Hostname: page-component-78c5997874-ndw9j Total loading time: 0 Render date: 2024-11-17T23:33:14.372Z Has data issue: false hasContentIssue false
  • English
  • Français

Genetic diversity analysis of Iranian Nigella sativa L. landraces using SCoT markers and evaluation of adjusted polymorphism information content

Published online by Cambridge University Press:  14 August 2015

Khaled Mirzaei  and
Ghader Mirzaghaderi
Khaled Mirzaei
Affiliation:
Department of Agronomy and Plant Breeding, University of Kurdistan, PO Box 416, Sanandaj, Iran
Ghader Mirzaghaderi*
Affiliation:
Department of Agronomy and Plant Breeding, University of Kurdistan, PO Box 416, Sanandaj, Iran
*
*Corresponding author. E-mail: gh.mirzaghaderi@uok.ac.ir
Get access Rights & Permissions [Opens in a new window]

Abstract

The genetic diversity of 39 Iranian black cumin (Nigella sativa L.) landraces was analysed using 14 polymorphic Start Codon Targeted (SCoT) markers. A total of 106 bands ranging from 3 (for SCoT70) to 13 (for SCoT23) were observed. Of them, 33 (31%) bands were polymorphic with a mean of 1.65 bands per primer. Polymorphism information content (PIC) per primer ranged from 0.035 (for SCoT12) to 0.133 (for SCoT70), with an average of 0.078. Besides PIC, Simpson's diversity (D) index was also calculated for each SCoT marker as an indication of discrimination power across population. The D index was used to adjust the PIC of the SCoT markers. As the adjusted PIC (PICD= PIC × D) was calculated based on both the PIC and the rate of band dispersion, this reflected the informativeness of a dominant marker more precisely than PIC. Genetic relationships were estimated using Jaccard's similarity coefficient-generated values between different pairs of genotypes that varied from 80 to 97% with an average of 88%. These coefficients were applied to construct a dendrogram using the UPGMA algorithm. A high genetic similarity was observed that might be due to the fact that N. sativa is a self-pollinated plant not originated from Iran and might have been imported from the Mediterranean regions.

Keywords

genetic diversitypolymorphism information contentSimpson's diversity indexStart Codon Targeted polymorphism
Type
Research Article
Information
Plant Genetic Resources , Volume 15 , Issue 1 , February 2017 , pp. 64 - 71
Copyright
Copyright © NIAB 2015 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Ali, B and Blunden, G (2003) Pharmacological and toxicological properties of Nigella sativa . Phytotherapy Research 17: 299–305.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Botstein, D, White, RL, Skolnick, M and Davis, RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 32: 314.Google ScholarPubMed
Charlesworth, D (2003) Effects of inbreeding on the genetic diversity of populations. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences 358: 1051–1070.CrossRefGoogle ScholarPubMed
Collard, BCY and Mackill, DJ (2009) Start Codon Targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology Reporter 27: 86–93.CrossRefGoogle Scholar
De Riek, J, Calsyn, E, Everaert, I, Van Bockstaele, E and De Loose, M (2001) AFLP based alternatives for the assessment of Distinctness, Uniformity and Stability of sugar beet varieties. Theoretical and Applied Genetics 103: 1254–1265.CrossRefGoogle Scholar
Doyle, JJ and Doyle, JL (1990) Isolation of plant DNA from fresh tissue. Focus 12: 13–15.Google Scholar
Ghamarnia, H and Jalili, Z (2013) Water stress effects on different black cumin (Nigella sativa L.) components in a semi-arid region. International Journal of Agronomy and Plant Production 4: 753–762.Google Scholar
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.CrossRefGoogle ScholarPubMed
Hajmansoor, S, Bihamta, MR and Alisoltani, A (2013) Genetic diversity among and within Iranian and non-Iranian barely (Hordeum vulgare L.) genotypes using SSR and storage proteins markers. Biochemical Systematics and Ecology 46: 7–17.CrossRefGoogle Scholar
Hamilton, AC (2004) Medicinal plants, conservation and livelihoods. Biodiversity and Conservation 13: 1477–1517.CrossRefGoogle Scholar
Iqbal, MS, Qureshi, AS and Ghafoor, A (2010) Evaluation of Nigella sativa L. for genetic variation and ex-situ conservation. Pakistan Journal of Botany 42: 2489–2495.Google Scholar
Iqbal, MS, Ghafoor, A, Ahmad, H and Inamullah, (2013) Multivariate analysis and selection to enquire genetic variation patterns in Nigella sativa . International Journal of Agriculture and Biology 15: 443–450.Google Scholar
Jaccard, P (1912) The distribution of the flora in the alpine zone. New Phytologist 11: 37–50.CrossRefGoogle Scholar
Kamal, A, Arif, JM and Ahmad, IZ (2010) Potential of Nigella sativa L. seed during different phases of germination on inhibition of bacterial growth. Journal of Biotechnology and Pharmaceutical Research 1: 9–13.Google Scholar
Kapital, B, Feyissa, T, Petros, Y, Mohammed, S, Oumer, A, Yohannes, P, Kassahun, T, Abel, T and Endashaw, B (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 18: 1543–1551.Google Scholar
Liu, BH (1998) Statistical Genomics: Linkage, Mapping and QTL Analysis. Boca Raton: CRC Press.Google Scholar
Luo, C, He, X-H, Chen, H, Hu, Y and Ou, S-J (2012) Genetic relationship and diversity of Mangifera indica L.: revealed through SCoT analysis. Genetic Resources and Crop Evolution 59: 1505–1515.CrossRefGoogle Scholar
Mariette, S, Le Corre, V, Austerlitz, F and Kremer, A (2002) Sampling within the genome for measuring within-population diversity: trade-offs between markers. Molecular Ecology 11: 1145–1156.CrossRefGoogle ScholarPubMed
Rao, VR and Hodgkin, T (2002) Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell, Tissue and Organ Culture 68: 1–19.Google Scholar
Rohlf, FJ (1993) NTSYS-PC. Numerical Taxonomy and Multivariate Analysis System Version 1.80. New York: Exeter Software, Setauket.Google Scholar
Salem, ML (2005) Immunomodulatory and therapeutic properties of the Nigella sativa L. seed. International Immunopharmacology 5: 1749–1770.CrossRefGoogle ScholarPubMed
Satya, P, Karan, M, Jana, S, Mitra, S, Sharma, A, Karmakar, P and Ray, D (2015) Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species. Meta Gene 3: 62–70.CrossRefGoogle ScholarPubMed
Simpson, EH (1949) Measurement of diversity. Nature 163: 688.CrossRefGoogle Scholar
Speer, MJ (1999) Genetic linkage: concepts and methods. In: Albers, MJ (ed.) Genetics of Cerebrovascular Disease. Oxford: Blackwell, pp. 25–26.Google Scholar
Weiss, EA (2002) Spice Crops. Wallingford, Oxon, UK: CABI.CrossRefGoogle Scholar
Zhang, J, Xie, W, Wang, Y and Zhao, X (2015) Potential of start codon targeted (SCoT) markers to estimate genetic diversity and relationships among Chinese Elymus sibiricus accessions. Molecules 20: 5987–6001.CrossRefGoogle ScholarPubMed