Comparison of ISSR and AFLP markers in assessing genetic diversity among Nettle (Urtica dioica L.) populations.

Document Type : Original research paper

Authors

1 Department of Biotechnology and Plant Breeding, Sari Agricultural Sciences and Natural Resources University, Sari, Iran

2 Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, Sari, Iran

Abstract

Urtica dioica is an important medicinal plant which is widely distributed in Mazandaran province (North of Iran). In this study for the first time Amplified Fragment Length Polymorphism (AFLP) and Inter-simple Sequence Repeat (ISSR) markers were used for detection of genetic polymorphism in Mazandaran nettle. Ten AFLP primer combinations and seventeen ISSR markers were utilized. AFLP produced 830 scorable bands out of which 90.21% were polymorphic. ISSR primers amplified 234 bands, 181 being polymorphic (77.3%). Average heterozygosity for AFLP and ISSR markers were 0.25, 0.23 respectively. Marker Index obtains 22.25 for AFLP and 15.57 for ISSR. The number of cluster computed was same for both molecular makers but location of samples in branch were different. The total compare of these two marker systems shown AFLP marker was a useful tool for detection of U. dioica’sgenetic diversity. This plant is very variable and is genetically distinct in east, west and north of Mazandaran.

Keywords

[1]      Bharmauria, V., Narang, N., Verma, V., and Sharma, Sh. 2009. Genetic variation and polymorphism in the Himalayan nettle plant Urtica dioica based on RAPD marker. Journal of Medicinal Plants Research. 3: 166-170.
 [2]     Boczkowska, M., Bulin´ska-Radomska, Z., Nowosielski, J. 2012. AFLP analysis of genetic diversity in five accessions of Polish runner bean (Phaseolus coccineus L.). Genetic resources and crop evolution. 59: 473–478.
 [3]     Doyle, JJ. and Doyle, JL. 1990.  Isolation of plant DNA from fresh tissue. Focus. 12: 13–15.
 [4]     Grime, J. P., Hodgson, J. G., Hunt, R. 2007. Comparative Plant Ecology: A Functional Approach to Common British Species, 2 nd edn. Castlepoint Press, Colvend, UK.
 [5]     Guil-Guerrero, J. L., Rebolloso-Fuentes, M.M., Isasa, M.T. 2003. Fatty acids and carotenoids from Stinging Nettle (Urtica dioica L.). Journal of Food Composition and Analysis, 16: 111-119.
 [6]     Jaccard, P. 1912. The distribution of the flora in the alpine zone. New phytologist 11: 37-50.
 [7]     Jianming, G., Shougong, Z., Liwanag, Q., Young, Z., Chunguo., W ., Wenqin,  S. 2006. ISSR and AFLP identification and genetic relationships of Chinese elite accessions from the Populus. Annals of forest science. 63: 499-506.
 [8]     Kalpana, D., Choi, S.H., Choi, T.K., Senthil, K., Lee, Y. S. 2012. Assessment of genetic diversity among varieties of mulberry using RAPD and ISSR fingerprinting. Scientia Horticulturae. 134: 79–87.
 [9]     Liu, L.W., Zhao, L.P., Gong, Y.Q., Wang, M.X., Chen, L.M., Yang, J.L., Wang, Y., Yu, F.M., Wang, L.Z. 2008. DNA fingerprinting and genetic diversity analysis of late-bolting radish cultivars with RAPD, ISSR and SRAP markers. Scientia Horticulturae. 116: 240–247.
 [10]   Lu, Z.X., Wang, Y.H., Peng, Y.H., Korpelainen, H., Li, C.Y. 2006. Genetic diversity of Populus cathayana Rehd populations in southwestern china revealed by ISSR markers. Plant Science. 170: 407–412.
 [11]   Mantel, N.A. 1967. The detection of disease clustering and a generalized regression approach. Cancer research. 27: 209–220.
 [12]   Maras, M., Sustar-Vozilc, J., Javornik, B., Meglic. V. 2008. The efficiency of AFLP and SSR markers in genetic diversity estimation and gene pool classification of common bean (Phaseolus vulgaris L). Acta agriculturae slovenica. 91: 87-96.
 [13]   Mardi, M., Naghavi, M.R., Pirseyedi, S.M., Kazemi Alamooti, M., Rashidi Monfared, S., Ahkami, A.H., Omidbakhsh, M.A., Alavi, N.S., Salehi Shanjani, P., Katsiotis, A. 2011. Comparative Assessment of SSAP, AFLP and SSR Markers for Evaluation of Genetic Diversity of Durum Wheat (Triticum turgidum L. var. durum). Journal of Agricultural Science and Technology. 13: 905-920.
 [14]   Moghaddama M., Omidbiagi, R., Naghavi, M.R. 2011. Evaluation of genetic diversity among Iranian accessions of Ocimum spp. using AFLP markers. Biochemical Systematics and Ecology 39: 619–626.
 [15]   Muminovic, J., Merz, A., Melchinger, A. E. 2005. Genetic structure and diversity among Radish varieties as Inferred from AFLP and ISSR analysis. Journal of the American Society for Horticultural Science. 130: 19-87.
 [16]   Potokina, E., Blattner, F.R., Alexandrova, T., Bachmann, K. 2002. AFLP diversity in the common vetch (Vicia sativa L.) on the world scale. Theor Appl Genet 105: 58–67.
 [17]   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. Molecular breeding. 2: 225–238.
 [18]   Qian, W., Ge, S., Hong, D. Y. 2001. Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers. Theoretical and Applied Genetics. 102: 440–44.
 [19]   Reddy, M.P., Sarla, N., Siddiq, E.A. 2002. Inter-simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128: 9–17.
 [20]   Roldan-Ruiz, I., Dendauw, J., Van Bockstaele, E., Depicker, A., De Loose, M. 2000. AFLP markers reveal high polymorphic rates in rye grasses (Lolium spp.). Molecular Breeding 6:125–134.
 [21]   Sarwat, M., Das, S., Srivastava, P.S. 2008. Analysis of genetic diversity through AFLP, SAMPL, ISSR and RAPD markers in Tribulus terrestris, a medicinal herb. Plant cell reports. 27: 519–528.
 [22]   Shahi-Gharahlar, F.A., Zamani, Z., Fatahi, R., Bouzari, N. 2011. Estimation of genetic diversity in some Iranian wild Prunus subgenus Cerasus accessions using inter-simple sequence repeat (ISSR) markers Biochemical Systematics and Ecology. 39: 826–833.
 [23]   Srutek, M. and Teckelmann, M. 1998. Review paper: Arbuscular mycorrhiza: Biological, chemical, and molecular aspects. Journal of chemical ecology 29: 1955-1979.
 [24]   Stace, C.A., 2004. Interactive Flora of the British Isles (DVD-ROM). ETI Information Services Ltd., University of Amsterdam, Amsterdam, The Netherlands.
 [25]   Taylor, K. 2009. Biological Flora of the British Isles: Urtica dioica L. Journal of Ecology. 97: 1436–1458.
 [26]   Vos, P., Hogers, R., Bleeker, M., Reijans, M., van de Lee, T., Hornes, M., Frijters, A., Pot, J., Peleman, J., Kulper, M., Zabeau, M. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research. 23:  4407-4414.
 [27]   Williams, J. G., Kubelik, A.R., Livak, K.J., Rafalski, J.A., Tingery, S.V. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research. 18: 6531-6535.
 [28]   Xiu-qin, Ci., Jun-qiu, Chen., Qiao-ming, Li., Jie, Li. 2008. AFLP and ISSR Analysis Reveals High Genetic Variation and Inter-population Differentiation in Fragmented Populations of the Endangered Litsea szemaois (Lauraceae) from South-West China. Plant Systematics and Evolution. 273: 237-246.
 [29]   Zietkiewicz, E., Rafalski, A., Labuda, D. 1994. Genome finger printing by simple sequence repeat (SSR) – anchored polymerase chain reaction amplification. Genomics. 20: 176–183.
Volume 4, Issue 1
June 2016
Pages 10-16
  • Receive Date: 05 October 2015
  • Revise Date: 01 May 2016
  • Accept Date: 16 May 2016
  • First Publish Date: 01 June 2016