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Assessment of Genetic Diversity in Sugarcane Germplasm Using ISSR and SSR Markers

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Abstract

Molecular diversity within and between Saccharum species clones and elite commercial hybrid varieties was studied using intersimple sequence repeat (ISSR) and simple sequence repeat (SSR) markers. The present study was performed to characterize 81 sugarcane genotypes. A total of 13 ISSR primers used and produced 65 amplified fragments, of which 63 (96.5 %) were polymorphic. The Polymorphic Information Content (PIC) value ranged from 0.11 (UBC824) to 0.45 (UBC825) primers with an average value of 0.28. The primer UBC 817 and UBC 825 exhibited highest resolving power (Rp) value 3.8 among thirteen primers. Genetic similarity (GS) by Jaccard’s similarity coefficient ranged from 0.23 to 0.95 with a mean of 0.59. Of the 79 alleles amplified by 28 SSRs primers showed 76 alleles, which were found to be polymorphic (96.2 %). The PIC value ranged from 0.06 (VSICRAD4) to 0.55 (VSICRAD26) primers with an average value of 0.17. The primer VSICRAD23 exhibited highest resolving power (Rp) value 4.3 among 28 primers. The GS by Jaccard’s similarity coefficient ranged from 0.11 to 0.91 with a mean of 0.51. Dendrograms constructed using the UPGMA cluster analysis revealed low level of correlation between genetic similarities based on pedigree and DNA profiles. The ISSR and SSR amplification proved to be valuable method for assessing genetic diversity among sugarcane complex and their related wild varieties and for identification of the cultivars.

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References

  • Aljanabi, S.M., L. Froget, and A. Dookun. 1999. An improved and rapid protocol for the isolation of polysaccharide and polyphenol free sugarcane DNA. Plant Molecular Biology Reporter 17: 1–8.

    Article  Google Scholar 

  • Al-Janabi, S.M., M. McClelland, C. Petersen, and B.W.S. Sobral. 1994. Phylogenetic analysis of organellar DNA sequences in the Andropogoneae: Saccharinae. Theoretical and Applied Genetics 98: 933–944.

    Google Scholar 

  • Alwala, S., A. Suman, J.A. Arro, J.C. Veremis, and C.A. Kimbeng. 2006. Target region amplified polymorphism (TRAP) for assessing genetic diversity in sugarcane germplasm collections. Crop Science 46: 448–455.

    Article  CAS  Google Scholar 

  • Barrett, B.A., K.K. Kidwell, and P.N. Fox. 1998. Comparison of AFLP and pedigree based genetic diversity assessment methods using wheat cultivars from the Pacific Northwest. Crop Science 38: 1271–1278.

    Article  CAS  Google Scholar 

  • Benchimol, L.L., C.L. Souza Jr, A.A.F. Garcia, P.M.S. Kono, C.A. Mangolim, A.M.M. Barbosa, A.S.G. Coelho, and A.P. Souza. 2000. Genetic diversity in tropical maize inbred lines: Heterotic group assignment and hybrid performance determined by RFLP markers. Plant Breeding 119(6): 491–496.

    Article  CAS  Google Scholar 

  • Bess, P., G. Taylor, B. Carroll, N. Berbing, D. Burner, and C.L. McLntyre. 1998. Assessing genetic diversity in a sugarcane germplasm collection using an automated AFLP analysis. Genetica 104: 143–153.

    Article  Google Scholar 

  • Burnquist, W.L., M.E. Sorrells, and S.D. Tanksley. 1995. Characterization of genetic variability in Saccharum germplasm by means of Restriction Fragment Length Polymorphism (RFLP) analysis. Proceedings of the International Society of Sugar Cane Technology 21: 355–365.

    Google Scholar 

  • Cordeiro, G.M., G.O. Taylor, and R.J. Henry. 2000. Characterization of microsatellite markers from sugarcane (Saccharum sp.) a highly polyploid species. Plant Science 155: 161–168.

    Article  PubMed  CAS  Google Scholar 

  • Costa, L.M.L., Lidiane L.Barbosa. Amorim, Alberto V.C. Onofre, Luiz J.O. Tavares de Melo, Maria Betânia M. de Oliveira, Reginaldo de Carvalho, and Ana M. Benko-Iseppon. 2011. Assessment of genetic diversity in contrasting sugarcane varieties using Inter-Simple Sequence Repeat (ISSR) markers. American Journal of Plant Science 2: 425–432.

    Article  Google Scholar 

  • Creste, S., D.M. Sansoli, A.C.S. Tardiani, D.N. Silva, F.K. Goncalves, T.M. Favero, C.N.F. Medeiros, C.S. Festucci, L.A. Carlini-Garcia, M.G.A. Landell, and L.R. Pinto. 2010. Comparison of AFLP, TRAP and SSRs in the estimation of genetic relationships in sugarcane. Sugar Tech 12(2): 150–154.

    Article  CAS  Google Scholar 

  • D’Hont, A., L. Grivet, P. Feldmann, J.C. Glaszmann, S. Rao, and N. Berrding. 1996. Characterization of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Molecular and General Genetics 250: 405–413.

    PubMed  Google Scholar 

  • D’Hont, A., Y.H. Lu, P. Feldmann, and J.C. Glaszmann. 1993. Cytoplasmic diversity in sugar cane revealed by heterologous probes. Sugarcane 1: 12–15.

    Google Scholar 

  • Daniels, J., and B.T. Roach. 1987. Taxonomy and evolution. In Sugarcane improvement through breeding, ed. D.J. Heinz, 7–84. Amsterdam: Elsevier Press.

    Google Scholar 

  • Daniels, J., P. Smith, N. Paton, and C.A. Williams. 1975. The origin of the genus Saccharum. Sugarcane Breeding Newsletter 36: 24–39.

    Google Scholar 

  • Garcia, A.A.F., L.L. Benchimol, A.M.M. Barbosa, I.O. Geraldi, C.L. Souza Jr., and A.P. Souza. 2004. Comparision of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines. Genetics and Molecular Biology 27(4): 579–588.

    Article  CAS  Google Scholar 

  • Graner, A., W.F. Ludwig, and A.E. Melchinger. 1995. Relationship among European barley germplasm. II. Comparison of RFLP and pedigree data. Crop Science 34: 1199–1205.

    Article  Google Scholar 

  • Harvey, M., and F.C. Botha. 1996. Use of PCR-based methodologies for the determination of DNA diversity between Saccharum varieties. Euphytica 89: 257–265.

    Article  CAS  Google Scholar 

  • Kawar, P.G., R.M. Devarumath, and Y.S. Nerkar. 2009. Use of RAPD markers for assessment of genetic diversity in sugarcane cultivars. Indian Journal of Biotechnology 8: 67–71.

    CAS  Google Scholar 

  • Lima, M.L.A., A.A.F. Garcia, K.M. Oliverira, S. Motsuoka, H. Arizono, C.L. De Souza Jr., and A.P. de Souza. 2002. Analysis of genetic similarity detected by AFLP and coefficient of parentage among genotypes of sugarcane (Saccharum spp.). Theoretical and Applied Genetics 104: 30–38.

    Article  PubMed  CAS  Google Scholar 

  • Lu, Y.H., A. D’Hont, D.I.T. Walker, P.S. Rao, P. Feldmann, and J.C. Glaszmann. 1994. Relationships among ancestral species of sugarcane revealed with RFLP using single copy maize nuclear probes. Euphytica 78: 7–18.

    Article  Google Scholar 

  • Mondal, S., S.R. Sutar, and A.M. Badigannavar. 2009. Assessment of genetic diversity in cultivated groundnut (Arachis hypogaea L.) with differential responses to rust and late leaf spot using ISSR markers. Journal of Genetics and Plant Breeding 63(3): 219–224.

    Google Scholar 

  • Mukherjee, S.K. 1957. Origin and distribution of Saccharum. Botanical Gazette 19: 55–61.

    Article  Google Scholar 

  • Nair, N.V., S. Nair, T.V. Sreenivasan, and M. Mohan. 1999. Analysis of genetic diversity and phylogeny in Saccharum and related genera using RAPD markers. Genetic Resources and Crop Evolution 46: 73–79.

    Article  Google Scholar 

  • Nair, N.V., A. Selvi, T.V. Sreenivasan, and K.N. Pushpalatha. 2002. Molecular diversity in Indian sugarcane varieties as revealed by randomly amplified DNA polymorphisms. Euphytica 127: 219–225.

    Article  CAS  Google Scholar 

  • Prevost, A., and M.J. Wilkinson. 1999. A new system of comparing primers applied to ISSR fingerprinting of potato cultivars. Theoretical and Applied Genetics 98: 107–112.

    Article  CAS  Google Scholar 

  • Rohlf, F.J. 2000. NTSYSpc numerical taxonomy and multivariate analysis system. New York: Exeter Software.

    Google Scholar 

  • Selvi, A., N.V. Nair, N. Balasundaram, and T. Mohapatra. 2003. Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane. Genome 46: 394–403.

    Article  PubMed  CAS  Google Scholar 

  • Selvi, A., N.V. Nair, J.L. Noyer, N.K. Singh, N. Balasundaram, K.C. Bansal, K.R. Koundal, and T. Mohapatra. 2006. AFLP analysis of the phenetic organization and genetic diversity in the sugarcane complex, Saccharum and Erianthus. Genetic Resources and Crop Evolution 53: 831–842.

    Article  CAS  Google Scholar 

  • Singh, R.K., S. Srivastava, S.P. Singh, M.L. Sharma, T. Mohopatra, N.K. Singh, and S.B. Singh. 2008. Identification of new microsatellite DNA markers for sugar and related traits in sugarcane. Sugar Tech 10(4): 327–333.

    Article  CAS  Google Scholar 

  • Sobral, B.W.S., D.P. Braga, E.S. Lahood, and P. Keim. 1994. Phylogenetic analysis of chloroplast restriction enzyme site mutations in the Saccharinae Griseb. Subtribe of the Andropogoneae Dumort Tribe. Theoretical and Applied Genetics 87: 843–853.

    Article  CAS  Google Scholar 

  • Sreenivasan, T.V., B.S. Ahloowalia, and D.J. Heinz. 1987. Cytogenetics. In Sugarcane improvement through breeding, ed. D.J. Heinz, 211–253. Amsterdam: Elsevier.

    Google Scholar 

  • Srivastava, S., and P. Gupta. 2008. Inter simple sequence repeat profile as a genetic marker system in sugarcane. Sugar Tech 10(1): 48–52.

    Article  CAS  Google Scholar 

  • Weir B.S. 1990. Genetic data analysis. Sunderland, Mass.: Sinauer Associates.

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Acknowledgments

We are thankful to the Director General and Director (AS&T), Vasantdada Sugar Institute, Pune India, for providing research facility. We are also thankful to Dr. R. S. Hapase, Principal Scientist, Plant Breeding section, for providing the leaf samples.

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Authors and Affiliations

  1. Molecular Biology and Genetic Engineering Division, Vasantdada Sugar Institute, Manjari (Bk), 412307, Pune, India

    Rachayya M. Devarumath, Sachin B. Kalwade & Prashant G. Kawar

  2. Plant Breeding Division, Vasantdada Sugar Institute, Manjari (Bk), 412307, Pune, India

    Kapil V. Sushir

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  1. Rachayya M. Devarumath
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  2. Sachin B. Kalwade
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  3. Prashant G. Kawar
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  4. Kapil V. Sushir
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Correspondence to Rachayya M. Devarumath.

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Devarumath, R.M., Kalwade, S.B., Kawar, P.G. et al. Assessment of Genetic Diversity in Sugarcane Germplasm Using ISSR and SSR Markers. Sugar Tech 14, 334–344 (2012). https://doi.org/10.1007/s12355-012-0168-7

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