Abstract
Fifty one Sequence tagged microsatellite sites (STMS) primer pairs were employed to assess the genetic diversity and relationships with morphological characters among the sixty-eight chickpea (Cicer arietinum L.) cultivars of India. A total of 32 out of 51 STMS primers were found polymorphic and a total of 121 alleles were generated out of which 102 (83 %) were detected for the 32 polymorphic STMS markers with an average of 2.22 alleles per locus. The PIC values of all the polymorphic loci ranged from 0.15 (TS82) to 0.69 (TS29) with the mean value of 0.27. Three primers showed PIC value of more than 0.60. The highest PIC value was observed for the primer TS29 (0.69), succeeded by the primer GA 11 (0.61) and TS71 (0.60). Gene diversity (He) was observed in the range of 0.16 (TS82) to 0.74 (TS29) with an average value of 0.33. The heterozygosity (Ho) was observed to be 0.39 (average) with a range of 0.04 (TA18) to 1.00 (TA76, STMS 5, TA72 and TA122). Based on the above STMS marker analysis by considering the parameters of PIC value (≥0.55), gene diversity (≥0.62), and polymorphic alleles (≥4), six highly polymorphic STMS loci GA11, TA76S, TA89, TS29, TS43 and TS71 were observed which can effectively be used in further molecular studies. Dendrogram generated by the UPGMA analysis and POWER MARKER v3.0 showed similar results and there was no clear demarcation of Kabuli and Desi genotypes. The present study resulted in identification of highly distinct genotypes JG 130 and C 235 (57 %) followed by two pairs of genotypes B 108 and JG 11 (57.8 %) and, JG 315 and RSG 2 (59 %) which can be used effectively in a breeding programs in order to develop transgressive segregants with wider genetic base and better promising genotypes. Effective use of these three pairs of chickpea genotypes is expected to give better products for the development of higher yielding Kabuli and Desi genotypes with tolerance/resistance to biotic and abiotic stresses and quality traits.
Similar content being viewed by others
Abbreviations
- STMS:
-
Sequence tagged microsatellite sites
- PIC:
-
Polymorphism information content
- CTAB:
-
Cetyl trimethyl ammonium bromide
- UPGMA:
-
Unweighted pair-group method with arithmetic average
References
Agrawal PK, Katiyar AK (2008) Validation of chickpea SSR markers in lentil and DNA fingerprinting of the lentil (Lenus culinaris subsp. Culinaris) cultivars of India. Indian J Genet 68:149–156
Agrawal PK, Srivastava A (2010) Assessment of genetic diversity among chickpea cultivars of India using RAPD markers. Indian J Genet 70(3):264–270
Bhagyawant SS, Srivastava N (2008) Genetic fingerprinting of chickpea (Cicer arietinum L.) germplasm using ISSR markers and their relationships. Afri J of Biotechnol 7:4428–4431
Bharadwaj C, Chauhan SK, Rajguru G, Srivastava R, Satyavathi CT, Yadav S, Rizvi AH, Kumar J, Solanki RK (2010) Diversity analysis of chickpea (Cicer arietinum L.) cultivars using STMS markers. Indian J Agri Sci 80:947–951
Choudhary S, Niroj Kumar S, Shokeen B, Bhatia S (2009) Development of chickpea EST-SSR markers and analysis of allelic variation across related species. Theor Appl Genet 118:591–608
Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An Introduction to markers, quantitative trait loci (QTL), mapping and marker assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196
Datta J, Lal N (2011) Characterization of genetic diversity in Cicer arietinum L. and Cajanus cajan L. Millspaugh using random amplified polymorphic DNA and simple sequence repeat markers. Genom Quant Genet 3:30–41
Fertilizer statistics (2011–12) The fertilizer association of India, 57th Edition, New Delhi
Gawel NJ, Jarret RL (1991) A modified CTAB DNA extraction procedure for Musa and Ipomoea plant. Mol Biol Rep 9:262–266
Gil J, Cubero JI (1993) Inheritance of seed coat thickness in chickpea (Cicer arietinum L.) and its evolutionary implications. Plant Breed 111:257–260
Gil J, Nadal S, Diego L, Moreno TM, De Antonio H (1999) Variability of some physio-chemical characters in Desi and Kabuli chickpea types. J Sci Food Agri 71:179–184
Iruela M, Rubio J, Cubero JI, Gill J, Millan T (2002) Phylogenetic analysis in the genus Cicer and cultivated chickpea using RAPD and ISSR markers. Thoer Appl Genet 104:643–651
Jaccard P (1908) Nouvelles recherches surla distribution florale. Bull Soc Sci Nat 44:223–270
Liu K, Muse SV (2005) Powermarker: integrated analysis environment for genetic marker data. Bioinformatics 21(9):2128–2129
Moreno MT, Cubero JI (1978) Variation in cicer arietinum L. Euphytica 27:465–468
Robertson LD, Ocampo B, Singh KB (1997) Morphological variation in wild annual Cicer species in comparison to the cultigen. Euphytica 95:309–319
Rohlf FJ (1997) NTSYS-pc. Numerical taxonomy and Multivariate Analysis System. Version 2.0. State University of New York, New York
Sant VJ, Patankara AG, Saroden D, Mhasel B, Sainani MN, Deshmukh RB, Ranjekar PK, Gupta VS (1999) Potential of DNA markers in detecting divergence and in analysing heterosis in Indian elite chickpea cultivars. Theor Appl Genet 98:1217–1225
Sharma PC, Winter P, Bunger T, Huttel B, Weigand F, Weising K, Kahl G (1995) Abundance and polymorphism of di-, tri- and tetra-nucleotide tandem repeats in chickpea (Cicer arietinum L.). Theor Appl Genet 90:90–96
Singh R, Vibha S, Randhawa GJ (2008) Molecular analysis of chickpea (Cicer arietinum L.) cultivars using AFLP and STMS markers. J Plant Biochem Biotech 17:167–171
Sudupak MA (2004) Inter and Intra-species Inter Simple Sequence Repeats (ISSR) variartions in the genus Cicer. Euphytica 135:229–238
Sudupak M, Akkaya M, Kence A (2002) Analysis of genetic relationships among perennial and annual cicer species growing in turkey using RAPD markers. Thoer Appl Genet 105:1220–1228
Talebi R, Fayaz F, Mardi M, Pirsyedi SM, Naji AM (2008) Genetic relationships among chickpea (Ci-cer arietinum) elite line based on RAPD and agronomic markers. Int J Agri Biol 10:301–305
Thomas MR, Scott NS (1993) Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theor Appl Genet 86:985–990
Udupa SM, Robertson LD, Weigand F, Baum M, Kahl G (1999) Allelic variation at (TAA)n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm. Mol Gen Genet 261:354–363
Upadhyaya HD, Dwivedi SL, Baum M, Varshney RK, Udupa SM, Gowda CLL, Hoisington D, Singh S (2008) Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.). BMC Plant Biol 8:106–117
Winter P, Pfaff T, Udupa SM, Huttel B, Sharma PC, Sahi S, Arreguin-Espinoza R, Weigand F, Muehlbauer FJ, 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
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Rizvi, H., Babu, B.K. & Agrawal, P.K. Molecular analysis of kabuli and desi type of Indian chickpea (Cicer arietinum L.) cultivars using STMS markers. J. Plant Biochem. Biotechnol. 23, 52–60 (2014). https://doi.org/10.1007/s13562-012-0187-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13562-012-0187-1