocnemum strobilaceum (Pall.) M.Bieb. (Amaranthaceae) in South-West Iran: Insights from Molecular Markers and DNA Barcoding

Document Type : Research Paper

Authors

1 Department of Plant Production and Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran

2 Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran

Abstract

The Earth hosts a complex and diverse array of plant species, and analyzing their genetic diversity is essential for advancing biodiversity conservation. In this study, we investigated the genetic variation of Halocnemum strobilaceum in Khuzestan Province, located in southwestern Iran, a region characterized by extreme heat and belonging to the Saharo-Sindian floristic zone. To assess the genetic structure of the species, we employed ISSR, SCoT, and DNA barcoding markers (ITS and trnH-psbA). Accessions were categorized based on ecogeographic differences between inland saline and coastal marsh habitats. Both marker systems revealed considerable variation, and barcoding identified three distinct ITS and two trnH-psbA haplotypes. These results enhance our understanding of genetic differentiation in H. strobilaceum and inform conservation planning. As a halophyte with potential medicinal and economic uses, preserving its genetic resources is vital for sustainable utilization. In the face of escalating environmental threats, such integrative studies are key to protecting vulnerable plant taxa in extreme habitats.

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References

  1. 1. Brondizio E.S., Settele J., Díaz S., Ngo H.T. IPBES. Global Assessment Report on Biodiversity and Ecosystem Services. Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, IPBES secretariat. 2019. http://doi.org/10.5281/zenodo.3831673
  2. 2. Ozturk M., Altay V., Nazish M., Ahmad M., Zafar M. Some Representative Medicinal Halophytes in Asia Halophyte Plant Diversity and Public Health, Springer. 2023. https://doi.org/10.1007/978-3-031-21944-3_2
  3. 3. Pourabdollah-Kaleybar V., Pourabdollah-Kaleybar P., Eskandani M., Nazemiyeh H. Toxicity of bioactive compounds from Halocnemum strobilaceum against A549 lung cancer cells. Toxicon. 2025;253:108186. https://doi.org/10.1016/j.toxicon.2024.108186
  4. 4. Al-Mailem D., Sorkhoh N., Marafie M., Al-Awadhi H., Eliyas M., Radwan S. Oil phytoremediation potential of hypersaline coasts of the Arabian Gulf using rhizosphere technology. Bioresource Technology. 2010;101(15):5786-5792. https://doi.org/10.1016/j.biortech.2010.02.082
  5. 5. Bobtana F., Elabbar F., Bader N. Evaluation of Halocnemum strobilaceum and Hammada scoparia plants performance for contaminated soil phytoremediation. Journal of Medicinal and Chemical Sciences. 2019;3:126-29. https://doi.org/10.26655/jmchemsci.2019.8.1
  6. 6. Firouzabadi A., Jafari M., Assareh M., Arzani H., Javadi S. Investigation on the potential of halophytes as a source of edible oil (case study: Suaeda aegyptiaca and Halocnemum strobilaceum). International Journal of Biological Sciences. 2014;5(10):87-93. https://doi.org/10.22092/ijrdr.2017.114900
  7. 7. Zahran M.A., El-Amier Y.A. Non-traditional fodders from the halophytic vegetation of the deltaic Mediterranean coastal desert, Egypt. Journal of Biological Sciences. 2013;13(4):226-233. https://doi.org/10.3923/jbs.2013.226.233
  8. 8. Akhani H. Plants and Vegetation of North-West Persian Gulf: The coasts and Islands of Khore Musa, Mahshahr and Adjacent Areas, University of Tehran Press. 2015.
  9. 9. Ghazanfar S.A., Böer B., Al Khulaidi A.W., El-Keblawy A., Alateeqi S. Plants of Sabkha ecosystems of the Arabian Peninsula. Sabkha Ecosystems. 2019;49:55-80. http://dx.doi.org/10.1007/978-3-030-04417-6_5
  10. 10. Hernández-Ledesma P., Berendsohn W.G., Borsch T., Von Mering S., Akhani H., Arias S., Castañeda-Noa I., Eggli U., Eriksson R., Flores-Olvera H., Fuentes-Bazán S., Kadereit G., Klak C., Korotkova N., Nyffeler R., Ocampo G., Ochoterena H., Oxelman B., Rabeler R.K., Sanchez A., Schlumpberger B.O., Uotila P. A taxonomic backbone for the global synthesis of species diversity in the angiosperm order Caryophyllales. Willdenowia. 2015;45(3):281-383. https://doi.org/10.3372/wi.45.45301
  11. 11. Dinarvand M., Keneshloo H., Fayaz M., Khaksarian F., Arami S.A., Haydari K. Species diversity of desert and relationship to soil properties in dust sources of Khuzestan, southwest of Iran. Journal of Rangeland Science. 2022;13(3):1-12. https://doi.org/10.57647/j.jrs.2023.1303.1601
  12. 12. Frankham R., Briscoe D.A., Ballou J.D. Introduction to Conservation Genetics, Cambridge University Press. 2002. https://doi.org/10.1017/CBO9780511808999
  13. 13. DeWoody J.A., Harder A.M., Mathur S., Willoughby J.R. The long‐standing significance of genetic diversity in conservation. Mol Ecol. 2021;30(17):4147-4154. https://doi.org/10.1111/mec.16051
  14. 14. Hughes A.R., Inouye B.D., Johnson M.T., Underwood N., Vellend M. Ecological consequences of genetic diversity. Ecology Letters. 2008;11(6):609-23. https://doi.org/10.1111/j.1461-0248.2008.01179.x
  15. 15. Govindaraj M., Vetriventhan M., Srinivasan M. Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genetics Research International. 2015;2015:431487. https://doi.org/10.1155/2015/431487
  16. 16. Dar A.A., Mahajan R., Sharma S. Molecular markers for characterization and conservation of plant genetic resources. The Indian Journal of Agricultural Sciences. 2019;89(11):1755-63. https://doi.org/10.56093/ijas.v89i11.95286
  17. 17. Amiteye S. Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon. 2021;7(10):e08093. https://doi.org/10.1016/j.heliyon.2021.e08093
  18. 18. Bidyananda N., Jamir I., Nowakowska K., Varte V., Vendrame W.A., Devi R.S., Nongdam P. Plant genetic diversity studies: insights from DNA marker analyses. International Journal of Plant Biology. 2024;15(3):607-640. https://doi.org/10.3390/ijpb15030046
  19. 19. Antiqueira L. Application of microsatellite molecular markers in studies of genetic diversity and conservation of plant species of Cerrado. Journal of Plant Sciences. 2013;1(1):1-5. https://doi.org/10.11648/j.jps.20130101.11
  20. 20. Collard B., Mackill D. Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology Reporter. 2009;27:86-93. https://doi.org/10.1007/s11105-008-0060-5
  21. 21. Rai M.K. Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects. Planta. 2023;257(2):34. https://doi.org/10.1007/s00425-023-04067-6
  22. 22. Li X., Yang Y., Henry R.J., Rossetto M., Wang Y., Chen S. Plant DNA barcoding: from gene to genome. Biological Reviews of the Cambridge Philosophical Society. 2015;90(1):157-166. https://doi.org/10.1111/brv.12104
  23. 23. Mahima K., Sunil Kumar K.N., Rakhesh K.V., Rajeswaran P.S., Sharma A., Sathishkumar R. Advancements and future prospective of DNA barcodes in the herbal drug industry. Frontiers in Pharmacology. 2022;13: 947512. https://doi.org/10.3389/fphar.2022.947512
  24. 24. Kress W.J., Wurdack K.J., Zimmer E.A., Weigt L.A., Janzen D.H. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America. 2005;102(23):8369-8374. https://doi.org/10.1073/pnas.0503123102
  25. 25. Letsiou S., Madesis P., Vasdekis E., Montemurro C., Grigoriou M.E., Skavdis G., Moussis V., Koutelidakis A.E., Tzakos A.G. DNA barcoding as a plant identification method. Applied Sciences. 2024;14(4):1415. https://doi.org/10.3390/app14041415
  26. 26. Álvarez I., Wendel J.F. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution. 2003;29(3):417-434. https://doi.org/10.1016/s1055-7903(03)00208-2
  27. 27. Lazareva V.G., Goryaev I.A. On the problem of spatial demographic structure and Ontogenesis of Halocnemum Strobilaceum [(PALL.) BIEB.] in the Republic of Kalmykia. South Of Russia-ecology Development. 2016;11(1):193-198. http://dx.doi.org/10.18470/1992-1098-2016-1-193-198
  28. 28. Rohlf F.J. NTSYS-pc: numerical taxonomy and multivariate analysis system, version 2.1. New York: Exeter Software. 2000.
  29. 29. Serrote C.M.L., Reiniger L.R.S., Silva K.B., dos Santos Rabaiolli S.M., Stefanel C.M. Determining the Polymorphism Information Content of a molecular marker. Gene. 2020;726:144175. https://doi.org/10.1016/j.gene.2019.144175
  30. 30. Powell W., Morgante M., Andre C., Hanafey M., Vogel J., Tingey S., Rafalski A. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding. 1996;2:225-238. https://doi.org/10.1007/BF00564200
  31. 31. Peakall R., Smouse P.E. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes. 2006;6(1):288-95. https://doi.org/10.1111/j.1471-8286.2005.01155.x
  32. 32. Tamura K., Stecher G., Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution. 2021;38(7):3022-3027. https://doi.org/10.1093/molbev/msab120
  33. 33. Rozas J., Ferrer-Mata A., Sánchez-DelBarrio J.C., Guirao-Rico S., Librado P., Ramos-Onsins S.E., Sánchez-Gracia A. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution. 2017;34(12):3299-3302. https://doi.org/10.1093/molbev/msx248
  34. 34. Perrier X., Jacquemoud-Collet J.P. DARwin software. http://darwin.cirad.fr/darwin. 2006.
  35. 35. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. 1999;41:95-98.
  36. 36. Aly S., Fouad N., Mohamed H.M., Abdel-Hamid A., Saad M.E. Molecular characterization of some Egyptian halophytes. South African Journal of Botany. 2025;180:265-273. https://doi.org/10.1016/j.sajb.2025.03.022
  37. 37. Samaha G., Sayed L., Tawfik M. Agro-physiological and genetic characterization of halophyte species and their impact on salt-affected soil. SABRAO Journal of Breeding and Genetics. 2024;56(1):76-88. http://doi.org/10.54910/sabrao2024.56.1.7.
  38. 38. ElSenosy N.K., Younis R., Khalil R., Abd El-Maboud M.M. Antioxidant enzymes and molecular markers associated with salinity tolerance of Halocnemum strobilaceum (Pall.) Bieb. American-Eurasian Journal of Agricultural & Environmental Sciences. 2015;15:648-658. http://dx.doi.org/10.5829/idosi.aejaes.2015.15.4.12618
  39. 39. Gogoi B., Wann S., Saikia S. Comparative assessment of ISSR, RAPD, and SCoT markers for genetic diversity in Clerodendrum species of North East India. Molecular Biology Reports. 2020;47(10):7365-7377. https://doi.org/10.1007/s11033-020-05792-x
  40. 40. Dar B.A., Al-Doss A.A., Assaeed A.M., Javed M.M., Ghazy A.I., Al-Rowaily S.L., Abd-ElGawad A.M. Genetic variation among Aeluropus lagopoides populations growing in different saline regions. Diversity. 2024;16(1):59. https://doi.org/10.3390/d16010059
  41. 41. Liu S., Zhu L., Jiang W., Qin J., Lee H.-S. Research on the effects of soil petroleum pollution concentration on the diversity of natural plant communities along the coastline of Jiaozhou bay. Environmental Research. 2021;197:111127. https://doi.org/10.1016/j.envres.2021.111127
  42. 42. Tahmasebi A., Nasrollahi F. Morphologic and genetic study of Halocnemum strobilaceum (Amaranthaceae) in rangeland ecosystems of Golestan province. Rostaniha. 2021;22(1):134-146. https://doi.org/10.22092/botany.2021.355344.1260
  43. 43. Zhu Z., Zhang L., Gao L., Tang S., Zhao Y., Yang J. Local habitat condition rather than geographic distance determines the genetic structure of Tamarix chinensis populations in Yellow River Delta, China. Tree Genetics and Genomes. 2016;12(1):14. https://doi.org/10.5061/dryad.p502g
  44. 44. Ma S., Shen Y., Li M., Jiang R., Cai L., Wu T., Gao L., Wu M., He P. Establishment of Novel Simple Sequence Repeat Markers in Phragmites australis and Application in Wetlands of Nanhui Dongtan, Shanghai. Biology. 2025;14(4):356. https://doi.org/10.3390/biology14040356
  45. 45. Chapman S.C., Chakraborty S., Dreccer M.F., Howden S.M. Plant adaptation to climate change opportunities and priorities in breeding. Crop & Pasture Science. 2012;63(3):251-268. http://dx.doi.org/10.1071/CP11303
  46. 46. Hulshof C.M., Spasojevic M.J. The edaphic control of plant diversity. Global Ecology and Biogeography. 2020;29(10):1634-1650. http://dx.doi.org/10.1111/geb.13151
  47. Phillips J.D., Gillis D.J., Hanner R.H. Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecology and Evolution. 2019;9(5):2996-3010. https://doi.org/10.1002/ece3.4757
  48. Piirainen M., Liebisch O., Kadereit G. Phylogeny, biogeography, systematics and taxonomy of Salicornioideae (Amaranthaceae/Chenopodiaceae) A cosmopolitan, highly specialized hygrohalophyte lineage dating back to the Oligocene. Taxon. 2017;66(1):109-132. https://doi.org/10.12705/661.6
  49. Mao X., Xie W., Li X., Shi S., Guo Z. Establishing community-wide DNA barcode references for conserving mangrove forests in China. BMC Plant Biology. 2021;21(1):571. https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-021-03349-z
  50. White T.J., Bruns T., Lee S., Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (Eds), PCR Protocols: A Guide to Methods and Applications. Academic Press. 1990. http://dx.doi.org/10.1016/B978-0-12-372180-8.50042-1
  51. Genievskaya Y., Abugalieva S., Zhubanysheva A., Turuspekov Y. Morphological description and DNA barcoding study of sand rice (Agriophyllum squarrosum, Chenopodiaceae) collected in Kazakhstan. BMC Plant Biology. 2017;17(1):1-8. https://doi.org/10.1186/s12870-017-1132-1
  52. Tate J.A., Simpson B.B. Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species. Systematic Botany. 2003;28(4):723-737. http://dx.doi.org/10.1043/02-64.1
  53. Sang T., Crawford D.J., Stuessy T.F. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany. 1997;84(8):1120-1136. http://dx.doi.org/10.2307/2446155
Journal of Medicinal plants and By-products
Volume 15, Issue 1
January and February 2026
Pages 70-77

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