Genetic assessment of some populations of the medicinal plant Caraway (Carum carvi) using RAPD and ISSR markers
Subject Areas : Geneticleila fahmideh 1 , Lila Jani pour 2 , Bahman Fazeli-Nasab 3
1 - Department of Plant Breeding and Biotechnology, University of Zabol, Zabol, Iran
2 - Department of Plant Breeding and Biotechnology, University of Zabol, Zabol, Iran
3 - Agricultural Research Center of Zabol University, Zabol, Iran
Keywords: Cluster analysis, genetic diversity, Carum carvi, Diversity Index, RAPD and ISSR markers,
Abstract :
RAPD and ISSR markers were used in the present study to determine genetic relationship and distance between some populations of Carum carvi. Amplification of genomic DNA all population using RAPD analysis yielded 126 fragments, where TIBMBA02 and TIBMBA08 had the minimum number of fragments (7) and TIBMBC05 had the maximum number of fragments, (22). ISSR marker yielded 79 fragments, where UBC112 and UBC809had the minimum (1) and maximum (15) fragments, respectively. The Diversity Index value of RAPD primers ranged from 0.8 (TIBMBA02) to 0.94 (TIBMBC05) and also Shanoon Diversity and Nei diversity were 0.57 and 0.38, respectively. In ISSR primers The Diversity Index value ranged from 0.0 (UBC112) to 0.92 (UBC809) and also Shanoon Diversity and Nei diversity were 0.57 and 0.39 respectively. According to ISSR and RAPD markers in combination, maximum genetic similarity (0.48) was observed between Kerman and Jandagh Carum carvi while the minimum similarity (0.115) was observed between Kerman and Neishabour Carum carvi with average 0.315. Also, cluster analysis segregated all populations into 3 groups according to geographical zone.
Agarwal, M., Shrivastava, N. and Padh, H. (2008). Advances in molecular marker techniques and their applications in plant sciences. Plant cell reports. 27 (4): 617-631.
Agrama, H., and Tuinstra, M. (2003). Phylogenetic diversity and relationships among sorghum accessions using SSRs and RAPDs. African Journal of Biotechnology. 2 (10): 334-340.
Alamdary, S, Safarnejad, A. and Nematzadeh, G. (2012). Using RAPD Marmer For Genetic Diversity Assessment of Several Thymus Species. Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research. 20(40):192- 201.
Anderson, J.A., Churchill, G., Autrique, J., Tanksley, S. and Sorrells, M. (1993). Optimizing parental selection for genetic linkage maps. Genome. 36 (1): 181-186.
Assessment, G.M. (2012). Recent Publications of F. James Rohlf. Evolution. 44: 665-683.
Bahmani, K., Noori, S. A. S., Darbandi, A. I. and Akbari, A. (2015). Molecular mechanisms of plant salinity tolerance: a review. Australian Journal of Crop Science. 9 (4): 321.
Bahraminejad, A., Mohammadi-Nejad, G., Abdul Kadir, K., Bin Yusop, M.R. and Samia, M. A. (2012). Molecular diversity of Cumin ('Cuminum cyminum' L.) using RAPD markers. Australian Journal of Crop Science. 6 (2): 194.
Bohn, M., Utz, H.F. and Melchinger, A.E. (1999). Genetic similarities among winter wheat cultivars determined on the basis of RFLPs, AFLPs, and SSRs and their use for predicting progeny variance. Crop Science. 39 (1): 228-237.
Botstein, D., White, R.L., Skolnick, M. and Davis, R.W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics. 32 (3): 314.
Dehghan-kohestani, S., Amin-Baghizadeh, A.G., Ranjbar, A. and Babaeian-jelodar, N. (2008). Genetic diversity of germplasm cumin [Bunium persicum (Boiss.) B. Fedtsch.] Kerman province using molecular markers RAPD. Quarterly Scientific-Research Medicinal and Aromatic Plants of Iran. 24 (4): 414-427.
Dellaporta, S.L., Wood, J. and Hicks, J.B. (1983). A plant DNA minipreparation: version II. Plant Molecular Biology Reporter. 1 (4): 19-21.
Domblides, A., Domblides, Kharchenko, E. V. and Potekhin, G. (2010). Study of genetic variation among parsley (Petroselinum crispum (Mill.) Nym.) samples using RAPD and ISSR markers. Moscow University Biological Sciences Bulletin. 65 (4): 152-154.
Echeverrigaray, S. and Agostini, G. (2006). Genetic relationships between commercial cultivars and Brazilian accessions of Salvia officinalis L. based on RAPD markers. Revista Brasileira de Plantas Medicinais, 8 (esp).
Fazeli-nasab, B. and Naghavi, M.R. (2011). Identification of Rust resistance among wheat cultiras by using SSRs markers. Journal of Agronomy Science. 4 (5): 81-88.
Gupta, P. (2010). Elements of biotechnology: Rastogi Publications.
Hashemi, H. and Safarnejad, A. (2010). The use of RAPD markers dor assessing the genetic diversity of Bunium persicum (Boiss) B. FEDTSCH populations. International Journal of Science and Nature. 1(2):202-208.
Jaccard, P. (1912). The distribution of the flora in the alpine zone. New Phytologist. 11 (2): 37-50.
Kafi, M., M.H, R.M., Kochaki, A. and Mplafiaei, A. (2000). Cumin, Produced and production technology: Ferdowsi University of Mashhad Institute Press.
Khaled, A., Motawea, M. and Said, A. (2015). Identification of ISSR and RAPD markers linked to yield traits in bread wheat under normal and drought conditions. Journal of Genetic Engineering and Biotechnology, 13(2): 243-252.
Lewontin, R.C. (1972). The apportionment of human diversity. In Evolutionary biology: Springer, 381-398.
Maccaferri, M., Stefanelli, S. Rotondo, F. Tuberosa, R. and Sanguineti, M.C. (2007). Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data. Genome, 50 (4):373-384.
Momeni, S., Shiran, B. and Razmjoo, K. (2006). Genetic variation in Iranian mints on the bases of RAPD analysis. Pakistan Journal of Biological Sciences. 9(10): 1898-1904.
Naghavi, M. R., Ghareyazi, B. and Hoseinisalekdeh, G. (2007). Molecular markers: Tehran University Press.
Nei, M. (1973). Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences. 70 (12): 3321-3323.
Nei, M. and Li, W.H. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences. 76 (10): 5269-5273.
Parashar, M., Jakhar, M. and Malik, C. (2014). A review on biotechnology, genetic diversity in cumin (Cuminum cyminum). International Journal of Life Science and Pharma Research. 4 (4): L17-L34.
Pasqualone, A., Lotti, C. and Blanco, A. (1999). Identification of durum wheat cultivars and monovarietal semolinas by analysis of DNA microsatellites. European Food Research and Technology. 210 (2): 144-147.
Prasad, M., Varshney, R., Roy, J., Balyan H. and Gupta, P. (2000). The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theoretical and Applied Genetics. 100 (3-4): 584-592.
Ranjbarian, P., Sadeghian, S., Shirazi, M., SarafNejad, A., Fazeli, M., Majlesi, G.O., Kashani, K.M. and Kooraki, M. (2004). Evaluation of antibacterial effect of 4 plant extract on heliobacterpilori with Difusion disk and focitometery methods. Scientific Journal of Hamedan University of Medical Sciences. 3 (42-47).
Roder, M.S., Plaschke, J., König, S. U., Börner, A.M., Sorrells, E. Tanksley, S.D. and Ganal, M.W. (1995). Abundance, variability and chromosomal location of microsatellites in wheat. Molecular and General Genetics MGG. 246 (3): 327-333.
Rostami-Ahmadvandi, H., Cheghamirza, K. Kahrizi, D. and Bahraminejad, S. (2013). Comparison of morpho-agronomic traits versus RAPD and ISSR markers in order to evaluate genetic diversity among Cuminum cyminum L. accessions. Australian Journal of Crop Science. 7 (3): 361.
Sarwat, M., Das, S. and Srivastava, P. (2008). Analysis of genetic diversity through AFLP, SAMPL, ISSR and RAPD markers in Tribulus terrestris, a medicinal herb. Plant cell reports. 27 (3): 519-528.
Seguin, M., Flori, A. Legnate, H., Clément-Demange, A., Hamon, P., Perrier, X. and Glaszmann Jean, C. (2003). Rubber tree (Hevea brasiliensis). Genetic Diversity of Cultivated Tropical Plants: 277.
Seidler-Łożykowska, K., Kuczyńska, A., Mikołajczyk, K. Nowakowska, J. and Bocianowski, J. (2014). Estimation of genetic distance among genotypes of caraway (Carum carvi L.) using RAPD-PCR. Acta Scientiarum. Agronomy. 36 (2): 183-188.
Sharifi, M. and Pouresmael, M. (2006). Breaking seed dormancy in Bunium persicum by stratification and chemical substances. Asian Journal of Plant Sciences.8:695-699.
Sheidai, M., Ahmadian, P. and Poorseyedy, S. (1996). Cytological Studies in Iran Zira from Three Genus: Bunium, Carum and Cuminum. Cytologia. 61 (1): 19-25.
Subramanyam, K., Muralidhararao, D. and Devanna, N. (2009). Novel molecular approach for optimization of DNA isolation and PCR protocol for RAPD analysis and genetic diversity assessment of Jatropha curcas (Euphorbiaceae). Current Biotica. 3 (1):1-13.
Terzopoulos, P. and Bebeli, P. (2008 a). DNA and morphological diversity of selected Greek tomato (Solanum lycopersicum L.) landraces. Scientia Horticulturae. 116 (4): 354-361.
Terzopoulos, P. and Bebeli, P. (2008 b). Genetic diversity analysis of Mediterranean faba bean (Vicia faba L.) with ISSR markers. Field Crops Research. 108 (1): 39-44.
Williams, J.G., Kubelik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research. 18 (22): 6531-6535.
Yang, K.-J., Zhang, X.-P., Zhang, Z.-X. and Gong, Y.-x. (2007). Analysis of actuality of Emmenopterys henryi community in Tiantangzhai of Anhui Province. Journal of Plant Resources and Environment. 16 (1):79.
Ye, Y., Zhang, J. Ning, G. and Bao, M. (2008). A comparative analysis of the genetic diversity between inbred lines of Zinnia elegans using morphological traits and RAPD and ISSR markers. Scientia Horticulturae. 118 (1): 1-7.
Zabeti, S.M., Ismaeili, A., Madah-arefi, H., Nazaryan-firouzabadi, F., Rezaeinezhad, A. and Mojori, F. (2013). Genetic diversity thyme, Thymus Pubescens based on indicator species RAPD. New Journal of Cellular and Molecular Biology Biotechnology. 4(13): 25-31.
Zhou, H.-F., Xie, Z.-W. and Ge, S. (2003). Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China. Theoretical and Applied Genetics. 107 (2): 332-339.
Zietkiewicz, E., Rafalski, A. and Labuda, D. (1994). Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics. 20 (2): 176-183.
Zinodini, A., Farshadfar, M., Safari, H., Moradi, F. and Shirvani, H. (2013). Study of Genetic Relationships of Some Mint Species Using R-ISSR Markers. Crop Biotechnology. 5: 11-21.
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Agarwal, M., Shrivastava, N. and Padh, H. (2008). Advances in molecular marker techniques and their applications in plant sciences. Plant cell reports. 27 (4): 617-631.
Agrama, H., and Tuinstra, M. (2003). Phylogenetic diversity and relationships among sorghum accessions using SSRs and RAPDs. African Journal of Biotechnology. 2 (10): 334-340.
Alamdary, S, Safarnejad, A. and Nematzadeh, G. (2012). Using RAPD Marmer For Genetic Diversity Assessment of Several Thymus Species. Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research. 20(40):192- 201.
Anderson, J.A., Churchill, G., Autrique, J., Tanksley, S. and Sorrells, M. (1993). Optimizing parental selection for genetic linkage maps. Genome. 36 (1): 181-186.
Assessment, G.M. (2012). Recent Publications of F. James Rohlf. Evolution. 44: 665-683.
Bahmani, K., Noori, S. A. S., Darbandi, A. I. and Akbari, A. (2015). Molecular mechanisms of plant salinity tolerance: a review. Australian Journal of Crop Science. 9 (4): 321.
Bahraminejad, A., Mohammadi-Nejad, G., Abdul Kadir, K., Bin Yusop, M.R. and Samia, M. A. (2012). Molecular diversity of Cumin ('Cuminum cyminum' L.) using RAPD markers. Australian Journal of Crop Science. 6 (2): 194.
Bohn, M., Utz, H.F. and Melchinger, A.E. (1999). Genetic similarities among winter wheat cultivars determined on the basis of RFLPs, AFLPs, and SSRs and their use for predicting progeny variance. Crop Science. 39 (1): 228-237.
Botstein, D., White, R.L., Skolnick, M. and Davis, R.W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics. 32 (3): 314.
Dehghan-kohestani, S., Amin-Baghizadeh, A.G., Ranjbar, A. and Babaeian-jelodar, N. (2008). Genetic diversity of germplasm cumin [Bunium persicum (Boiss.) B. Fedtsch.] Kerman province using molecular markers RAPD. Quarterly Scientific-Research Medicinal and Aromatic Plants of Iran. 24 (4): 414-427.
Dellaporta, S.L., Wood, J. and Hicks, J.B. (1983). A plant DNA minipreparation: version II. Plant Molecular Biology Reporter. 1 (4): 19-21.
Domblides, A., Domblides, Kharchenko, E. V. and Potekhin, G. (2010). Study of genetic variation among parsley (Petroselinum crispum (Mill.) Nym.) samples using RAPD and ISSR markers. Moscow University Biological Sciences Bulletin. 65 (4): 152-154.
Echeverrigaray, S. and Agostini, G. (2006). Genetic relationships between commercial cultivars and Brazilian accessions of Salvia officinalis L. based on RAPD markers. Revista Brasileira de Plantas Medicinais, 8 (esp).
Fazeli-nasab, B. and Naghavi, M.R. (2011). Identification of Rust resistance among wheat cultiras by using SSRs markers. Journal of Agronomy Science. 4 (5): 81-88.
Gupta, P. (2010). Elements of biotechnology: Rastogi Publications.
Hashemi, H. and Safarnejad, A. (2010). The use of RAPD markers dor assessing the genetic diversity of Bunium persicum (Boiss) B. FEDTSCH populations. International Journal of Science and Nature. 1(2):202-208.
Jaccard, P. (1912). The distribution of the flora in the alpine zone. New Phytologist. 11 (2): 37-50.
Kafi, M., M.H, R.M., Kochaki, A. and Mplafiaei, A. (2000). Cumin, Produced and production technology: Ferdowsi University of Mashhad Institute Press.
Khaled, A., Motawea, M. and Said, A. (2015). Identification of ISSR and RAPD markers linked to yield traits in bread wheat under normal and drought conditions. Journal of Genetic Engineering and Biotechnology, 13(2): 243-252.
Lewontin, R.C. (1972). The apportionment of human diversity. In Evolutionary biology: Springer, 381-398.
Maccaferri, M., Stefanelli, S. Rotondo, F. Tuberosa, R. and Sanguineti, M.C. (2007). Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data. Genome, 50 (4):373-384.
Momeni, S., Shiran, B. and Razmjoo, K. (2006). Genetic variation in Iranian mints on the bases of RAPD analysis. Pakistan Journal of Biological Sciences. 9(10): 1898-1904.
Naghavi, M. R., Ghareyazi, B. and Hoseinisalekdeh, G. (2007). Molecular markers: Tehran University Press.
Nei, M. (1973). Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences. 70 (12): 3321-3323.
Nei, M. and Li, W.H. (1979). Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences. 76 (10): 5269-5273.
Parashar, M., Jakhar, M. and Malik, C. (2014). A review on biotechnology, genetic diversity in cumin (Cuminum cyminum). International Journal of Life Science and Pharma Research. 4 (4): L17-L34.
Pasqualone, A., Lotti, C. and Blanco, A. (1999). Identification of durum wheat cultivars and monovarietal semolinas by analysis of DNA microsatellites. European Food Research and Technology. 210 (2): 144-147.
Prasad, M., Varshney, R., Roy, J., Balyan H. and Gupta, P. (2000). The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theoretical and Applied Genetics. 100 (3-4): 584-592.
Ranjbarian, P., Sadeghian, S., Shirazi, M., SarafNejad, A., Fazeli, M., Majlesi, G.O., Kashani, K.M. and Kooraki, M. (2004). Evaluation of antibacterial effect of 4 plant extract on heliobacterpilori with Difusion disk and focitometery methods. Scientific Journal of Hamedan University of Medical Sciences. 3 (42-47).
Roder, M.S., Plaschke, J., König, S. U., Börner, A.M., Sorrells, E. Tanksley, S.D. and Ganal, M.W. (1995). Abundance, variability and chromosomal location of microsatellites in wheat. Molecular and General Genetics MGG. 246 (3): 327-333.
Rostami-Ahmadvandi, H., Cheghamirza, K. Kahrizi, D. and Bahraminejad, S. (2013). Comparison of morpho-agronomic traits versus RAPD and ISSR markers in order to evaluate genetic diversity among Cuminum cyminum L. accessions. Australian Journal of Crop Science. 7 (3): 361.
Sarwat, M., Das, S. and Srivastava, P. (2008). Analysis of genetic diversity through AFLP, SAMPL, ISSR and RAPD markers in Tribulus terrestris, a medicinal herb. Plant cell reports. 27 (3): 519-528.
Seguin, M., Flori, A. Legnate, H., Clément-Demange, A., Hamon, P., Perrier, X. and Glaszmann Jean, C. (2003). Rubber tree (Hevea brasiliensis). Genetic Diversity of Cultivated Tropical Plants: 277.
Seidler-Łożykowska, K., Kuczyńska, A., Mikołajczyk, K. Nowakowska, J. and Bocianowski, J. (2014). Estimation of genetic distance among genotypes of caraway (Carum carvi L.) using RAPD-PCR. Acta Scientiarum. Agronomy. 36 (2): 183-188.
Sharifi, M. and Pouresmael, M. (2006). Breaking seed dormancy in Bunium persicum by stratification and chemical substances. Asian Journal of Plant Sciences.8:695-699.
Sheidai, M., Ahmadian, P. and Poorseyedy, S. (1996). Cytological Studies in Iran Zira from Three Genus: Bunium, Carum and Cuminum. Cytologia. 61 (1): 19-25.
Subramanyam, K., Muralidhararao, D. and Devanna, N. (2009). Novel molecular approach for optimization of DNA isolation and PCR protocol for RAPD analysis and genetic diversity assessment of Jatropha curcas (Euphorbiaceae). Current Biotica. 3 (1):1-13.
Terzopoulos, P. and Bebeli, P. (2008 a). DNA and morphological diversity of selected Greek tomato (Solanum lycopersicum L.) landraces. Scientia Horticulturae. 116 (4): 354-361.
Terzopoulos, P. and Bebeli, P. (2008 b). Genetic diversity analysis of Mediterranean faba bean (Vicia faba L.) with ISSR markers. Field Crops Research. 108 (1): 39-44.
Williams, J.G., Kubelik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research. 18 (22): 6531-6535.
Yang, K.-J., Zhang, X.-P., Zhang, Z.-X. and Gong, Y.-x. (2007). Analysis of actuality of Emmenopterys henryi community in Tiantangzhai of Anhui Province. Journal of Plant Resources and Environment. 16 (1):79.
Ye, Y., Zhang, J. Ning, G. and Bao, M. (2008). A comparative analysis of the genetic diversity between inbred lines of Zinnia elegans using morphological traits and RAPD and ISSR markers. Scientia Horticulturae. 118 (1): 1-7.
Zabeti, S.M., Ismaeili, A., Madah-arefi, H., Nazaryan-firouzabadi, F., Rezaeinezhad, A. and Mojori, F. (2013). Genetic diversity thyme, Thymus Pubescens based on indicator species RAPD. New Journal of Cellular and Molecular Biology Biotechnology. 4(13): 25-31.
Zhou, H.-F., Xie, Z.-W. and Ge, S. (2003). Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China. Theoretical and Applied Genetics. 107 (2): 332-339.
Zietkiewicz, E., Rafalski, A. and Labuda, D. (1994). Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics. 20 (2): 176-183.
Zinodini, A., Farshadfar, M., Safari, H., Moradi, F. and Shirvani, H. (2013). Study of Genetic Relationships of Some Mint Species Using R-ISSR Markers. Crop Biotechnology. 5: 11-21.
