A comparative analysis of RAPD and ISSR markers for assessing genetic diversity in Iranian populations of Nigella sativa L.

Samira Hosseini KorehKhosravi; Asad Masoumiasl; Masoud Dehdari

doi:10.14715/cmb/2018.64.1.10

Issue

Vol. 64 No. 1: Issue 1

Issue Published : February 7, 2018

The undersigned hereby assign all rights, included but not limited to copyright, for this manuscript to CMB Association upon its submission for consideration to publication on Cellular and Molecular Biology. The rights assigned include, but are not limited to, the sole and exclusive rights to license, sell, subsequently assign, derive, distribute, display and reproduce this manuscript, in whole or in part, in any format, electronic or otherwise, including those in existence at the time this agreement was signed. The authors hereby warrant that they have not granted or assigned, and shall not grant or assign, the aforementioned rights to any other person, firm, organization, or other entity. All rights are automatically restored to authors if this manuscript is not accepted for publication.

A comparative analysis of RAPD and ISSR markers for assessing genetic diversity in Iranian populations of Nigella sativa L.

https://doi.org/10.14715/cmb/2018.64.1.10

Samira Hosseini KorehKhosravi

Department of Agronomy and Plant Breeding, Yasouj University, Iran

Asad Masoumiasl

Department of Agronomy and Plant Breeding, Yasouj University, Iran

Masoud Dehdari

Department of Agronomy and Plant Breeding, Yasouj University, Iran

Corresponding Author(s) : Asad Masoumiasl

masoumiasl@yu.ac.ir

Cellular and Molecular Biology, Vol. 64 No. 1: Issue 1
Article Published : January 31, 2018

Abstract

The genetic diversity of 18 Iranian populations of Nigella sativa L. was tested using RAPD (10 primers) and ISSR (12 primers) molecular markers. RAPD primers produced 103 acceptable bands and out of them, 42 bands were polymorphic and the total percentage of polymorphism was estimated 40.5%. Out of the 12 ISSR primers, only 5 of them produced acceptable bands. Five ISSR primers generated 39 amplified products and out of them, 19 bands were polymorphic and the total percentage of polymorphism was estimated 57.4%. As a result, the level of polymorphism obtained from the ISSR markers was higher than of the RAPD markers. Mean of marker index (MI) (0.822 for RAPD and 0.74 for ISSR) and Polymorphic information content (PIC) (0.402 for RAPD and 0.35 for ISSR) for each of the marker systems indicated that both markers were effective for evaluating genetic diversity. Cluster analysis classified the populations into 5 groups for both DNA markers. By integration and analyzing of the two marker systems, the populations were classified into 4 groups. The results of this research showed that RAPD and ISSR molecular markers can be useful for identifying and classifying the Iranian Nigella sativa L. populations.

Keywords

Black cumin Genetic distance Polymorphic information content Similarity.

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, 64(1), 52–59. https://doi.org/10.14715/cmb/2018.64.1.10

Download Citation

References

Morikawa T, Xu F, Kashima Y, Matsuda H, Ninomiya K., Oshikawa M. Novel dolabellane-type diterpene alkaloids with lipid metabolism promoting activities from the seeds of Nigella sativa. Org Lett 2004; 6: 869-872.
Riyaz M, Syed M, Chaudhary FM. Chemistry of the medicinal plants of the genus Nigella sativa L. Hamdard Med 1996; 39(2): 40-45.
Salamati MA, Zeinali H. Assessment genetic variation of some accessions of Nigella sativa L. using morphological and agronomic traits. Iranian J Med Aroma Plants 2013; 29(1): 201-214.
Mohammadi SA, Prasanna BM. Analysis of genetic diversity in crop plants–salient statistical tools and considerations. Crop Sci 2003; 43:1235-1248.
Dominique VD. Molecular markers in plant genetics and biotechnology. Taylor & Francis Inc. USA 2003; 248 pp.
Han YC, Teng CZ, Zhong Sh, Zhou MQ. Genetic variation and clonal diversity in populations of Nelumbo nucifera (nelumbonaceae) in central china detected by ISSR markers. Aquat Bot 2007; 86: 69- 75.
Roose ML, Fang DQ. Identification of closely related citrus cultivars with inter-simple sequence repeats markers. Theor Appl Genet 1997; 95(3):408-417.
Domblides AS, Domblides EA, Kharchenko VA, Potekhin GA. Study of genetic variation among Parsley (Petroselinum Crispum (Mill.) Nym.) samples using RAPD and ISSR markers. Moscow Univ Biol Sci Bullet 2010; 4: 25-28.
Gajera HP, Tomar RS, Patel SV, Viradia RR, Golakiya BA. Comparison of RAPD and ISSR markers for genetic diversity analysis among different endangered Mangifera indica genotypes of Indian Gir forest region. J Plant Biochem Biotechnol 2011; 10:1000-1007.
Morales RGF, Resende JTV, Faria MV, Andrade MC, Resende LV, Carla Andrea Delatorre CA, da Silva PR. Genetic similarity among strawberry cultivars assessed by RAPD and ISSR markers. Sci Agr 2011; 68(6): 665-670.
Moradi A, Chogamirza K. Evaluation of genetic diversity in different genotypes of durum wheat using RAPD and ISSR markers. Proceeding of the 5th National Biotechnol Cong Islamic Republic of Iran in 2007; Tehran.
Murray MG, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 1980; 8: 4321–4326.
Garcia E, Jamilena M, Alvarez JI, Arnedo T, Oliver JL, Lozano R. Genetic relationships among melon breeding lines revealed by RAPD markers and agronomic traits. Theor Appl Genet 1998; 96: 878-885.
Al-Huqail A, Al-Saad F. DNA Fingerprinting and genotyping of four Black seed (Nigella sativa L.) taxa. Environ Arid Land Agr Sci 2010; 21(1): 93-108.
Williames JGK, Kubelik AE, Livak KJ, Rafalski JA, Tingey SC. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 1990; 18: 6531-6535.
Peakall R, Smouse PE. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 2006; 6: 288-295.
Kumar M, Mishra GP, Singh R, Kumar J, Naik PK, Singh ShB. Correspondence of ISSR and RAPD markers for comparative analysis of genetic diversity among different apricot genotypes from cold arid deserts of trans-Himalayas. Physiol Molecul Biol Plants 2009; 15(3): 225-236.
Altintas S, Toklu F, Kafkas S, Kilian B, Brandolini A, zkan HO. Estimating genetic diversity in durum and bread wheat cultivars from Turkey using AFLP and SAMPL markers. Plant Breed 2008; 127(1): 9-14.
Huang L, Chen Z, Zhang X, Wang Z, Liu C. A comparative analysis of molecular diversity of Erect Milkvetch (Astragalus adsurgens) germplasm from north China using RAPD and ISSR markers. Biochem Genet 2009; 47: 92–99.
Chengxin FU, Yingxiong Q, Hanghui K. RAPD analysis for genetic diversity in Changium smyrnioides (Apiaceae), an endangered plant. Botan Bullet Academia Sinica 2003; 44: 13-18.
Pezhmanmehr M, Hassani ME, Jahansooz F, Najafi AA, Sefidkon F, Mardi M, Pirseiedi M. Assessment of genetic diversity in some Iranian populations of Bunium persicum using RAPD and AFLP markers. Iranian J Biotechnol 2009; 7(2): 92-100.
Fabriki Orang S, Shams-Bakhsh M, Jalali-Javaran M, Ahmadi J. Assessment genetic variation of endemic accessions of Iranian melon (Cucumis melo L.) using molecular inter sequence repeat (ISSR) markers. Iranian Biol J 2009; 22(2): 271-281.
Feyzian A, Jalali-Javaran M, Dehgani H, Zamiad H. Assessment genetic variation of some endemic melons in Iran using morphological and molecular RAPD markers. J Sci Technol Agri Nat Resour 2007; 41(11): 151-162.
Martins-Lopes P, Lima-Brito J, Gomes S, Meirinhos J, Santos L, Guedes-Pinto H. RAPD and ISSR molecular markers in Olea europaea L.: Genetic variability and molecular cultivar identification. Genet Resour Crop Evol 2007; 54:117–128.
Sadigova S, Sadigov H, Eshghi R, Salayeva S, Ojaghi J. Application of RAPD and ISSR markers to analyses molecular relationship in Azerbaijan wheat accessions (Triticum aestivum L.). Bulgarian J Agri Sci 2014; 20 (1): 87-95.
Elmeer Kh, Alghanem M, Al-Latifi L, Alhemairi H. Efficiency of RAPD and ISSR Markers for the Detection of Polymorphisms and Genetic Relationships in Date Palm. Biotechnol 2017; 16(1): 19-26.
Goulao L, Cabrita L, Oliveira CM, Leitao JM. Comparing RAPD and AFLP analysis in discrimination and estimation of genetic similarities among apple (Malus domestica Borkh) cultivars. Euphytica 2001; 119: 259–270.

References

Morikawa T, Xu F, Kashima Y, Matsuda H, Ninomiya K., Oshikawa M. Novel dolabellane-type diterpene alkaloids with lipid metabolism promoting activities from the seeds of Nigella sativa. Org Lett 2004; 6: 869-872.

Riyaz M, Syed M, Chaudhary FM. Chemistry of the medicinal plants of the genus Nigella sativa L. Hamdard Med 1996; 39(2): 40-45.

Salamati MA, Zeinali H. Assessment genetic variation of some accessions of Nigella sativa L. using morphological and agronomic traits. Iranian J Med Aroma Plants 2013; 29(1): 201-214.

Mohammadi SA, Prasanna BM. Analysis of genetic diversity in crop plants–salient statistical tools and considerations. Crop Sci 2003; 43:1235-1248.

Dominique VD. Molecular markers in plant genetics and biotechnology. Taylor & Francis Inc. USA 2003; 248 pp.

Han YC, Teng CZ, Zhong Sh, Zhou MQ. Genetic variation and clonal diversity in populations of Nelumbo nucifera (nelumbonaceae) in central china detected by ISSR markers. Aquat Bot 2007; 86: 69- 75.

Roose ML, Fang DQ. Identification of closely related citrus cultivars with inter-simple sequence repeats markers. Theor Appl Genet 1997; 95(3):408-417.

Domblides AS, Domblides EA, Kharchenko VA, Potekhin GA. Study of genetic variation among Parsley (Petroselinum Crispum (Mill.) Nym.) samples using RAPD and ISSR markers. Moscow Univ Biol Sci Bullet 2010; 4: 25-28.

Gajera HP, Tomar RS, Patel SV, Viradia RR, Golakiya BA. Comparison of RAPD and ISSR markers for genetic diversity analysis among different endangered Mangifera indica genotypes of Indian Gir forest region. J Plant Biochem Biotechnol 2011; 10:1000-1007.

Morales RGF, Resende JTV, Faria MV, Andrade MC, Resende LV, Carla Andrea Delatorre CA, da Silva PR. Genetic similarity among strawberry cultivars assessed by RAPD and ISSR markers. Sci Agr 2011; 68(6): 665-670.

Moradi A, Chogamirza K. Evaluation of genetic diversity in different genotypes of durum wheat using RAPD and ISSR markers. Proceeding of the 5th National Biotechnol Cong Islamic Republic of Iran in 2007; Tehran.

Murray MG, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 1980; 8: 4321–4326.

Garcia E, Jamilena M, Alvarez JI, Arnedo T, Oliver JL, Lozano R. Genetic relationships among melon breeding lines revealed by RAPD markers and agronomic traits. Theor Appl Genet 1998; 96: 878-885.

Al-Huqail A, Al-Saad F. DNA Fingerprinting and genotyping of four Black seed (Nigella sativa L.) taxa. Environ Arid Land Agr Sci 2010; 21(1): 93-108.

Williames JGK, Kubelik AE, Livak KJ, Rafalski JA, Tingey SC. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 1990; 18: 6531-6535.

Peakall R, Smouse PE. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 2006; 6: 288-295.

Kumar M, Mishra GP, Singh R, Kumar J, Naik PK, Singh ShB. Correspondence of ISSR and RAPD markers for comparative analysis of genetic diversity among different apricot genotypes from cold arid deserts of trans-Himalayas. Physiol Molecul Biol Plants 2009; 15(3): 225-236.

Altintas S, Toklu F, Kafkas S, Kilian B, Brandolini A, zkan HO. Estimating genetic diversity in durum and bread wheat cultivars from Turkey using AFLP and SAMPL markers. Plant Breed 2008; 127(1): 9-14.

Huang L, Chen Z, Zhang X, Wang Z, Liu C. A comparative analysis of molecular diversity of Erect Milkvetch (Astragalus adsurgens) germplasm from north China using RAPD and ISSR markers. Biochem Genet 2009; 47: 92–99.

Chengxin FU, Yingxiong Q, Hanghui K. RAPD analysis for genetic diversity in Changium smyrnioides (Apiaceae), an endangered plant. Botan Bullet Academia Sinica 2003; 44: 13-18.

Pezhmanmehr M, Hassani ME, Jahansooz F, Najafi AA, Sefidkon F, Mardi M, Pirseiedi M. Assessment of genetic diversity in some Iranian populations of Bunium persicum using RAPD and AFLP markers. Iranian J Biotechnol 2009; 7(2): 92-100.

Fabriki Orang S, Shams-Bakhsh M, Jalali-Javaran M, Ahmadi J. Assessment genetic variation of endemic accessions of Iranian melon (Cucumis melo L.) using molecular inter sequence repeat (ISSR) markers. Iranian Biol J 2009; 22(2): 271-281.

Feyzian A, Jalali-Javaran M, Dehgani H, Zamiad H. Assessment genetic variation of some endemic melons in Iran using morphological and molecular RAPD markers. J Sci Technol Agri Nat Resour 2007; 41(11): 151-162.

Martins-Lopes P, Lima-Brito J, Gomes S, Meirinhos J, Santos L, Guedes-Pinto H. RAPD and ISSR molecular markers in Olea europaea L.: Genetic variability and molecular cultivar identification. Genet Resour Crop Evol 2007; 54:117–128.

Sadigova S, Sadigov H, Eshghi R, Salayeva S, Ojaghi J. Application of RAPD and ISSR markers to analyses molecular relationship in Azerbaijan wheat accessions (Triticum aestivum L.). Bulgarian J Agri Sci 2014; 20 (1): 87-95.

Elmeer Kh, Alghanem M, Al-Latifi L, Alhemairi H. Efficiency of RAPD and ISSR Markers for the Detection of Polymorphisms and Genetic Relationships in Date Palm. Biotechnol 2017; 16(1): 19-26.

Goulao L, Cabrita L, Oliveira CM, Leitao JM. Comparing RAPD and AFLP analysis in discrimination and estimation of genetic similarities among apple (Malus domestica Borkh) cultivars. Euphytica 2001; 119: 259–270.

Author biographies is not available.