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Molecular Characterization of Primary Gene Pool of Chickpea Based on ISSR Markers

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Abstract

Genetic diversity and relationships within and among members of the primary gene pool of chickpea, including 38 accessions of Cicer arietinum, six of C. reticulatum,, and four of C. echinospermum, were investigated using 31 ISSR markers. The study revealed moderate diversity, detecting 141 fragments, of which 79 (56%) were polymorphic. Averages were 0.125 for polymorphic information content, 0.350 for marker index, and 0.715 for resolving power. The UPGMA dendrogram and the principal coordinate analysis revealed a clear differentiation between wild and cultivated accessions. The clustering pattern did not strictly follow the grouping of accessions by geographic origin but was in good agreement with the pedigree data and the seed type. The study demonstrates that ISSRs provide promising marker tools in revealing genetic diversity and relationships in chickpea and can contribute to efficient identification, conservation, and utilization of germplasm for plant improvement through conventional as well as molecular breeding approaches.

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References

  • Abbo S, Berger J, Turner NC (2003) Evolution of cultivated chickpea: four bottlenecks limit diversity and constrain adaptation. Funct Plant Biol 30:1081–1087

    Article  Google Scholar 

  • Ahmad F, Khan AI, Awan FS, Sadia B, Sadaqat HA, Bahadur S (2010) Genetic diversity of chickpea (Cicer arietinum L.) germplasm in Pakistan as revealed by RAPD analysis. Genet Mol Res 9:1414–1420

    Article  PubMed  CAS  Google Scholar 

  • Berger J, Abbo S, Turner NC (2003) Ecogeography of annual Cicer species: the poor state of the world collection. Crop Sci 43:1076–1090

    Article  Google Scholar 

  • Bhagyawant SS, Srivastava N (2008) Genetic fingerprinting of chickpea (Cicer arietinum L.) germplasm using ISSR markers and their relationships. Afr J Biotechnol 7:4428–4431

    CAS  Google Scholar 

  • Bohn MH, Utz F, Melchinger AE (1999) Genetic similarities among winter wheat cultivars determined on the basis of RFLPs, AFLPs and SSRs and their use for predicting progeny variance. Crop Sci 39:228–237

    Article  CAS  Google Scholar 

  • Choudhary P, Khanna SM, Jain PK, Bharadwaj C, Kumar J, Lakhera PC, Srinivasan R (2012) Genetic structure and diversity analysis of the primary gene pool of chickpea using SSR markers. Genet Mol Res 11:891–905

    Article  PubMed  CAS  Google Scholar 

  • Choumane W, Winter P, Weigand F, Kahl G (2000) Conservation and variability of sequence tagged microsatellite sites (STMSs) from chickpea (Cicer aerietinum L.) within the genus Cicer. Theor Appl Genet 101:269–278

    Article  CAS  Google Scholar 

  • Chowdhury MA, Vandenberg B, Warkentin T (2002) Cultivar identification and genetic relationship among selected breeding lines and cultivars in chickpea (Cicer arietinum L.). Euphytica 127:317–325

    Article  CAS  Google Scholar 

  • Croser JS, Ahmad F, Clarke HJ, Siddique KHM (2003) Utilization of wild Cicer in chickpea improvement–progress, constraints and prospects. Aust J Agri Res 54:429–444

    Article  Google Scholar 

  • dos Santos LF, de Oliveira EJ, dos Santos Silva A, de Carvalho FM, Costa JL, Pádua JG (2011) ISSR markers as a tool for the assessment of genetic diversity in Passiflora. Biochem Genet 49:540–554

    Article  PubMed  CAS  Google Scholar 

  • FAO (2010) Agriculture Data. United Nations Food and Agriculture Organization. http://faostat.fao.org/site/567/default.aspx. Accessed 1 Jan 2012

  • Fernandez E, Figueiras M, Benito C (2002) The use of ISSR and RAPD markers for detecting DNA polymorphism, genotype identification and genetic diversity among barley cultivars with known origin. Theor Appl Genet 104:845–851

    Article  PubMed  CAS  Google Scholar 

  • Glaszmann JC, Kilian B, Upadhyaya HD, Varshney RK (2010) Accessing genetic diversity for crop improvement. Curr Opin Plant Biol 13:1–7

    Article  Google Scholar 

  • Grativol C, da Fonseca Lira-Medeiros C, Hemerly AS, Ferreira PCG (2011) High efficiency and reliability of inter-simple sequence repeats (ISSR) markers for evaluation of genetic diversity in Brazilian cultivated Jatropha curcas L. accessions. Mol Biol Rep 38:4245–4256

    Article  PubMed  CAS  Google Scholar 

  • Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  • Millan T, Clarke HJ, Siddique KHM, Buhariwalla HK, Gaur PM, Kumar J, Kahl G, Winter P (2006) Chickpea molecular breeding: new tools and concepts. Euphytica 147:81–103

    Article  Google Scholar 

  • Muminovic J, Melchinger AE, Lübberstedt T (2004) Genetic diversity in corn salad (Valerianella locusta) and related species as determined by AFLP markers. Plant Breed 123:460–466

    Article  CAS  Google Scholar 

  • Nguyen TT, Taylor PWJ, Redden RJ, Ford R (2004) Genetic diversity estimates in Cicer using AFLP analysis. Plant Breed 123:173–179

    Article  CAS  Google Scholar 

  • Powell W, Margenta M, Andre C, Hanfrey M, Vogel J, Tingey S, Rafalsky A (1996) The utility of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98:107–112

    Article  CAS  Google Scholar 

  • Rafalski JA, Vogel JM, Morgante M, Powell W, Andre C, Tingey SV (1996) Generating and using DNA markers in plants. In: Lai E (ed) Brain B. Nonmammalian Genomic Analysis, A Practical Guide, pp 75–134

    Google Scholar 

  • Rao LS, Rani PU, Deshmukh PS, Kumar PA, Panguluri SK (2007) RAPD and ISSR fingerprinting in cultivated chickpea (Cicer arietinum L.) and its wild progenitor Cicer reticulatum Ladizinsky. Genet Resour Crop Evol 54:1235–1244

    Article  CAS  Google Scholar 

  • Ratnaparkhe MB, Santra DK, Tullu A, Muehlbauer FJ (1998) Inheritance of inter-simple-sequence-repeat polymorphisms and linkage with a fusarium wilt resistance gene in chickpea. Theor Appl Genet 96:348–353

    Article  CAS  Google Scholar 

  • Reddy MP, Sarla N, Siddiq EA (2002) Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128:9–17

    Article  Google Scholar 

  • Rohlf FJ (2000) NTsys-PC version 2.1: Numerical Taxonomy and Multivariate Analysis System. Exeter Publications, New York

  • Roldan-Ruiz I, Dendauw J, VanBockstaele E, Depicker A, De Loose M (2000) AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol Breed 6:125–134

    Article  CAS  Google Scholar 

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length in barley: mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014–8018

    Article  PubMed  CAS  Google Scholar 

  • Sefera T, Abebie B, Gaur PM, Assefa K, Varshney RK (2011) Characterisation and genetic diversity analysis of selected chickpea cultivars of nine countries using simple sequence repeat (SSR) markers. Crop Pasture Sci 62:177–187

    Article  Google Scholar 

  • Singh R, Sharma P, Varshney RK, Sharma SK, Singh NK (2008) Chickpea improvement: role of wild species and genetic markers. Biotechnol Genet Eng Rev 25:267–314

    Article  PubMed  CAS  Google Scholar 

  • Sudupak MA (2004) Inter- and intraspecies inter simple sequence repeat (ISSR) variation in the genus Cicer. Euphytica 135:229–238

    Article  CAS  Google Scholar 

  • Sudupak MA, Akkaya MS, Kence A (2002) Analysis of genetic relationships among perennial and annual Cicer species growing in Turkey using RAPD markers. Theor Appl Genet 105:1220–1228

    Article  PubMed  CAS  Google Scholar 

  • Talebi R, Naji AM, Fayaz F (2008) Geographical patterns of genetic diversity in cultivated chickpea (Cicer arietinum L.) characterized by amplified fragment length polymorphism. Plant Soil Environ 54:447–452

    CAS  Google Scholar 

  • Udupa SM, Sharma A, Sharma RP, Pai RA (1993) Narrow genetic variability in Cicer arietinum L. as revealed by RFLP analysis. J Plant Biochem Biotechol 2:83–86

    Article  CAS  Google Scholar 

  • Upadhyaya HD, Dwivedi SL, Baum M, Varshney RK, Udupa SM, Gowda CLL, Hoisington DA, 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

    Article  PubMed  Google Scholar 

  • Upadhyaya HD, Thudi M, Dronavalli N, Gujaria N, Singh S, Sharma S, Varshney RK (2011) Genomic tools and germplasm diversity for chickpea improvement. Plant Genet Resour 9:45–58

    Article  CAS  Google Scholar 

  • Varshney RK, Horres R, Molina C, Nayak S, Jungmann R, Swamy P, Winter P, Jayashree B, Kahl G, Hoisington DA (2007) Extending the repertoire of microsatellite markers for genetic linkage mapping and germplasm screening in chickpea. J SAT Agri Res 5(1):3

    Google Scholar 

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Acknowledgments

The authors gratefully acknowledge the Indian Council of Agricultural Research (ICAR) Network Project on Transgenics in Crops (Functional Genomics component) for providing the financial support for this study.

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Authors and Affiliations

  1. National Research Center on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India

    Pooja Choudhary, Suruchi M. Khanna, Pradeep K. Jain & Ramamurthy Srinivasan

  2. Division of Genetics, Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110012, India

    Chellapilla Bharadwaj & Jitendra Kumar

  3. Department of Biotechnology, Hemwati Nandan Bahuguna Garhwal University, Srinagar, Pauri Garhwal, 246 174, Uttarakhand, India

    Pooja Choudhary & Pramesh C. Lakhera

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  1. Pooja Choudhary
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  2. Suruchi M. Khanna
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  3. Pradeep K. Jain
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  4. Chellapilla Bharadwaj
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  5. Jitendra Kumar
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  6. Pramesh C. Lakhera
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  7. Ramamurthy Srinivasan
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Correspondence to Ramamurthy Srinivasan.

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Choudhary, P., Khanna, S.M., Jain, P.K. et al. Molecular Characterization of Primary Gene Pool of Chickpea Based on ISSR Markers. Biochem Genet 51, 306–322 (2013). https://doi.org/10.1007/s10528-012-9564-7

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  • DOI: https://doi.org/10.1007/s10528-012-9564-7

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