Genetic variation among different populations of Centaurea virgata from Iran using start codon targeted (SCoT) markers

Document Type : Research Paper

Authors

1 MSc Graduate in Biochemistry, Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran

2 Assistant Prof., Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Kashan, Iran

10.22092/bot.j.iran.2024.366800.1397

Abstract

The aim of the present study is the identification of the genetic variation of Centaurea virgata (Asteraceae) through start codon targeted (SCoT) markers. Forty-two specimens of said species were collected from 11 different regions of Iran. Ten primers revealed 131 amplifications ranging from 200 bp to 3 kbp, of which 102 (77.86%) were polymorphic. Polymorphism information content (PIC) ranged from 0.37 to 0.50 with an average of 0.43, effective multiplex ration (EMR) from 1 to 4.11 and marker index (MI) from 0.006 to 0.59. Based on the analysis of molecular variance (AMOVA), the genetic variation within populations (72%) was higher than that of those among populations (28%). Overall, the highest mean for Nei’s gene diversity (0.18), Shannon index (0.27) and percentage of polymorphic loci (47.83) were observed in W. Azarbaijan populations, similarly the highest mean of total heterozygosity (HT) and subpopulation heterozygosity (HS) were found to be 0.18 and 0.07 in W. Azarbaijan and Golestan populations, respectively. The high genetic differentiation (GST = 1) showed significant genetic variation in Razavi Khorasan, N. Khorasan, Kurdistan, and Hamedan populations. Neighbor-Joining and population structure analysis divided C. virgata populations into six main clusters. The current study showed that, SCoT marker was efficient in assessing the genetic variation among different populations of the studied species.

Keywords

Main Subjects


Article Title [Persian]

تنوع ژنتیکی بین جمعیت‌های مختلف گل‌گندم بوته‌ای در ایران با استفاده از نشانگرهای SCoT

Authors [Persian]

  • الهه قاسمی 1
  • زینب طلوعی 2
1 دانش‌آموخته کارشناسی ارشد بیوشیمی، گروه زیست‌شناسی سلولی و مولکولی، دانشکده شیمی، دانشگاه کاشان، کاشان، ایران
2 استادیار گروه زیست‌شناسی سلولی و مولکولی، دانشکده شیمی، دانشگاه کاشان، کاشان، ایران
Abstract [Persian]

هدف از مطالعه حاضر، شناسایی تنوع ژنتیکی گیاه گل‌گندم بوته‌ای (Centaurea virgata Lam.) متعلق به کاسنیان از طریق نشانگر SCoT است. به این منظور، 42 نمونه از گونه مذکور از 11 منطقه مختلف ایران جمع‌آوری شد. ده پرایمر 131 باند از اندازه 200 تا 3000 جفت باز را ایجاد کردند که 102 باند (86/77%) چندشکل بودند. محتوای اطلاعاتی چندشکلی (PIC) 37/0 تا 50/0 با میانگین 43/0، نسبت چندگانه مؤثر (EMR) از 1 تا 11/4 و شاخص نشانگر (MI) از 006/0 تا 59/0 متغیر بود. براساس تجزیه و تحلیل واریانس مولکولی (AMOVA) تنوع ژنتیکی، در درون جمعیت‌ها (72%) بیشتر از بین جمعیت‌ها (28%) وجود داشت. در مجموع، بیشترین میانگین تنوع ژنی Nei (18/0)، شاخص شانون (27/0) و درصد جایگاه‌های چندشکلی (83/47) در جمعیت‌های آذربایجان‌غربی مشاهده شد. همچنین، بیشترین میانگین هتروزیگوتی کل (HT) و هتروزیگوتی درون جمعیتی (Hs) به ترتیب با میزان 18/0 و 07/0 در جمعیت‌های آذربایجان‌غربی و گلستان به دست آمد. تمایز ژنتیکی بالا (GST = 1) تنوع ژنتیکی قابل‌توجهی را در جمعیت‌های خراسان‌رضوی، خراسان‌شمالی، کردستان و همدان نشان داد. آنالیز خوشه‌ای با روش NJ و تحلیل ساختار جمعیت، جمعیت‌های C. virgata را به شش خوشه اصلی تقسیم کرد. مطالعه حاضر نشان داد که نشانگر SCoT در ارزیابی تنوع ژنتیکی در بین جمعیت‌های مختلف گونه مورد بررسی کارآمد است. 
 

Keywords [Persian]

  • انگشت‌نگاری دی‌اِن‌اِی
  • چندشکلی
  • فاصله ژنتیکی
  • کاسنیان
  • نشانگر مولکولی
Abd-dada, H., Bouda, S., Khachtib, Y.  Bella, Y.A. & Haddioui, A. 2023. Use of ISSR markers to assess the genetic diversity of an endemic plant of Morocco (Euphorbia resinifera O. Berg). Journal of Genetic Engineering and Biotechnology 21(1): 91. DOI: 10.1186/s43141-023-00543-4.
Adhikari, S., Biswas, A., Saha, S., Bandyopadhyay, T.K. & Ghosh, P. 2022. AFLP-based assessment of genetic variation in certain Indian elite cultivars of Cymbopogon species. Journal of Applied Research on Medicinal and Aromatic Plants 29: 100372. DOI: 10.1016/j.jarmap.2022.100372.
Agarwal, M., Shrivastava, N. & Padh, H. 2008 Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports 27: 617–631. DOI: 10.1007/s00299-008-0507-z.
Atasagun. B. 2022. Assessment of the genetic diversity of a critically endangered species Centaurea amaena (Asteraceae). Archives of Biological Sciences 74(4): 325–332. DOI: 10.2298/ABS220826031A.
Atia, M.A.M., El-Moneim, D.A., Abdelmoneim, T.K., Reda, E.H., Shakour, Z.T.A., El-Halawany, A.M., El-Kashoury, E.S.A., Shams, K.H., Abdel-Azim, N.S. & Hegazy, M.E.F. 2021. Evaluation of genetic variability and relatedness among eight Centaurea species through CAAT-box derived polymorphism (CBDP) and start codon targeted polymorphism (SCoT) markers. Biotechnology & Biotechnological Equipment 35(1): 1230–1237. DOI: 10.1080/13102818.2021.1960891.
Bassin, S., Kölliker, R., Cretton, C., Bertossa, M., Widmer, F., Bungener, P. & Fuhrer, J. 2004. Intra-specific variability of ozone sensitivity in Centaurea jacea L., a potential bioindicator for elevated ozone concentrations. Environmental Pollution 131(1): 1–12. DOI: 10.1016/j.envpol.2004.02.014.
Burridge, A.J., Winfield, M., Przewieslik-Allen, A., Edwards, K.J., Siddique, I., Barral-Arca, R., Griffiths, S., Cheng, S., Huang, Z., Feng, C., Dreisigacker, S., Bentley, A.R., Brown-Guedira, G. & Barker, G.L. 2024. Development of a next generation SNP genotyping array for wheat. Plant Biotechnology Journal 22(8): 2235–2247. DOI: 10.1111/pbi.14341.
Collard, B.C.Y. & Mackill, D.J. 2009. Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology Reports 27: 86–93. DOI: 10.1007/s11105-008-0060-5.
Essa, N.M., Ibrahim, A.A. & Soliman, M.I. 2024. Association study between some cultivated species and their wild relatives from Apiaceae, Asteraceae and Brassicaceae families based on molecular and DNA barcoding in Egypt. Genetic Resources and Crop Evolution 71: 1125–1143. DOI: 10.1007/s10722-023-01681-x.
Etminan, A., Pour-Aboughadareh, A., Noori, A., Ahmadi-Rad, A., Shooshtari, L., Mahdavian, Z. & Yousefiazar-Khanian, M. 2018. Genetic relationships and diversity among wild Salvia accessions revealed by ISSR and SCoT markers. Biotechnology & Biotechnological Equipment 32(3): 610e617. DOI: 10.1080/13102818.2018.1447397.
Evanno, G., Regnaut, S. & Goudet, J. 2005. Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology 14: 2611e2620. DOI: 10.1111/j.1365-294X.2005.02553.x.
Falush, D., Stephens, M. & Pritchard, J.K. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164(4): 1567–1587. DOI: 10.1093/genetics/164.4.1567.
Ferriol, M., Garmendia, A., Ruiz, J.J., Merle, H. & Boira, H. 2012. Morphological and molecular analysis of natural hybrids between the diploid Centaurea aspera L. and the tetraploid C. seridis L. (Compositae). Plant Biosystems 146(Suppl.):
86–100.‏ DOI: 10.1080/11263504.2012.727878.
Freville, H., Justy, F. & Olivieri, I. 2001. Comparative allozyme and microsatellite population structure in a narrow endemic plant species, Centaurea corymbosa Pourret (Asteraceae). Molecular Ecology 10(4): 879–89. DOI: 10.1046/j.1365-294x.2001.01249.x.
Funk, V.A., Bayer, R.J., Keeley, S., Chan, R., Watson, L., Gemeinholzer, B., Schilling, E., Panero, J.L., Baldwin, B.G., Garcia- Jacas, N., Susanna, A. & Jansen, R.K. 2005. Everywhere but Antarctica: using a super tree to understand the diversity and distribution of the Compositae. Biologiske Skrifter 55: 343–374. https://repository.si.edu/handle/10088/11397.
Garcia-Jacas, N., Susanna, A., Mozaffarian, V. & Ilarslan, R. 2000. The natural delimitation of Centaurea (Asteraceae: Cardueae): ITS sequence analysis of the Centaurea jacea group. Plant Systematics and Evolution 223(3): 185–199. DOI: 10.1007/BF00985278.
Ghasemi, E. & Toluei, T. 2020. Intraspecific variations and biological relationships of different populations of Centaurea virgata Lamark (Asteraceae) in Iran. Iranian Journal of Genetics and Plant Breeding 9(1): 61–69. DOI: 20.1001.1.22519610.2020.9.1.7.9.
Gulsen, O., Sever-Mutlu, S., Mutlu, N., Tuna, M., Karaguzel, O., Shearman, R.C., Riordan, T.P. & Heng-Moss, T.M. 2009. Polyploidy creates higher diversity among Cynodon accessions as assessed by molecular markers. Theoretical and Applied Genetics 118: 1309–1319. DOI: 10.1007/s00122-009-0982-9.
Hellwig, F.H. 2004. Centaureinae (Asteraceae) in the Mediterranean-history of ecogeographical radiation. Plant Systematics and Evolution 246(3–4): 137–162.‏ DOI: 10.1007/s00606-004-0150-2.
Huang, W., Zhao, X., Li, Y. & Lian, J. 2016. Effects of environmental factors on genetic diversity of Caragana microphylla in Horqin sandy land, northeast China. Ecology and Evolution 6(22): 8256–8266. DOI: 10.1002/ece3.2549.
Ismail, R.Y., Muhammed, J.J. & Sinjare, D.Y. 2024. Phylogenetic study of ten species from Centaurea (Asteraceae) in Duhok city, Kurdistan region-Iraq. Science Journal of University of Zakho 12(3): 277–284. DOI: 10.25271/sjuoz.2024.12.3.1279.
Jedrzejczyk, I. 2020. Genome size and SCoT markers as tools for identification and genetic diversity assessment in Echinacea genus. Industrial Crops and Products 144: 112055. DOI: 10.1016/j.indcrop.2019.112055.
Jèssica, R., López-Pujol, J., Carnicero, P., Susanna, A. & Garcia-Jacas, N. 2020. The Centaurea alba complex in theIberian Peninsula: gene flow, introgression, and blurred genetic boundaries. Plant Systematics and Evolution 306(2): 1–21. DOI: 10.1007/s00606-020-01669-5.
Kader, A., Sinha, S.N. & Ghosh, P. 2023. ISSR markers endorsed genetically stable plants regeneration of neem (Azadirachta indica A. Juss.) through indirect organogenesis using different explants. Molecular Biology Reports 50(9): 7305–7317. DOI: 10.1007/s11033-023-08655-3.
Kazemeini, F., Asri, Y., Mostafavi, G., Kalvandi, R. & Mehregan, I. 2020. RAPD-based evaluation of genetic diversity among populations of the Iranian endemic species Rhabdosciadium aucheri Boiss. (Apiaceae). Molecular Biology Reports 47(12): 9345–9352. DOI: 10.1007/s11033-020-06028-8.
Khanam, S., Sham, A., Bennetgen, J.L. & Mohammed, A.M.A. 2012. Analysis of molecular marker-based characterization and genetic variation in date palm (Phoenix dactylifera L.). Australian Journal of Crop Science 6(8): 1236–1244. https://www.cropj.com/khanam_6_8_2012_1236_1244.pdf.
Lopez, L. & Barreiro, R. 2013. Genetic guidelines for the conservation of the endangered polyploid Centaurea borjae (Asteraceae). Journal of Plant Research 126(1): 81–93.‏ DOI: 10.1007/s10265-012-0497-3.
López-Vinyallonga, S., López-Pujol, J., Constantinidis, T., Susanna, A. & Garcia-Jacas, N. 2015. Mountains and refuges: Genetic structure and evolutionary history in closely related, endemic Centaurea in continental Greece. Molecular Phylogenetics and Evolution 92: 243–54. DOI: 10.1016/j.ympev.2015.06.018.
Lovejoy, T.E & Hannah, L.J. 2005. Climate Change and Biodiversity, Yale University Press, New Haven, CT. 
Mallón, R., Rodríguez-Oubiña, J. & González, M.L. 2010. In vitro propagation of the endangered plant Centaurea ultreiae: assessment of genetic stability by cytological studies, flow cytometry and RAPD analysis. Plant Cell, Tissue and Organ Culture 101(1): 31–39.‏ DOI: 10.1007/s11240-009-9659-y.
Mameli, G., Filigheddu, R., Binelli, G. & Meloni, M. 2008. The genetic structure of the remnant populations of Centaurea horrida in Sardinia and associated islands. Annals of Botany 101(5): 633–640.‏ DOI: 10.1093/aob/mcn012.
Moreyra, L.D., Márquez, F., Susanna, A., Garcia-Jacas, N., Vázquez, F.M. & López-Pujol, J. 2021. Genesis, evolution, and genetic diversity of the hexaploid, narrow endemic Centaurea tentudaica. Diversity 13(2): 72. DOI: 10.3390/d13020072.
Mukhopadhyay, M., Mondal, T.K. & Chand, P.K. 2016. Biotechnological advances in tea (Camellia sinensis [L.] O. Kuntze): a review. Plant Cell Reports 35(2): 255–287. DOI: 10.3390/d13020072.
Nei, M. & Li, W.H. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. The Proceedings of the National Academy of Sciences 76(10): 5269–5273. DOI: 10.1073/pnas.76.10.5269.
Novakovi´c, J., Jana´ckovi´c, P., Susanna, A., Lazarevi´c, M., Borši´c, I., Milanovici, S., Lakuši´c, D., Zlatkovi´c, B., Marin, P.D. & Garcia-Jacas, N. 2022. Molecular insights into the Centaurea Calocephala complex (Compositae) from the Balkans - Does phylogeny match systematics? Diversity 14(5): 394. DOI: 10.3390/d14050394.
Nurmansyah Alghamdi, S.S., Migdadi, H.M., Khan, M.A. & Afzal, M. 2020. AFLP-based analysis of variation and population structure in mutagenesis induced Faba Bean. Diversity 12(8): 303. DOI: 10.3390/d12080303.
Page, R.D. 1996. Tree View: an application to display phylogenetic trees on personal computers. Bioinformatics 12(4): 357–358. DOI: 10.1093/bioinformatics/12.4.357.
Peakall, R. & Smouse, P.E. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28(19): 2537–2539. DOI: 10.1093/bioinformatics/bts460.
Plants of the World Online (POWO). Facilitated by the Royal Botanic Gardens, Kew [Published
on the Internet, cited 5 Aug. 2024]. https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:330045-2.
Pritchard, J.K., Stephens, M. & Donnelly, P. 2000. Inference of population structure using multi locus genotype data. Genetics 155(2): 945–959. DOI: 10.1093/genetics/155.2.945.
Quinones-Perez, C.Z., Saenz Romero, C. & Wehenkel, C. 2014. Genetic diversity and conservation of Picea chihuahuana Martinez: a review. African Journal of Biotechnology 13(28): 2786–2795. DOI: 10.5897/AJB2014.13645.
Rai, MK. 2023. Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects. Planta 257(2): 34. DOI: 10.1007/s00425-023-04067-6.
Rechinger, K.H. 1987. Flora iranica: Akademische Druck-u. Verlagsanstalt: Graz.
Doyle, J.J. & Doyle, J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11–15. https://worldveg.tind.io/record/33886.
Samarina, L.S., Malyarovskaya, V.I., Reim, S., Yakushina, L.G., Koninskaya, N.G., Klemeshova, K.V., Shkhalakhova, R.M., Matskiv, A.O., Shurkina, E.S., Gabueva, T.Y., Slepchenko, N.A. & Ryndin, A.V. 2021. Transferability of ISSR, SCoT and SSR markers for Chrysanthemum × Morifolium Ramat and genetic relationships among commercial Russian cultivars. Plants 10(7): 1302. DOI: 10.3390/plants10071302.
Serrote, C.M.L., Reiniger, L.R.S., Silva, K.B., Rabaiolli, S.M.D.S. & Stefanel, C.M. 2020. Determining the polymorphism information content of a molecular marker. Gene 726: 144175. DOI: https://doi.org/10.1016/j.gene.2019.144175.
Smith, J.S.C., Chin, E.C., Shu, H., Smith, O.S., Wall, S.J., Senior, M.L., Mitchell, S.E., Kresovich, S. & Ziegle, J. 1996. An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.) comparisons with data from RFLPs and pedigree. Theoretical and Applied Genetics 95: 163–173. DOI: 10.1007/s001220050544.
Sözen, E. & Özaydın, B. 2009. A preliminary study on the genetic diversity of the critically endangered Centaurea nivea (Asteraceae). Annales
Botanici Fennici 46(6): 541–548. DOI: 10.5735/085.046.0606.
Sozen, E. & Ozaydin, B. 2010. A study of genetic variation in endemic plant Centaurea wiedemanniana by using RAPD markers. Ecology 19(77): 1–8.‏ DOI: 10.5053/ekoloji.2010.771.
Swofford, D.L. 2003. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
Uysal, T., Özel, E., Bozkurt, M. & Ertuğrul, K. 2012. Genetic diversity in threatened populations of the endemic species Centaurea lycaonica Boiss. & Heldr. (Asteraceae). Research Journal of Biological Sciences 2(3): 110–116. https://api.semanticscholar.org/CorpusID:73718811.
Wang, H., Bai, Y. & Biligetu, B. 2024. Effects of SNP marker density and training population size on prediction accuracy in alfalfa (Medicago sativa L.) genomic selection. The Plant Genome 17: e20431. DOI: 10.1002/tpg2.20431.
Wolanin, M., Klichowska, E., Jedrzejczyk, I., Rewers, M. & Nobis, M. 2023. Taxonomy and distribution of Taraxacum sect. Erythrosperma (Asteraceae) in Poland. PhytoKeys 224: 1–88. DOI: 10.3897/phytokeys.224.99463.
Wu, K., Liu, Y., Yang, B., Kung, Y., Chang, K. & Lee, M. 2022. Rapid discrimination of the native medicinal plant Adenostemma lavenia from its adulterants using PCR-RFLP. Peer Journal 10: e13924. DOI: 10.7717/peerj.13924.
Yeh, F.C. & Boyle, T.J.B. 1997. Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belgian Journal of Botany 129: 157–163. https://www.sid.ir/paper/571184/en.
 
Volume 25, Issue 2 - Serial Number 71
December 2024
Pages 157-172
  • Receive Date: 24 August 2024
  • Revise Date: 01 October 2024
  • Accept Date: 12 October 2024
  • Publish Date: 28 December 2024