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Genetic diversity and relationship between cultivated clones of Dalbergia sissoo of wide geographical origin using RAPD markers

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Abstract

Random Amplified Polymorphic DNA (RAPD) polymorphism was employed to assess the genetic diversity in the elite germplasm of Dalbergia sissoo. Sixty-seven clones that are under cultivation in northern India, originated from six different states of India and Nepal were analyzed with 30 RAPD primers that generated a total of 342 fragments out of which 290 were polymorphic. Total genetic diversity (Ht) varied between 0.01 and 0.37, with an average of 0.19. Shannon’s Information index (I) varied between 0.02 and 0.54, with an average of 0.31. Marker attributes like Polymorphism Information Content (PIC), Marker Index (MI) and Effective Multiplex Ratio (EMR) values were calculated to assess the discriminatory power of 30 primers used. The PIC values ranged from 0.01 to 0.37 with an average of 0.17 per primer and the EMR ranged from 0.17 to 21.00 with a mean of 8.66 across all genotypes. Closely related clones were C49 and C51 with similarity index of 0.86 while the least similar or most dissimilar clones were C14 and S-DB showing similarity index of 0.58. The UPGMA-phenogram categorized the 67 clones into six clusters based on genetic similarity and dissimilarity. The clustering of clones in relation to their geographical location has been discussed.

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References

  • Arif M, Zaidi NW, Singh YP, Haq QMR, Singh US. 2009. A comparative analysis of ISSR and RAPD markers for study of genetic diversity in Shisham (Dalbergia sissoo). Plant Mol Biol Rep, 27(4): 488–495.

    Article  CAS  Google Scholar 

  • Ashraf M, Abdul SM, Rabia R, Sobia T. 2010. A molecular study of genetic diversity in shisham (dalbergia sissoo) plantation of NWFP, Pakistan. Pakistan Journal of Botany, 42(1): 79–88.

    CAS  Google Scholar 

  • Boland DJ. 1981. Eucalypt seed for Indian populations from better Australian natural seed sources. Indian Forester, 107(3): 125–134.

    Google Scholar 

  • Caron H, Bandou E, Kremer A. 2004. Multilocus assessment of levels of genetic diversity in tropical trees in Paracou stands. In: Gourlet FS, Guehl JM, Laroussinie O (eds), Ecology and Management of a Neotropical Rainforest. Amsterdam: Elsevier, Pp. 160–171.

    Google Scholar 

  • Castiglione S, Wang G, Damini G, Bandi C, Bisoffi S, Sala F. 1993. RAPD fingerprints for identification and for taxonomic studies of elite poplar (Populus spp.) clones. Theor Appl Genet, 87: 54–59.

    Article  CAS  Google Scholar 

  • Cavers S, Navarro C, Lowe AJ. 2004. A combination of molecular markers (cpDNA, PCR-RFLP, AFLP) identifies evolutionarily significant units in Cedrela odorata L. (Meliaceae) in Costa Rica. Conserv Genet, 4: 571–580.

    Article  Google Scholar 

  • Deshwal RPS, Singh R, Malik K, Randhawa GJ. 2005. Assessment of genetic diversity and genetic relationships among 29 population of Azadirachta indica A. Jess. using RAPD markers. Genetic Resources and Crop Evolution, 52: 285–292.

    Article  CAS  Google Scholar 

  • Dhillon RS, Bisla, Dhanda SK, Singh VP. 1995. Genetic variation and heritability of some growth traits in shisham (Dalbergia sissoo ROXB.). Annals of Biol, 11(1): 107–110.

    Google Scholar 

  • Esselman EJ, Li JQ, Crawford D, Winduss JL, Wolfe AD. 1999. Clonal diversity in the rare Calamagrostis porteri ssp. Insperata (Poaceae): comparative results for allozymes and random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Mol Ecol, 8: 443–451.

    Article  CAS  Google Scholar 

  • Ginwal HS, Maurya SS. 2008. RAPD markers for genetic diversity in Eucalyptus tereticornis Sm. of Australian and Papua New Guinea origin. In: Ansari SA, Narayanan C, Mandal AK (eds.), Forest Biotechnology in India. Delhi: Satish Serial Publishing House, 75–87.

    Google Scholar 

  • Ginwal HS, Maurya SS. 2010. Evaluation and optimization of DNA extraction method for Dalbergia sissoo leaf. Indian Journal of Biotechnology, 9: 69–73.

    CAS  Google Scholar 

  • Gupta PK, Varshney RK. 2000. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica, 113: 163–185.

    Article  CAS  Google Scholar 

  • Heybroek HM. 1978. Primary considerations: multiplication and genetic diversity. Unasylva 30: 27–33.

    Google Scholar 

  • Keil M, Griffin AR. 1994. Use of random amplified polymorphic DNA (RAPD) markers in the discrimination and verification of genotypes in Eucalyptus. Theor Appl Genet, 88: 116–122.

    Google Scholar 

  • Kremer A, Caron H, Cavers S, Colpaert N, Gheysen G, Gribel R, Lemes M, Lowe AJ, Margis R, Navarro C, Salgueiro F. 2005. Monitoring genetic diversity in tropical trees with multilocus dominant markers. Heredity, 95: 274–280.

    Article  PubMed  CAS  Google Scholar 

  • Li A, Ge S. 2001. Genetic variation and clonal diversity of Psammochloa villosa (Poaceae) detected by ISSR markers. Ann Bot, 87: 585–590.

    Article  CAS  Google Scholar 

  • Libby WJ. 1982. What is a safe number of clones per plantation? In: H.M. Heybroek, B.R. Stephan and K. von Weissenberg (Eds.), Resistance to Diseases and Pests. The Netherlands: Pudoc. Wageningen, pp. 342–360.

    Google Scholar 

  • Libby WJ. 1985. Potential of clonal forestry. In: L. Zsuffa, R.M. Rauter, and C.W. Yeatman (Eds.), Clonal Forestry: its Impact on Tree Improvement and our Future Forests. Proc. 19th Meeting Canadian Tree Improvement Association, Part 2, pp.1–11.

  • Lowe AJ, Jourde B, Breyne P, Colpaert N, Navarro C, Cavers S. 2003. Fine scale genetic structure and gene flow within Costa Rican populations of Mahogany (Swietenia macrophylla). Heredity, 90: 268–275.

    Article  PubMed  CAS  Google Scholar 

  • Margis R, Felix DB, Caldas JF, Salgueiro F, Dearaujo DSD, Breyne P, et al. 2002. Biodiversity on three neighboring populations of Eugenia uniflora (pitanga) from Brazilian Atlantic rain forest accessed by AFLP markers. Biodivers and Conserv, 11: 149–163.

    Article  Google Scholar 

  • Mosseler A, Egger KN, Hughes GA. 1992. Low levels of genetic diversity in red pine confirmed by Random Amplified Polymorphic DNA markers. Can J For Res, 22: 1332–1337.

    Article  CAS  Google Scholar 

  • Nanda MR, Nayak S, Rout GR. 2004. Studies on genetic relatedness of Acacia tree species using RAPD markers. Biologia Bratislava, 59: 115–120.

    CAS  Google Scholar 

  • Nei M. 1973. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, USA 70: 3321–3323.

    Article  CAS  Google Scholar 

  • Nei M, Li WH. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Nat Acad Sci USA, 76: 5269–5273.

    Article  PubMed  CAS  Google Scholar 

  • Okun DO, Kenya EU, Oballa PO, Odee DW, Muluvi GM. 2008. Analysis of genetic diversity in Eucalyptus grandis (Hill ex Maiden) seed sources using inter simple sequence repeats (ISSR) molecular markers. African Journal of Biotechnology, 7(13): 2119–2123.

    CAS  Google Scholar 

  • Parajuli AV, Bhatta B, Adhikari MK, Tuladhar J, Thapa HB. 1999. Causal agents responsible for the die-back of Dalbergia sissoo in Nepal’s eastern Terai. Ban Ko Janakari, 9(1).

  • Parsons BJ, Newbury HJ, Jackson MT, Ford-Lloyd BV. 1997. Contrasting genetic diversity relationships are revealed in rice (Oryza sativa L.) using different marker types. Mol Breed, 3: 115–125.

    Article  CAS  Google Scholar 

  • Rajgopal J, Bashyam L, Bhatia S, Khurana DK, Srivastava PS, Lakshmikumaran M. 2000. Evaluation of genetic diversity in the Himalyan Poplar using RAPD markers. Silvae Genetica, 49(2): 60–66.

    Google Scholar 

  • Rohlf FJ. 1997. NTSYSpc: numerical taxonomy and multivariate analysis system, version 2.02. Exeter Software, Setauket, New York, USA.

    Google Scholar 

  • 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 

  • Rout GR, Bhatacharya D, Nanda RM, Nayak S, Das P. 2003. Evaluation of genetic relationships in Dalbergia species using RAPD markers. Biodiversity and Conservation, 12: 197–206.

    Article  Google Scholar 

  • Sagta HC, Nautiyal. 2001. Growth performance and genetic divergence of various provenances of Dalbergia Sissoo ROXB. at nursery stage. Silvae Genetica, 50(3–4): 93–99.

    Google Scholar 

  • Scheepers D, Eloy MC, Briquet M. 1997. Use of RAPD patterns for clone verification and in studying provenance relationship in Norway spruce (Picea abies). Theor Appl Genet, 94: 480–485.

    Article  CAS  Google Scholar 

  • Schnell RJ, Ronning CM, Knight RJ, Jr. 1995. Identification of cultivars and validation of genetic relationship in Mangifera indica L. using RAPD markers. Theor Appl Genet, 90: 269–274.

    Article  CAS  Google Scholar 

  • Shiv-Kumar P, Banerjee AC. 1986. Provenance trials of Acacia nilotica. J Tree Sci, 5(1): 53–56.

    Google Scholar 

  • Ude GN, Kenworthy WJ, Costa JM, Cregan PB, Alvernaz J. 2003. Genetic diversity of soybean cultivars from China, Japan, North America, and North American ancestral lines determined by amplified fragment length polymorphism. Crop Sci, 43: 1858–1867.

    Article  CAS  Google Scholar 

  • Upadhyay A, Jayadev K, Manimekalai R, Parthasarathy VA. 2004. Genetic relationship and diversity in Indian coconut accessions based on RAPD markers. Scientia Horticulturae, 99: 353–362.

    Article  CAS  Google Scholar 

  • Vaishali, Khan S, Sharma V. 2008. RAPD based assessment of genetic diversity of Butea monosperma from different agro-ecological regions of India. Indian Journal of Biotechnology, 7: 320–327.

    CAS  Google Scholar 

  • Varshney RK, Chabane K, Hendre PS, Aggarwal RK, Graner A. 2007. Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys. Plant Sci, 173: 638–649.

    Article  CAS  Google Scholar 

  • Whitkus R, Cruz ML, Bravo M, Gomez-Pompa A. 1998. Genetic diversity and relationships of cacao (Theobroma cacao L.) in southern Mexico. Theor Appl Genet, 96: 621–627.

    Google Scholar 

  • Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nuc Ac Res, 18: 6531–6535.

    Article  CAS  Google Scholar 

  • Zehdi S, Sakka H, Mohamed Salem AO, Rhouma A, Marrakchi M, Trifi M. 2004. Molecular polymorphism and genetic relationships in a Tunisian date palm (Phoenix dactylifera L.) collection using ISSR amplification fingerprinting. IPGR News Lett, 144: 39–44.

    Google Scholar 

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Authors and Affiliations

  1. Division of Genetics and Tree Propagation, Forest Research Institute, P.O. I.P.E Kaulagarh Road, Dehradun, 248195, Uttarakhand, India

    H. S. Ginwal, S. S. Maurya & P. Chauhan

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  1. H. S. Ginwal
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  2. S. S. Maurya
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  3. P. Chauhan
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Correspondence to H. S. Ginwal.

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Ginwal, H.S., Maurya, S.S. & Chauhan, P. Genetic diversity and relationship between cultivated clones of Dalbergia sissoo of wide geographical origin using RAPD markers. Journal of Forestry Research 22, 507–517 (2011). https://doi.org/10.1007/s11676-011-0171-y

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