Assessment of SCoT and DAMD molecular markers in genetic diversity and species delimitation of three moss species grown in Iran

Document Type : Research paper


1 Young Researchers and Elite Club, North Branch, Islamic Azad University, P. O. Box: 16511-53311, Tehran, Iran.

2 Young Researchers and Elite Club, North Branch, Islamic Azad University, P. O. Box: 16511-53311, Tehran, Iran


This study was conducted to assess the efficacy of SCoT and DAMD molecular markers in genetic diversity of three moss species and compare them with ISSR marker. Another objective was to evaluate the suitability of these DNA markers in species identification (delimitation) in three moss species, including Neckera complanata, Homalothecium sericeum and Neckera crispa. To prevent ecological impact on results, all samples were collected from one locality. PIC and MI in three markers showed closely ranged values. Our results revealed that the average values of Rp and the number of species-specific bands in SCoT primers were more than those of DAMD and ISSR. It showed considerable capability of SCoT marker in discriminating individuals. The highest value of genetic parameters Na (1.08), He (0.15) and I (0.23) were obtained with SCoT marker showing the power of this marker in genetic diversity analysis. Moreover, dendrograms produced from SCoT and DAMD data indicated similar results in the placement of closely related species. ‏SCoT markers were shown to be more efficient than DAMD and ISSR markers based on the multiplex ratio (EMR), Rp, genetic diversity parameters (Na, He, I) and the number of species-specific bands. The findings demonstrated that the SCoT and DAMD markers could be applied for the estimation of genetic relationships and separation of two closely related genera. This is the first report of its type on the genetic diversity of mosses by application of SCoT and DAMD.


Amirmoradi B., Talebi R., and Karami E. (2012). Comparison of genetic variation and differentiation among annual Cicer species using start codon targeted (SCoT) polymorphism, DAMD-PCR, and ISSR markers. Plant Systematics and Evolution, 298(9): 1679-1689.
Atherton I., Bosanquet S. D. S., and Lawley M. (2010). Mosses and liverworts of Britain and Ireland - a field guide. British Bryological Society.
Bhattacharyya P., Kumaria S., Kumar S., and Tandon P. (2013). Start Codon Targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl. an endangered medicinal orchid species. Gene, 529: 21–26.
Boisselier-Dubayle M. C., and Bischler H. (1994). A combination of molecular and morphological characters for delimitation of taxa in European Porella. Journal of Bryology,18: 1–11.
Boisselier-Dubayle M. C., Jubier M. F., Lejeune B., and Bischler H. (1995). Genetic variability in the three subspecies of Marchantia polymorpha (Hepaticae) isozymes, RFLP and RAPD markers. Taxon,44: 363–376.
Budke M., Bernard E. C., Gray D.J., Huttunen S., Piechulla B., and Trigiano R. N. (2018). Introduction to the Special Issue on Bryophytes. Critical Reviews in Plant Sciences, 37: 101-112.
Crespo Pardo D., Terracciano S., Giordano S., and Spagnuolo V. (2014). Molecular Markers Based on PCR Methods: A Guideline for Mosses. Cryptogamie, Bryologie, 35(3): 229-246.
Etminan A, Pour-Aboughadareh A, and Mohammadi R. (2016). Applicability of start codon targeted (SCoT) and inter-simple sequence repeat (ISSR) markers for genetic diversity analysis in durum wheat genotypes. Biotechnology & Biotechnological Equipment, 30: 1075–1081.
Freeland J. R., Kirk H., and Peterson S. D. (2011). Molecular ecology. 2nd ed. UK: Wiley-Blackwell.
Ghasemzadeh Baraki S.,Nikzat Siahkolaee S., and Mousavi,A. (2018). Optimization of the genomic DNA extraction in some mosses. Rostaniha, 19(2): 165–175.
Glime, J. M. (2017). Bryophyte Ecology. Ebook sponsored by Michigan Technological University and the International Association of Bryologists.
Gorji A. M., Poczai P., Polgar Z., and Taller J. (2011). Efficiency of arbitrarily amplified dominant markers (SCoT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato. Am Potato, 88: 226–237.
Guo D-L., Zhang J. Y., and Liu C. H. (2012). Genetic diversity in some grape varieties revealed by SCoT Analyses. Molecular Biology Reports, 39: 5307–5313.
Hammer O. M, Harper D. A. T., and Ryan P. D. (2012). PAST: Paleontological Statistics software package for education and data analysis. Palaeontologia Electa, 4: 9.
Heidari S. H., Azizinezhad R., and Haghparast R. (2017). Investigation of genetic diversity in Triticum turgidum L. var. durum using agro-morphological characters and molecular markers. Indian Journal of Genetics, 77(2): 242-250.
Heikrujam M., Kumar J., and Agrawal V. (2015). Genetic diversity analysis among male and female Jojoba genotypes employing gene targeted molecular markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) markers. Meta Gene, 5: 90-97.
Luo C. H., Chen X. H., Ou Shi-jin H., Mei-ping G., Brown S. J., Tondo C. T., and Schnell R. J. (2011). Genetic diversity of mango cultivars estimated using SCoT and ISSR markers. Biochemical Systematics and Ecology, 39: 676–684.
Mcdaniel S. F., Willis J. H., and Shaw A. J. (2007). Linkage map reveals a complex basis for segregation distortion in an interpopulation cross in the moss Ceratodon purpureus. Genetics, 176: 2489-2500.
Nagy S., Poczai P., Cernák I, Gorji A. M, Hegedűs G., and Taller J. (2012). PICcalc: an online program to calculate polymorphic information content for molecular genetic studies. Biochemical Genetics., 50(9-10): 670-672.
Natcheva R., and Cronberg N. (2007). Recombination and introgression of nuclear and chloroplast genomes between the peat moss, Sphagnum capillifolium and Sphagnum quinquefarium. Molecular Ecology, 16: 811-818.
Oztopcu-Vatan P., Savaroglu F., Filik-Iscen C., Kabadere S., Ilhan S., and Ruhi U. (2011). Antimicronial and antiproliferative activities of Homalothecium sericeum (Hedw.) Schimp. Extracts. Fresenius Environmental Bulletin, 20: 2a.
Ozturk M., Gokler I., and Altay V. (2018). Medicinal bryophytes distributed in Turkey. Khalid Rehman Hakeem (Eds.), Plant and Human Health, 1: 323-348.
Pakseresht F., Talebi R., and 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. Physiology and Molecular Biology of Plants, 19(4): 563–574.
Peakall R., and Smouse P. E. (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6: 288-295.
Pour-Aboughadareh A., Ahmadi J., Mehrabi A. A., and Moghaddam M., and Etminan A. (2018). Insight into the genetic variability analysis and relationships among some Aegilops and Triticum species, as genome progenitors of bread wheat, using SCoT markers. Plant Biosystems, 152: 694-703.
Pour-Aboughadareh A., Mohmoudi A. M., Ahmadi J., Moghaddam M., and Mehrabi A. A. (2017). Agro-morphological and molecular variability in Triticum boeoticum accessions from Zagros Mountains. Iran Genet Resour Crop Evol, 64: 545–556.
Rajesh M. K.., Sabana A. A., Rachana K. E., Rahman, S., Jerard B. A., and Karun A. (2015). Genetic relationship and diversity among coconut (Cocos nucifera L.) accessions revealed through SCoT Analysis. 3 Bitech, 5: 999–1006.
Rosengren F., Cronberg N., Reitalu T., and Prentice H. C. (2013). Genetic variation in the moss Homalothecium lutescens in relation to habitat age and structure. Botany, 91: 431- 441.
Sawicki, J., and Szczecińska, M. (2011). A comparison of PCR-based markers for the molecular identification of Sphagnum species of the section Acutifolia. Acta Societatis Botanicorum Poloniae, 80(3): 185-192
Sivaprakash K. R., Prasanth S. R., Mohanty B. P., and Parida A. (2004). Genetic diversity of black gram landraces as evaluated by AFLP markers. Current Science, 86: 1411-1415.
Skotnicki M. L., Ninham J. A., and Selkirk P. M. (2000). Genetic diversity, mutagenesis and dispersal of Antarctic mosses—a review of progress with molecular studies. Antarctic Science, 12: 363–373.
Skotnicki M. L., Selkirk P. M., Broady P., Adam K. D., and Ninham J. A. (2001). Dispersal of the moss Campylopus pyriformis on geothermal ground near the summits of Mount Erebus and Mount Melbourne, Victoria Land, Antarctica. Antarctic Science,13: 280–285.
Spagnuolo V., Muscariello L., Cozzolino S., Giordano S., Castaldo., and Cobianchi R. (2002). Polimorfismo di lunghezza di trnL (cpDNA) nel muschio Pleurochaete squarrosa (Brid.) Lindb. Proceedings of Annual Congress of Societa` Botanica Italiana, Lecce (Italy), 24–26, September.
Terracciano S., Giordano S., Bonini I., Miserere L., and Spagnuolo V. (2012). Genetic variation and structure in endangered populations of Sphagnum palustre L. in Italy: a molecular approach to evaluate threats and survival ability. Botany, 90: 966-975.
Weising K., Nybom H., Wolff K., and Kahl G. (2005). DNA Fingerprinting in plants. Principles, methods, and applications. 2nd ed. Boca Rayton, Fl.
Xiong F., Zhong R., Han Z., Jiang J., He L., Zhuang W., and Tang R. (2011). Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut (Arachis hypogaea L.) genotypes. Molecular Biolology Reports, 38: 3487–3494.
Yadav Ch., and Malik C. P. (2016). Molecular Characterization of Fennel (Foeniculum vulgare Mill.) accessions using Start Codon Targeted (SCoT) markers. Journal of Plant Science and Research, 32(1): 37-44.