Document Type : Research paper


1 Department of Horticultural Science, Faculty of Agricultural Science and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran

2 Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University, P.O. Box 14115-365, Tehran, Iran


Black cumin (Nigella sativa L.) is one of the most important plants in terms of medicine and economics in the world. Breeding of black cumin genotypes by using biotechnology and phytochemistry has always been an important area of different studies. In this study, 24 ISSR molecular markers were used to evaluate the genetic diversity and population structure of Iranian black cumin genotypes. The primers produced a total number of 223 bands, of which 155 were polymorphic bands (indicating 69% polymorphism). By analyzing the similarity matrix based on the simple matching similarity coefficient, the similarity ranged from 0.46 to 0.84. The genotypes were classified into three main groups in the phylogenetic dendrogram, which was based on the similarity matrix and UPGMA algorithm. The average of Polymorphism Information Content, Marker Index, Resolving power, and Observed number of alleles, Effective number of alleles, Nei’s gene diversity, and Shannon's information index were 0.26, 1.56, 3.07, 15.79, 13.72, 0.26, and 0.38, respectively. In analyzing the population structure, when the K value was adjusted to range from 2 to 10, two subpopulations were revealed. However, there was a degree of inconsistency when comparing the results of the phylogenetic dendrogram with those of the population structure. The results of this study can expand future inquiries into the assessments of germplasms and provide opportunities for breeding black cumin genotypes.


Abdelmeguid N.E., Fakhoury R., Kamal S.M., Al Wafai R.J. 2010. Effects of Nigella sativa and thymoquinone on biochemical and subcellular changes in pancreatic β-cells of streptozotocin-induced diabetic rats. Journal of Diabetes 2, 256–266.
Abou Khalil N.S., Abd-Elkareem M., Sayed A.H. 2017. Nigella sativa seed protects against 4-nonylphenol-induced haematotoxicity in Clarias gariepinus (Burchell, 1822): oxidant/antioxidant rebalance. Aquaculture Nutrition 23, 1467–1474.
Alemi M., Sabouni F., Sanjarian F., Haghbeen K., Ansari, S. 2013. Anti-inflammatory effect of seeds and callus of Nigella sativa L. extracts on mix glial cells with regard to their thymoquinone content. AAPS PharmSciTech 14, 160–167.
Bakal S.N., Bereswill S., Heimesaat M.M. 2017. Finding novel antibiotic substances from medicinal plants-antimicrobial properties of Nigella sativa directed against multidrug-resistant bacteria. European Journal of Microbiology and Immunology 7, 92-98.
Barlianto W., Rachmawati M., Irawan M., Wulandari D. 2017. Effects of Nigella sativa oil on Th1/Th2, cytokine balance, and improvement of asthma control in children. Paediatrica Indonesiana 57, 223–228.
Benhaddou-Andaloussi A., Martineau L., Vuong T., Meddah B., Madiraju P., Settaf A. S Haddad P. 2011. The in vivo antidiabetic activity of Nigella sativa is mediated through activation of the AMPK pathway and increased muscle glut4 content. Evidence-based Complementary and Alternative Medicine 2011(1): 538671.
Boskabady M.H., Mohsenpoor N., Takaloo L. 2010. Antiasthmatic effect of Nigella sativa in airways of asthmatic patients. Phytomedicine 17, 707–713.
Bourgou S., Pichette A., Marzouk B., Legault J. 2011. Antioxidant, anti-inflammatory, anticancer and antibacterial activities of extracts from Nigella sativa (black cumin) plant parts. Journal of Food Biochemistry 36, 539–546.
Brünjes L. and Link, W. 2021. Paternal outcrossing success difers among faba bean genotypes and impacts breeding of synthetic cultivars. Theoretical and Applied Genetics 134, 2411–2427.
Cascella M., Bimonte S., Barbieri A., Del Vecchio V., Rosaria Muzio M., Vitale A., Benincasa G., Bella Ferriello A., Azzariti A., Arra C., Cuomo A. 2018. Dissecting the potential roles of Nigella sativa and its constituent thymoquinone on the prevention and on the progression of alzheimer’s disease. Frontiers in Aging Neuroscience 10, 1–10.
Chaieb K., Kouidhi B., Jrah H., Mahdouani K., Bakhrouf A. 2011. Antibacterial activity of thymoquinone, an active principle of Nigella sativa and its potency to prevent bacterial biofilm formation. BMC Complementary Medicine and Therapies 11, 1–6.
Chehl N., Chipitsyna G., Gong Q., Yeo C.J., Arafat H.A. 2009. Anti-inflammatory effects of the Nigella sativa seed extract, thymoquinone, in pancreatic cancer cells. International Hepato-Pancreato-Biliary Association 11, 373–381.
Czajkowska A., Gornowicz A., Pawłowska N., Czarnomysy R., Nazaruk J., Szymanowski W., Bielawska A., Bielawski K. 2017. Anticancer effect of a novel octahydropyrazino[2,1-a:5,4-a′]diisoquinoline derivative and its synergistic action with Nigella sativa in human gastric cancer cells. BioMed Research International 2017 (5), 1–13.
Effenberger K., Breyer S., Schobert R. 2010. Terpene conjugates of the Nigella sativa seed-oil constituent thymoquinone with enhanced efficacy in cancer cells. Chemistry & Biodiversity 7, 129–139.
Elkhayat E., Alorainy M., El-Ashmawy I., Fat’hi S., 2016. Potential antidepressant constituents of Nigella sativa seeds. Pharmacognosy Magazine 12, 27–31.
Evanno G., Regnaut S., Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology 14, 2611–2620.
Falush D., Stephens M., K Pritchard J. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164, 1567–1587.
Farmanpour Kalalagh K., Mohebodini M., Ghanbari A., Chamani E., Erfani M. 2016. Determination of genetic diversity among Arasbaran cornelian cherry (Cornus mas L.) genotypes based on quantitative and qualitative traits. Iranian Journal of Genetics and Plant Breeding 5, 32–40.
Farmanpour Kalalagh K., Mohebodini M., Ghanbari A. 2017. Analysis of genetic diversity, phylogenetic relationships and population structure of Arasbaran cornelian cherry (Cornus mas L.) genotypes using ISSR molecular markers. Journal of Plant Molecular Breeding 5, 60-67.
Ghonime M., Eldomany R., Abdelaziz A., Soliman H. 2011. Evaluation of immunomodulatory effect of three herbal plants growing in Egypt. Immunopharmacology and Immunotoxicology 33, 141–145.
Golkar P., Nourbakhsh V. 2019. Analysis of genetic diversity and population structure in Nigella sativa L.using agronomic traits and molecular markers (SRAP and SCoT). Industrial Crops & Products 130, 170-178.
Halamova K., Kokoska L., Flesar J.,  Sklenickova O., Svobodova B., Marsik P. 2010. In vitro antifungal effect of black cumin seed quinones against dairy spoilage yeasts at different acidity levels. Journal of food protection 73, 2291–2295.
Hosseini KorehKhosravi S., Masoumiasl, A., Dehdari M. 2018. A  comparative  analysis  of  RAPD  and  ISSR  markers for  assessing genetic  diversity  in  Iranian populations of Nigella sativa L. Cellular and Molecular Biology 31, 52-59.
Islam T.M., Guha B., Hosen S., Riaz T.A., Shahadat S., da Rocha Sousa L., Santos de Oliveira, JV Júnior da Silva, JJ de Lima R.M.T., Lima Braga A., dos Reis A.C., de Alencar M.V.O.B., de Carvalho Melo-Cavalcante A.A. 2017. Nigellalogy: a review on Nigella Sativa. MOJ Bioequivalence & Bioavailability 3, 167–181.
Islam M.T., Khan M.R., Mishra S.K. 2019. An updated literature-based review: phytochemistry, pharmacology and therapeutic promises of Nigella sativa L.. Orient Pharm Exp Med 19, 115–129.
Jrah Harzallah H., Grayaa R., Kharoubi W., Maaloul A., Hammami M., Mahjoub T. 2012. Thymoquinone, the Nigella sativa bioactive compound, prevents circulatory oxidative stress caused by 1,2-dimethylhydrazine in erythrocyte during colon postinitiation carcinogenesis. Oxidative Medicine and Cellular Longevity 2012, 1–6.
Kapital B., Feyissa T., Petros Y., Mohammed. S. 2015. Molecular diversity study of black cumin (Nigella sativa L.) from Ethiopia as revealed by inter simple sequence repeat (ISSR) markers. African Journal of Biotechnology 14, 1543-1551.
Mahboubi M., Mohammad Taghizadeh Kashani L., Mahboubi M. 2018. Nigella sativa fixed oil as alternative treatment in management of pain in arthritis rheumatoid. Phytomedicine 1–35.
Mahmoud S.S., Torchilin V.P. 2013. Hormetic/cytotoxic effects of Nigella sativa seed alcoholic and aqueous extracts on MCF-7 breast cancer cells alone or in combination with doxorubicin. Cell Biochemistry and Biophysics 66, 451–460.
Majdalawieh A.F., Fayyad M.W., Nasrallah G.K. 2017. Anti-cancer properties and mechanisms of action of thymoquinone, the major active ingredient of Nigella sativa. Critical Reviews in Food Science and Nutrition 53, 3911–3928.
Mariod A.A., Ibrahim R.M., Ismail M., Ismail N. 2009. Antioxidant activity and phenolic content of phenolic rich fractions obtained from black cumin (Nigella sativa) seedcake. Food Chemistry 116, 306–312.
Mateescu R.G., Zhang Z., Tsai K., Phavaphutanon J., Burton-Wurster N.I., Lust G., Quaas R., Murphy K., Acland G.M., Todhunter R.J. 2005. Analysis of allele fidelity, polymorphic information content, and density of microsatellites in a genome-wide screening fo hip dysplasia in a crossbreed pedigree. Journal of Heredity 96, 847–853.
Mehri N., Mohebodini M., Behnamian M. 2018. Diversity of back cumin (Nigella sativa L.) accessions using multivariate analysis methods. Journal of Crop Breeding 10 (26), 32-42. (in Persian)
Mirzaei Kh. Mirzaghaderi Gh. 2015. Genetic diversity analysis of Iranian Nigella sativa L. landraces using SCoT markers and evaluation of adjusted polymorphism information content. Plant Genetic Resources: Characterization and Utilization; 1–8.
Mohamed A.M., Metwally N.M., Mahmoud S.S. 2005. Sativa seeds against Schistosoma mansoni different stages. Memórias do Instituto Oswaldo Cruz 100, 205–211.
Muminovic J., Melchinger A.E., Lübberstedt T. 2004. Genetic diversity in cornsalad (Valerianella locusta) and related species as determined by AFLP markers. Plant Breeding 123, 460–466.
Nadaf N.H., Gawade S.S., Muniv A.S., Waghmare S.R., Jadhav D.B., Sonawane, K.D. 2015. Exploring anti-yeast activity of Nigella sativa seed extracts. Industrial Crops and Products 77, 624–630.
Namazi N., Larijani B., Ayati M.H., Abdollahi M., 2018. The effects of Nigella sativa L. on obesity: A systematic review and meta-analysis. Journal of Ethnopharmacology 219, 173–181.
Neela F.A., Parvin R., Mahato N.C., Uddin M., Ghosh L., Begum M.F. 2015. Antibacterial activity of pteridophytes and Nigella sativa against antibiotic resistant bacteria isolated from wastewater environment. Frontiers in Environmental Microbiology 1, 27–31.
Nikrouz-Gharamaleki A., Mohebodini M., Farmanpour-Kalalagh K. 2019. Multivariate and univariate analysis of genetic variation in Iranian summer savory (Satureja hortensis L.) accessions based on morphological traits. Iranian Journal of Genetics and Plant Breeding 8 (2), 21-32.
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.
Ramadan M.F. 2007. Nutritional value, functional properties and nutraceutical applications of black cumin (Nigella sativa L.): An overview. International Journal of Food Science & Technology 42, 1208–1218.
Raza M., Alghasham A.A., Alorainy M.S., El-Hadiyah T.M. 2008. Potentiation of valproate-induced anticonvulsant response by Nigella sativa seed constituents: The role of GABA receptors. International Journal of Health Sciences 2, 15–25.
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.
Rogozhin E.A., Oshchepkova Y.I., Odintsova T.I., Khadeeva N.V., Veshkurova O.N., Egorov T.A., Grishin E. V., Salikhov S.I. 2011. Novel antifungal defensins from Nigella sativa L. seeds. Plant Physiology and Biochemistry 49, 131–137.
Shaaban H.A., Sadek Z., Edris A.E., Saad-hussein A. 2015. Analysis and antibacterial activity of Nigella sativa essential oil formulated in microemulsion system. Journal of Oleo Science 64, 223–232.
Shuid A.N., Mohamed N., Mohamed I.N., Othman F., Suhaimi F., Mohd Ramli E.S., Muhammad N., Soelaiman I.N. 2012. Nigella sativa: A potential antiosteoporotic agent. Evidence-Based Complementary and Alternative Medicine 2012.
Siddiqui S.I., Chaudhry S.A. 2018. Nigella sativa plant based nanocomposite-MnFe2O4/BC: An antibacterial material for water purification. Journal of Cleaner Production 200, 996–1008.
Solati Z., Baharin B.S. 2014. Antioxidant effect of supercritical CO2 extracted Nigella sativa L. seed extract on deep fried oil quality parameters. Journal of Food Science and Technology 52, 3475–3484.
Spataro G., Tiranti B., Arcaleni P., Bellucci E., Attene G., Papa R., Zeuli P.S., Negri V. 2011. Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L. Theoretical and Applied Genetics 122, 1281–1291.
Srinivasan K. 2018. Cumin (Cuminum cyminum) and black cumin (Nigella sativa) seeds: traditional uses, chemical constituents, and nutraceutical effects. Food Quality and Safety 2, 1–16.
Sudhir S.P., Kumarappan A., Malakar J., Verma H. N. 2016. Genetic diversity of Nigella sativa from different geographies using RAPD markers. American Journal of Life Sciences 4, 175-180.
Tayman C., Cekmez F., Kafa I.M., Canpolat F.E., Cetinkaya M., Tonbul A., Uysal S., Tunc T., Sarici S.U. 2013. Protective effects of Nigella sativa oil in hyperoxia-induced lung injury. Archivos de Bronconeumología (English Edition) 49, 15–21.
Uz E., Bayrak O., Uz E., Kaya A., Bayrak R., Uz B., Turgut F.H., Bavbek N., Kanbay M., Akcay A. 2008. Nigella sativa oil for prevention of chronic cyclosporine nephrotoxicity: an Experimental Mmodel. American Journal of Nephrology 28, 517–522.
Yildiz F., Coban S., Terzi A., Savas M., Bitiren M., Celik H., Aksoy N. 2010. Protective effects of Nigella sativa against iischemia-reperfusion injury of kidneys. Renal Failure 32, 126–131.