Detection and Comparison of RAPD & SSR Primers in Genetic Diversity of Ocimum sanctum
S. R. Sutar *
Department of Plant Biotechnology, K. K. Wagh College of Agricultural Biotechnology, Nashik- 422003, Maharashtra, India.
S. D. Surbhaiyya
Department of Plant Biotechnology, K. K. Wagh College of Agricultural Biotechnology, Nashik- 422003, Maharashtra, India.
D. R. Dhumale
Department of Plant Biotechnology, K. K. Wagh College of Agricultural Biotechnology, Nashik- 422003, Maharashtra, India.
V. B. Kasar
Department of Plant Biotechnology, K. K. Wagh College of Agricultural Biotechnology, Nashik- 422003, Maharashtra, India.
A. P. Bhole
Department of Plant Biotechnology, K. K. Wagh College of Agricultural Biotechnology, Nashik- 422003, Maharashtra, India.
V. R. Kulkarni
Department of Plant Biotechnology, K. K. Wagh College of Agricultural Biotechnology, Nashik- 422003, Maharashtra, India.
*Author to whom correspondence should be addressed.
Abstract
Aims: To Analysis of genetic variability in Tulsi (Ocimum sanctum) genotypes by using RAPD & SSR Markers.
Place and Duration of Study: Department of Plant Biotechnology at K.K.Wagh College of Agricultural Biotechnology, Nashik.
Methodology: Ocimum tenuiflorum Linn., commonly known as Tulsi, is an aromatic plant with significant traditional and medicinal value. To assess the genetic diversity and relatedness of six Tulsi genotypes (Krishna, Ram, Lavangi, Pandharpuri, Daisil, and Kapoori), molecular techniques were employed. The genotypes were collected from Nagarjuna Medicinal and Aromatic Plant Park at Dr. P.D.K.V. Akola. DNA isolation was performed using alcohol fixation without liquid nitrogen, and the genotypes were analyzed using RAPD and SSR primers for molecular characterization.
Results: Genetic diversity analysis of six Tulsi genotypes (Krishna, Ram, Lavangi, Pandharpuri, Daisil, and Kapoori) was performed using RAPD and SSR markers. Five RAPD primers produced 15 bands, with 11 bands showing polymorphism (73.3%) and 4 bands showing monomorphism (26.7%). The PIC value ranged from 0.28 to 0.49 (average: 0.40). Four SSR primers generated 9 bands, with 8 bands showing polymorphism and 1 band showing monomorphism. The PIC value ranged from 0.24 to 0.57 (average: 0.39). The Jaccard coefficient revealed moderate to high similarity in RAPD (0.40 to 0.73) and SSR (0.44 to 0.88) analyses. The UPGMA dendrogram separated the genotypes into two main clusters. Cluster 1 included Krishna, Lavangi, Ram, Pandharpuri, and Daisil Tulsi, while cluster 2 consisted of Kapoori Tulsi. The SSR dendrogram also formed two clusters, with Krishna, Lavangi, Ram, Daisil, and Kapoori genotypes in cluster 1, and Pandharpuri Tulsi showing dissimilarity and forming cluster 2.
Keywords: Tulsi, diversity, RAPD, SSR, RNase, DNA fingerprinting
How to Cite
Downloads
References
Pistrick K. Phenology and genome variation in Allium L. - a tight correlation? Plant Biol. 2001;3:654-660
Mohan L, Amberkar M, Kumari M. Ocimum sanctum Linn. (Tulsi)- an overview. Int. J.Pharm. Sci. Rev. Res. 2011:7(1):51-53
Ahmad S, Khaliq I. Morpho-molecular variability and heritability in Ocimum sanctum genotypes from northern regions of pakistan. Pak. J. Biol. Sci. 2002;5:1084-1087
Biswas N, Biswas A. Evaluation of some leaf dusts as grain protectant against rice weevil Sitophilus oryzae (Linn). Environ. Ecol. 2005;23(3):485 – 488 553-571.
Borah R, Biswas S. Tulsi excellent source of phytochemicals. Int. J. Agric. Environ. Biotechnol. 2018;3(5):1732-1738.
24.Matasyoh L, Matasyoh J, Wachira F, Kinyua M, Thairu M, Mukiama T. Chemical composition and antimicrobial activity of the essential oil of Ocimumgratissimum L. growing in Eastern Kenya. Afr J. Biotechnol. 2007:6(6): 760-765.
Mullis KB, Ferre F, Gibbs RA. The Polymerase Chain Reaction 1994.
Muluvi G, Sprent J, Soranzo N, Provan J, Odee D, Folkard G, McNicol J, Powell W. Amplified fragment length polymorphism (AFLP) analysis of genetic variation in Moringa oleifera Lam. Mol Ecol. 1999:8:463-470
Cardoso S, Eloy N, Provan J, Cardoso M, Ferreira P. Genetic differentiation of Euterpe edulis Mart. populations estimated by AFLP analysis. Mol. Ecol. 2000;9: 1753-1760.
Lal S, Mistry K, Shah S, Thaker R, Vaidya P. Genetic diversity assessment in nine cultivars of Catharanthus roseus from Central Gujarat (India) through RAPD, ISSR and SSR markers. J. Biol Res. 2011;1(8):667-675.
Lei Y., Gao H., Tsering T., Shi S., Zhong Y. Determination of genetic variation in Rhodiolacrenulata from the Hengduan Mountains Region, China using inter-simple sequence repeats. Genetics Mol Biol. 2006:(29)2:339-344.
Chen X, Yang J, Tang J. Species-diversified plant cover enhances orchard ecosystem resistance to climatic stress and soil erosion in subtropical hillside. J. Zhejiang Univ. Sci. A. 2004:5(10):1191-1198
Lemos J, Passos X, Fernandes O, Paµla J, Ferri P, Souza L, Lemos A, Silva M. Antifungal activity from Ocimumgratissimum L. towards Cryptococcus neoformans. Mem Inst Oswaldo Cruz, Rio de Janeiro. 2005; 100(1):55‐58.
Li Q., Xu Z., He T. Ex-situ genetic conservation of endangered Vaticaguangxiensis (Dipterocarpaceae) in China. Biol Conserv. 2002;106:151-156.
Goswami M, Ranade S. Analysis of variations in RAPD profiles among accessions of Prosopis. J. Genetics. 1999; 78:141-147.
Adams R, Demeke T. Systematic relationships in Juniperus based on random amplified polymorphic DNAs (RAPDs). 1993.Taxon 42
Lopez, Sanchez P, Batlle R, Nerin C. Solid and vapor phase anti-microbial activities of six essential oils susceptibility of selected food borne bacterial and fungal strains. J. Agric Food Chem. 2005:53(17):6939-6946
Pearson C, Sinden R. Trinucleotide repeat DNA structures: dynamic mutations from dynamic DNA. Curr. Opin. Struct. Biol. 1998;8:321–330.
TaleyzzamanM,Jain P, Verma R, Iqbal Z, Mirza M. Eugenol as a potential drug candidate: a Review. Bentham Sci. Pub. 2021;1804-1815.
Williams J., Kubelik A., Livak K., Rafalski J. and Tingey S. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990; 18:6531-6535.
Dawson J, Chalmers K, Waugh R, Powell W. Detection and analysis of genetic variation in Hordeum spontaneum populations from Isreal using RAPD markers. Mol. Ecol. 1993;2:151-159.
Hu J, Quiros J. Identification of broccoli and cauliflowercultivars with RAPD markers. Plant Cell Rep. 1991;10:505-511.
Crawford D, Brauner S, Cosner M, Stuessy T. Use of RAPD markers to document the origin of the intergeneric hybrid x Margyrocaeneskottsbergii (Rosoceae) on the Juan Fernandez Island. Amer. J. of Bot. 1993;80:89-92.
Doyle J, Doyle J. Isolation of plant DNA from fresh tissue. Phytochemical Bulletin. 1990;19:11-15
Gupta P, Mishra A, Lal R, Dhawan S. DNA fingerprinting and genetic relationships similarities among the accessions/species of Ocimum using SCoT and ISSR markers system. Springer. 2021;446-457.
Harisaranraj R, Prasitha R, Saravana S, Suresh K. Analysis of inter-species relationships of Ocimum species using RAPD markers. Ethnobot. Leafl. 2008;12: 609-13.
Bardakci F. Random amplified polymorphic DNA (RAPD) markers. Turk J. Biol. 2001;25:185-196.
Patel H, Foughat R, Kumar S, Mistry J. and Kumar M. Detection of genetic variation in Ocimum species using RAPD and ISSR markers. Springer. 2014; 10:1007.
Rafalski J, Morgante M, Vogel J, Powell W, Tingey S. Generating and using DNA markers in plants. In: Birren B. and Lai, E (eds). Non-mammalian Genome Analysis: a practical guide. AP, London New York. 1995;75-134.
Rohlf F. NTSYS-Pc. Numerical taxonomy and multivariate analysis system version 2.02e. Exeter Software. New York; 1997.
SairkarP, Vijay N, Silawat N, Garg R, Chouhan S, Batav N, Sharma R, Mehrotra NN. Inter-species association of Ocimum genus as revealed through random amplified polymorphic DNA fingerprinting. Sci Secure J. Biotech. 2012;1(1):1-8.
35.Satyavathi C., Tiwari S., Bharadwaj C., Rao A., Bhat J., & Singh S.Genetic diversity analysis in a novel set of restorer lines of pearl millet [Pennisetum glaucum (L.) R. Br] using SSR markers. Vegetos. 2013:26(1):72-82.
Akande T, Omoigui L, Ikwebe J. Morphological variability and molecular characterization of thirty soybean genotypes using random amplified polymorphic DNA (RAPD) markers. Afr. J. Biotechnol. 2016;17(24).739747.
Bilal A. Molecular characterization of Ocimum species using random amplified polymorphic DNA method and gene identification using sanger sequencing method. J. Mol Biomark Diagn. 2020; 9: 423.
Jaccard P. Nouvelles Recherches sur la distribution florale. Bulletin Soc Vaud Sci Nat. 1908;44:223-270.
Chen S, Dai T, Chang Y, Wang S, Lin Y, Ku H. Genetic diversity among Ocimum specie as based on ISSR, RAPD and SRAP markers. Aust J Crop SCI. 2013; 1463-1471.
Opoola J, Oziegbe M. Characterization of Ocimum tenuiflorum (Linn.) Morpho-types Using RAPD Markers. Not. Sci. Biol. 2019; 11(4):417-420.