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Genetic diversity of Thymus daenensis subsp. daenensis using SRAP markers

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Abstract

Thymus daenensis subsp. daenensis is an aromatic medicinal plant endemic to Iran and generally grows in high altitudes in Zagros Mountains range. Molecular markers provide valuable information about relative genetic relationships for facilitate breeding programs. Here, we used SRAP markers to estimate the genetic diversity of 79 T. daenensis accessions from 16 regions in Iran, located at extremes and the central regions of the Zagros range. Fourteen SRAP primer combinations (PCs) amplified 240 stable and reproducible fragments, of which 198 (82.5%) were polymorphic for all accessions. The PIC value for PCs ranged from 0.195 to 0.333 with an average of 0.284. Neighbor-joining tree constructed from Dice’s similarity matrix of SRAP data revealed two major groups and verified with the results of AMOVA (P < 0.001; genetic distance = 0.98). The Tc and Te groups included the accessions collected from the center and the extremes of the Zagros Mountains, respectively. The results showed that the current scattered distribution area of Iranian thyme is probably recent due mainly to anthropic pressures and limited gene flow via seed and/or pollen dispersal.

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References

  • Bassam B.J., Caetano Anolles C.G. & Gresshoff P.M. 1991. Fast and sensitive silver staining of DNA in polyacrylamide gel. Anal. Biochem. 196: 80–83.

    Article  CAS  PubMed  Google Scholar 

  • Ben El Hadj Ali I., Guetat A. & Boussaid M. 2012a. Interspecific relationships among two Tunisian Thymus taxa: Thymus capitatus Hoffm. et Link, and Thymus algeriensis Boiss. et Reut. using molecular markers. Afr. J. Biotechnol. 11: 8810–8819.

    CAS  Google Scholar 

  • Ben El Hadj Ali I., Guetat A. & Boussaid M. 2012b. Genetic diversity, population structure and relationships of Tunisian Thymus algeriensis Boiss. et Reut. and Thymus capitatus Hoffm. et Link, assessed by isozymes. Ind. Crops Prod. 36: 149–163.

    Article  CAS  Google Scholar 

  • Budak H., Shearman R.C., Parmaksiz I. & Dweikat I. 2004. Comparative analysis of seeded and vegetative biotype buffalo-grasses based on phylogenetic relationship using ISSRs, SSRs, RAPDs, and SRAPs. Theor. Appl. Genet. 109: 280–288.

    Article  CAS  PubMed  Google Scholar 

  • Chen M., Feng F., Sui X., Li M., Zhao D. & Han S. 2010. Construction of a framework map for Pinus koraiensis Sieb.et Zucc. using SRAP, SSR and ISSR markers. Trees 24: 685–693.

    Article  CAS  Google Scholar 

  • Excoffier L. & Smouse P.E. 1994. Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics 136: 343–359.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Excoffier L., Smouse P. & Quattro J. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479–491.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Excoffier L., Laval G. & Schneider S. 2005. Arlequin 3.01: An integrated software package for population genetics data analysis. Evol. Bioinfo. Online 1: 47–50.

    Article  CAS  Google Scholar 

  • Ferriol M., Pico B. & Nuez F. 2003. Genetic diversity of a germplasm collection of Cucurbita pepo using SRAP and AFLP markers. Theor. Appl. Genet. 107: 271–282.

    Article  CAS  PubMed  Google Scholar 

  • Ghasemi Pirbalouti A., Karimi A., Yousefl M., Enteshari S.H. & Golparvar A.R. 2011. Diversity of Thymus daenensis Celak in central and west of Iran. J. Med. Plants Res. 5: 319–323.

    Article  Google Scholar 

  • Hamrick J.L. & Godt M.J. 1996. Effects of life history traits on genetic diversity in plant species. Phil. Trans R Soc. Lond. B. 351: 1291–1298.

    Article  Google Scholar 

  • Huang C.Q., Yong-Fa Zhang Y.F., Liu G.D., Bai C.J. & Wang W.Q. 2012. Genetic diversity of Cynodon radiatus assessed by sequence-related amplified polymorphism markers. Biochem. Syst. Ecol. 40: 56–61.

    Article  CAS  Google Scholar 

  • Jalili A. & Jamzad Z. 1999. Red data book of Iran. Research Institute of Forests and Rangelands, Tehran, Iran

    Google Scholar 

  • Li G. & Quiros C.F. 2001. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor. Appl. Genet. 103: 455–461.

    Article  CAS  Google Scholar 

  • Li Y., Fan X., Shi T., Zhang Q. & Zhang Z. 2009. SRAP marker reveals genetic diversity in tartary buckwheat in China. Front Agric. China 3: 383–387.

    Article  Google Scholar 

  • Liu L., Zhu X., Gong Y., Song X., Wang Y., Zhao L. & Wang L. 2007. Genetic diversity analysis of radish germplasm with RAPD, AFLP and SRAP markers. Acta Hortic. 760: 125–130.

    CAS  Google Scholar 

  • Li-Wang L., Li-Ping Z., Yi-Qin G., Ming-Xia W., Li-Ming C., Jin-Lan Y., Yan W., Fan-Min Y. & Long-Zh W. 2008. DNA fingerprinting and genetic diversity analysis of late-bolting radish cultivars with RAPD, ISSR and SRAP markers. Sci. Hortic. 116: 240–247.

    Article  Google Scholar 

  • Murray M.G. & Thompson W.F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8: 4321–4325.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nickavar B., Mojab F. & Dolat-Abadi R. 2005. Analysis of the essential oils of two Thymus species from Iran. Food Chem. 90: 609–611.

    Article  CAS  Google Scholar 

  • Noroozie M. 2000. Study on distribution and factors affecting the extinct of some medicinal plants in Esfahan province. In: Proceeding of the 1st international congress on traditional medicine and materia medica, 6 November, Tehran

    Google Scholar 

  • Rahimmalek M., Bahreininejad B., Khorrami M. & Sayed Tabatabaei B.E. 2009. Genetic variability and geographic differentiation in Thymus daenensis subsp. daenensis, an endangered medicinal plant, as revealed by inter simple sequence repeat (ISSR) markers. Biochem. Genet. 47: 831–842.

    Article  CAS  PubMed  Google Scholar 

  • Reynolds J., Weir B.S. & Cockerham C.C. 1983. Estimation of the coancestry coefficient: basis for a short term genetic distance. Genetics 105: 767–779.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rohlf F.J. 1998. NTSYS-PC Numerical taxonomy and multivariate analysis system, Version 2.02. Exter Publications, Setauket, NY, pp. 1–31.

    Google Scholar 

  • Sajjadi S.E. & Khatamsaz M. 2003. Composition of the essential oil of Thymus daenensis Cleak. ssp. lancifolius (Cleak) Jalas. J. Essent. Oil Res. 15: 34–35.

    Article  CAS  Google Scholar 

  • Sangwan R.S., Sangwan N.S., Jain D.C., Kumar S. & Ranade A.S. 1999. RAPD profile based genetic characterization of chemotypic variants of Artemisia annua L. Biochem. Mol. Biol. Int. 47: 935–944.

    CAS  PubMed  Google Scholar 

  • Smith J.S.C., Chin E.C.L., Shu H., Smith O.S., Wall S.J., Senior M.L., Mitchell S.E., Kresovich S. & Zeigle J. 1997. An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): Comparison with data from RFLPs and pedigree. Theor. Appl. Genet. 95: 163–173.

    Article  CAS  Google Scholar 

  • Swofford D.L. 1999. PAUP: Phylogenetic Analysis Using Parsimony, Version 4.0b4a. Smithsonian Institution, Washington, DC, USA.

    Google Scholar 

  • Tarayre M. & Thompson J.D. 2002. Populations genetic structure of the gynodioecious Thymus vulgaris L. (Labiatae) in southern France. J. Evol. Biol. 10: 157–174.

    Article  Google Scholar 

  • Xie W., Zhang X., Cai H., Liu W. & Peng Y. 2010. Genetic diversity analysis and transferability of cereal EST-SSR markers to orchardgrass (Dactylis glomerata L.). Biochem. Syst. Ecol. 38: 740–749.

    Article  CAS  Google Scholar 

  • Yeh F.C. & Yang R.C. 1999. POPGENE Version 1.31. University of Albert and Tim Boyle, Center for International Research.

    Google Scholar 

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Authors and Affiliations

  1. Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 8415683111, Iran

    Majid Talebi & Mohsen Norouzi

  2. Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 8415683111, Iran

    Mehdi Rahimmalek

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  1. Majid Talebi
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  2. Mehdi Rahimmalek
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  3. Mohsen Norouzi
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Correspondence to Majid Talebi.

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Talebi, M., Rahimmalek, M. & Norouzi, M. Genetic diversity of Thymus daenensis subsp. daenensis using SRAP markers. Biologia 70, 453–459 (2015). https://doi.org/10.1515/biolog-2015-0059

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