World Journal of Agricultural Research
ISSN (Print): 2333-0643 ISSN (Online): 2333-0678 Website: Editor-in-chief: Rener Luciano de Souza Ferraz
Open Access
Journal Browser
World Journal of Agricultural Research. 2015, 3(6), 192-197
DOI: 10.12691/wjar-3-6-2
Open AccessArticle

Molecular Diversity Assessment in Chickpea through RAPD and ISSR Markers

Sameer. S. Bhagyawant1, Neha Gupta1, Ajay Gautam1, S.K. Chaturvedi2 and Nidhi Shrivastava3,

1School of Studies in Biotechnology, Jiwaji University, Gwalior, India

2ICAR-Indian Institute of Pulses Research, Kanpur, India 3Department of Bioscience & Biotechnology, Banasthali University, India

32ICAR-Indian Institute of Pulses Research, Kanpur, India 3Department of Bioscience & Biotechnology, Banasthali University, India

Pub. Date: November 07, 2015

Cite this paper:
Sameer. S. Bhagyawant, Neha Gupta, Ajay Gautam, S.K. Chaturvedi and Nidhi Shrivastava. Molecular Diversity Assessment in Chickpea through RAPD and ISSR Markers. World Journal of Agricultural Research. 2015; 3(6):192-197. doi: 10.12691/wjar-3-6-2


Chickpea (Cicer arietinum L.) is a cool season food legume in the family of Fabaceae. The exploration of genetically variable accessions is the key source of germplasm conservation for future selecting parents for breeding. PCR based analysis employing RAPD and ISSR marker are one of the established techniques of estimation of genetic diversity. Twelve chickpea accessions were analyzed by ten RAPD and ISSR primers of which all primers gave amplification products. The results showed that the level of DNA polymorphism in these accessions is low. RAPD analysis yielded 5.9 bands per primer while ISSR analysis produce 2.8 bands per primer. The average percentage of molecular polymorphism as produced by RAPD and ISSR primers was 67%. The cluster dendrogram demonstrated a similarity coefficient range of 0.10 to 0.66 due to RAPD markers, whereas ISSR markers showed 0.60 to 0.80. The variability index worked out in the present study ranges from 0.49 to 0.78. The present study determines DNA polymorphism in chickpea accessions as revealed by RAPD and ISSR markers. Overall the study ascertained that RAPD and ISSR marker provide powerful tools in revealing genetic diversity in chickpea.

chickpea RAPD ISSR polymorphism

Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit


[1]  Talebi, R., Fayaz, F., Mardi, M., Pirsyedi, S.M. and Naji, A.M. Genetic Relationships among Chickpea (Cicer arietinum) Elite Lines Based on RAPD and Agronomic Markers. Int. J. Agri. Biol. 10, 301 -305. 2008.
[2]  Dwevedi, K.K. and Gaibriyal, M. Assessment of genetic diversity of cultivated chickpea (Cicer arietinum L.). Asian J. Agri. Sci. 1(1), 7-8. 2009.
[3]  Gupta, P.K. and Varshney, R.K. The development and use of microsatellite markers for genetics and plant breeding with emphasis on bread wheat. Euphytica 113, 163-185. 2000.
[4]  Lisek, A., Korbin, M. and Rozpara, E. Using simple generation RAPD Markers to distngushing between sweet cherry (Prunus avium L.) cultivars. J. Fruit Ornam. Plant Res. 14, 53-59. 2006.
[5]  Zietkiewicz, E., Rafalski, A. and Labuda, D. Genomic fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20, 176-118. 1994.
[6]  Godwin, I.D., Aitken, E.A.B. and Smith, L.W. Application of inter-simple sequence repeats (ISSR) markers to plant genetics. Electrophoresis 18, 1524-1528. 1997.
[7]  Varshney, R.K., Song, C., Saxena, R.K., Azam, S., Yu, S., Sharpe, A.G., Cannon, S., Baek, J., Rosen, B.D. and Tar'an, B. Draft genome sequence of chickpea (Cicer arietinum) provides a resource trait improvement. Nat Biotechnol 31(3), 240-246. 2013.
[8]  Willams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. DNA polymorphism amplified by arbitraray primers are useful as genetic markers. Nucleic Acids Res. 18, 6531-6535. 1990.
[9]  Welsh, J. and Mcclelland, M. Fingerprinting genomes using PCR with arbitrary primers. Nucl Acids Res. 18, 7213-7218. 1990.
[10]  Bhagyawant, S.S. and Srivastava, N. Genetic Fingerprinting of Chickpea (Cicer arietinum L.) Germplasm Using ISSR Markers and Their Relationships. African Journal of Biotechnology. 7, 4428-4431. 2008.
[11]  Jaccard, P. Nouvelles Researches Sur Ladistribution Florale. Bulletin de la Societe Vaudoise des Sciences Naturelles. 44, 223-270. 1908.
[12]  Pavlicek, A., Hrda, S. and Flegr, J. Free Tree: Freeware Program for Construction of Phylogenetic Trees on the Basis of Distance Data and Bootstrap/Jackknife Analysis of the Tree Robustness. Application in the RAPD Analysis of Genus Frenkelia. Folia Biologica (Praha). 45, 97-99. 1999.
[13]  Souframanien, J. and Gopalakrishna, T.G. A Comparative Analysis of Genetic Diversity in Black Gram Genotypes Using RAPD and ISSR Markers. Theoretical and Applied Genetics. 109, 1687-1693. 2004.
[14]  Dikshit, H.K., Jhang, T. Singh, N.K., Koundal, K.R., Bansal, K.C., Chandra, N., Tickoo, J.L. and Sharma, T.R. Genetic Differentiation of Vigna Species by RAPD, URP and SSR Markers. Biologia Plantarum. 3, 451-457. 2007.
[15]  Ravi, M., Geethanjali, S., Sammeyafarheen, F. and Maheswaran, M. Molecular Marker Based Genetic Diversity Analysis in Rice (Oryza sativa L.) Using RAPD and SSR Markers. Euphytica. 133, 243-253. 2003.
[16]  Pakseresht, F., Talebi, R. and Karami, E. Comprative assessment of ISSR, DAMD and SCoT markers for evaluation of genetic diversity and conservation of landrace Chickpea (Cicer arietinum L.) Genotypes Collected from North-West of Iran. Physiol Mol Biol of Plants. 19(4), 5, 63-574. 2013.
[17]  Iruela, M., Rubio, J., Cubero, J.I., Gil, J. and Mill├ín, T. Phylogenetic Analysis in the Genus Cicer and Cultivated Chickpea Using RAPD and ISSR Markers. Theoretical and Applied Genetics. 104, 643-651. 2002.
[18]  Rajesh, P.N., Sant V.J., Gupta V.S., Muehlbauer, F.J. and Rajesh, P.K. Genetic relationships among annual and perennial wild species of Cicer using inter simple sequence repeat (ISSR) polymorphism. Euphytica. 129, 15-23. 2002.
[19]  Rao, A.S., Usha, Rani, P., Deshmukh, P.S., Kumar, P.A., Panguluri, S.K. RAPD and ISSR fingerprinting in cultivated chickpea (Cicer arietinum L.) and its wild progenitor Cicer reticulatum L. Genet Resour Crop Ev. 54, 1235-1244. 2007.
[20]  Mei, Z., Zhang, C., Khan, M.A., Zhu, Y., Tania, M., Luo, P., Fu, J. Efficiency of improved RAPD and ISSR markers in assessing genetic diversity and relationships in Angelica sinensis (Oliv.) Diels varieties of China. Ele. J. of Biotech. 18, 96-102. 2015.
[21]  Ahmad, Z., Mumtaz, A.S., Ghafoor, A., Ali, A. and Nisar M. Marker Assisted Selection (MAS) for chickpea fusarium wilt resistant genotypes using PCR based molecular markers. Mol.Biol. Rep. 41, 6755-6762. 2014.