Achala Bakshi Vinay Kumar Sushma Sagar Sorabh Chaudhary Rajendra Kumar Mukesh Kumar


Chickpea (Cicer arietinum L.) commonly also known as gram, Chana, Bengal gram and Garbanzo beans is the second most important pulse crop of the world mainly grown in arid and semi-arid regions. Assessment of genetic variability in the base population is the first step in any breeding programme for selection of genetically divergent parents and their use in the crop improvement programme. In the present investigation 20 genotypes of chickpea were characterized using a specific set of 15 numbers of Sequence tagged microsatellite site (STMS) markers. The number of alleles, allelic distribution and their frequency was estimated and found that the 36 alleles amplified with 15 STMS loci having an average of 2.4 alleles per locus. The number of alleles amplified varied from 1 to 4. The Polymorphic information content value ranged from 0 to 0.965 with an average of 0.373 indicated the considerable efficiency of markers for studying the polymorphism level. All primer showed higher polymorphism among the genotypes except two primers namely, TAA59 and GA105 which were monomorphic in nature. Genetic similarity based on UPGMA clustering the dendrogram grouped the 20 genotypes in three clusters, cluster I, II, III comprised of 2, 4, 14 genotypes, respectively. The maximum similarity was found between genotypes ICRISAT-4183 and ICRISAT- 7722 (0.972). The present study provided an insight of the inter-relationship among the genotypes and highlights the genetic distance by STMS markers. The genetic diversity revealed in this study could be exploited for selective breeding programme of chickpea improvement.


Download data is not yet available.




Chickpea, Cicer aeritenum, Molecular diversity, Sequence tagged microsatellite markers

Agarwal, G. Jhanwar, S. Priya, P. Singh, V.K. Saxena, M.S. Parida, S.K. Garg, R. Tyagi, A.K. and Jain, M. (2012). Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional marker. PLoS One. 7 (12):e52443.
Bharadwaj, C. Chauhan, S.K. Rajguru, G. Srivastava, R. Satyavathi, C.T. Yadav, S. Rizvi, A.H. Kumar, J. and Solanki, R.K. (2010). Diversity analysis of chickpea (Cicer arietinum L.) cultivars using STMS markers. Indian J. Agri. Sci. 80: 947-951.
Bouhadida, M. Benjannet, R. Jendoubi, W. and Kharrat, M. (2015). Analysis of genetic diversity of chickpea cultivars using STMS markers. IOSR Journal of Applied Chemistry. 8(2):70-74.
Choumane, W. Winter, P. Weigand, F. and Kahl, G. (2000). Conservation and variability of sequence-tagged microsatellite sites (STMSs) from chickpea (Cicer arietinum L.) within the genus Cicer. Theor. Appl. Genet. 101(1-2):269-278.
Collard, B.C.Y. Jahufer, M.Z.Z. Brouwer, J.B. Pang, E.C.K. (2005). An Introduction to markers, quantitative trait loci (QTL), mapping and marker assisted selection for crop improvement: the basic concepts. Euphytica. 142:169-196.
Doddamani, D. Katta, M.A.V.S.K. Khan, A.W. Agarwal, G. Shah, T.M. and Varshney, R.K. (2014). CicAr-MiSatDB: the chickpea microsatellite database, BMC Genomics, 15: 212.
Doyle, J.J. and Doyle, J.L. (1987). A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochem. Bull., 19:11-15.
Flandez-Galvez, H. Ford, R. Pang, E.C.K. and Taylor, P.W. J. (2003). An intraspecific linkage map of the chickpea (Cicer arietinum L.) genome based on sequence tagged microsatellite site and resistance gene analog markers. Theor. Appl. Genet., 110(7):447-1456.
Gaur, P.M. Jukanti, A.K. and Varshney, R.K. (2012). Impact of genomic technologies on chickpea breeding strategies. Agronomy, 2:199-221.
Gawel, N.J. and Jarret, R.L. (1991). A modified CTAB DNA extraction procedure for Musa and Ipomoea plant. Mol. Biol. Rep., 9:262-266.
Huttel, B. Winter, P. Weising, K. Choumane, W. Weigand, F. and Kahl, G. (1999). Sequence tagged microsatellites site markers for chickpea (Cicer arietinum L.). Genome, 42:210-217.
Jaccard, P. (1908). Nouvelles recherches surla distribution florale. Bull. Soc. Sci. Nat., 44:223–270
Jukanti, A.K. Gaur, P.M. Gowda, C.L.L. and Chibbar, R.N. (2012). Nutritional quality and health benefits of chickpea (Cicer arientium L.): A review, Br. J. Nutr. 108 (Suppl. 1):S11-S16.
Kupitcha, F.K. (1977). The delimitation of the tribe Viceae (Leguminoeceae) and the relationship of Cicer. Botanical journal of Linnean Society, 74: 12-13.
Poncet, V., Rondeau, M., Tranchant, C., Cayrel, A., Hamon, S., Kochko, A.D. and Hamon, P. 2006. SSR mining in coffee tree databases: potential use of EST-SSRs as marker for the Coffea genus, Theor. Appl. Genet., 276: 436-449.
Powell, W. Marchy, G.C. and Provan, J. (1996a). Polymorphism revealed by simple sequence repeats. Trends Plant Sci., 1:215-222.
Powell, W. Morgante, M. Andes, C. Hangley, M. Vogel, J. Tingey, S. and Raflski, A. (1996b). The comparison of RFLP, RAPD, AFLP, and SSR microsatellites markers for germplasm analysis. Mol. Breed., 2: 225-238.
Rizvi, H. Kalyana Babu, B. and Agrawal, P.K. (2014). Molecular analysis of kabuli and desi type of Indian chickpea (Cicer arietinum L.) cultivars using STMS markers. J. Plant Biochem. Biotech., 23(1):52-60
Rohlf, F.J. (1989). NTSYS–pc (Numerical Taxonomy and Multivariate Analysis System).Ver.1.70. Exeter, Setauket, New York.
Senior, M.L. Murphi, J.P. Goodman, M.M. and Stuber, C.W. (1998). Utility of SSRs for determining genetic similarities and relationship in Maize using an Agarose gel system. Crop Sci., 38:1088-1098.
Sethy, N.K. Choudhary, S. Shokeen, B. and Bhatia, S. (2005). Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis. Theor. Appl. Genet., 112(2):347-357.
Singh, R., Vibha, S. and Randhawa, G.J. (2008). Molecular analysis of chickpea (Cicer arietinum L.) cultivars using AFLP and STMS markers. J. Plant Biochem. Biotech. 17: 167-171.
Sneath, P.H.A. and Sokal, R.R. (1973). Numerical Taxonomy WH Truman & Co San Francisco.
Varshney, R.K. and Tuberosa, R. (2013). Genomics applications in crop breeding for biotic stress tolerance, an introduction. In: Varshney, R.K., Tuberosa, R. (eds.) Translational Genomics for Crop Breeding: Biotic Stress, vol I. Willey Blackwell, Hoboken, 1-9.
Weir, B.S. and Buckleton, J.S. (1996). Statistical issues in DNA profiling. Advances in Haemogenetics, 6:457-464.
Winter, P. Pfaff, T. Udupa, S.M. Huttel, B. Sharma, P.C. Sahi, S. Arreguin-Espinoza, R. Weigand. F. Muehlbauer, F.J. and Kahl, G. (1999). Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol. Gen. Genet. 262 (1):90–101.
Citation Format
How to Cite
Bakshi, A., Kumar, V., Sagar, S., Chaudhary, S., Kumar, R., & Kumar, M. (2016). Molecular characterization of chickpea (Cicer arietinum L.) genotypes using sequence tagged microsatellite site (STMS) markers. Journal of Applied and Natural Science, 8(2), 1068-1074. https://doi.org/10.31018/jans.v8i2.922
More Citation Formats:
Research Articles