Skip to main content
SpringerLink
Log in

Analysis of Genetic Diversity of Saccharum Complex Using Chloroplast Microsatellite Markers

  • Research Article
  • Published:
Sugar Tech Aims and scope Submit manuscript

An Erratum to this article was published on 23 June 2015

Abstract

A basic understanding of the cytoplasmic diversity of Saccharum complex comprising of Saccharum species and related genera is essential for broadening the cytoplasmic base of sugarcane cultivars. In the present study markers generated by nine chloroplast microsatellite primer pairs designed from sugarcane chloroplast genome were used to establish the genetic relationship and phylogeny among 43 accessions belonging to different species of Saccharum and related genera representing the Saccharum complex. The polymorphic primer pairs amplified an average of six alleles per loci and possess relatively high polymorphism information content. Molecular diversity was estimated using 54 polymorphic markers. The overall chloroplast genetic diversity in the Saccharum complex was found to be 53 %. The genetic diversity among Saccharum species was 22 %. Among the Saccharum species S. spontaneum was found to be distinct from other species of Saccharum and cpSSR markers could efficiently distinguish S. spontaneum from rest of the Saccharum spcies. Ripidium, one of the most primitive among the Saccharum complex showed the highest genetic diversity (90 %) with Saccharum. Miscanthus, another primitive genus of Saccharum complex was found to be more closely related to Saccharum than Erianthus. In view of the high genetic diversity, the present study supports the utilization of different species of Erianthus in the sugarcane breeding programmes for broadening the cytoplasmic base of the sugarcane varieties.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Al-Janabi, S.M., M. McClelland, C. Petersen, and B.W.S. Sobral. 1994. Phylogenetic analysis of organellar DNA sequences in the Andropogoneae: Saccharine. Theoretical and Applied Genetics 88: 933–944.

    Article  CAS  PubMed  Google Scholar 

  • Anderson, J.A., G.A. Churchill, J.E. Autroque, S.D. Tanksley, and M.E. Swells. 1993. Optimizing parental selection for genetic linkage maps. Genome 36: 181–186.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Asano, T., T. Tsudzuki, S. Takahashi, H. Shimada, and K. Kadowaki. 2004. Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: A comparative analysis of four monocot chloroplast genomes. DNA Research 11: 93–99.

    Article  CAS  PubMed  Google Scholar 

  • Bakshi Ram, N.V. Nair, C.M. Radhakrishnan, N. Singh, and B.K. Sahi. 2007. Effect of cytoplasmic diversity on performance of sugarcane hybrids. The Indian Journal of Genetics 67: 229–231.

  • 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 Technologists 21: 355–365.

    Google Scholar 

  • Clegg, M.T. 1993. Chloroplast gene sequences and the study of plant evolution. Proceedings of the National Academy of Sciences of the United States of America 90: 363–367.

    Article  CAS  PubMed  PubMed Central  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.

    Chapter  Google Scholar 

  • Devarumath, R., S. Kalwade, P. Bundock, F.G. Eliott, and R. Henry. 2013. Independent target region amplification polymorphism and single-nucleotide polymorphism marker utility in genetic evaluation of sugarcane genotypes. Plant Breeding 132: 736–747.

    Article  CAS  Google Scholar 

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

    Google Scholar 

  • Irvine, J.E. 1999. Saccharum species as horticultural classes. Theoretical and Applied Genetics 98: 186–194.

    Article  Google Scholar 

  • Liu, P., Y. Que, and Y.-B. Pan. 2011. Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Tech 13(2): 129–136.

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Mangelsdorf, A.J. 1983. Cytoplasmic diversity in relation to pest and pathogens. Sugarcane Breeders Newsletter 45: 45–49.

    Google Scholar 

  • Marshall, H.D., C. Newton, and K. Ritland. 2001. Sequence-repeat polymorphisms exhibit the signature of recombination in lodgepole pine chloroplast DNA. Molecular Biology and Evolution 18: 2136–2138.

    Article  CAS  PubMed  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. 1999. Production and cyto-morphological analysis of intergeneric hybrids of Sorghum x Saccharum. Euphytica 108: 187–191.

    Article  Google Scholar 

  • Powell, W., G.C. Machray, and J. Provan. 1996. Polymorphism revealed by simple sequence repeats. Trends in Plant Science 1: 215–222.

    Article  Google Scholar 

  • Rajendrakumar, P., A.K. Biswal, S.M. Balachandran, K. Srinivasarao, and R.M. Sundaram. 2007. Simple sequence repeats in organellar genomes of rice: Frequency and distribution in genic and intergenic regions. Bioinformatics 23: 1–4.

    Article  CAS  PubMed  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 sugar cane. Genome 46: 394–403.

    Article  CAS  PubMed  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 Erianthum. Genetic Resources and Crop Evolution 53: 831–842.

    Article  CAS  Google Scholar 

  • Selvi, A., O. Garsmeur, and A. D’Hont. 2008. Phylogenetic analysis of sugarcane. In: Deputation report of the Department of Biotechnology overseas associateship, submitted to the Department of Biotechnology, India, p. 3.

  • Singh, R.K., S.K. Mishra, S.P. Singh, N. Mishra, and M.L. Sharma. 2010. Evaluation of microsatellite markers for genetic diversity analysis among sugarcane species and commercial hybrids. Australian Journal of Crop Science 4: 115–124.

    Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Suman, A., C.A. Kimbeng, S.J. Edme, and J. Vermis. 2008. Sequence related amplified polymorphism (SRAP) markers for accessing genetic relationship and diversity in sugarcane germplasm collections. Plant Genetic Resources 6: 222–231.

    Article  Google Scholar 

  • Takahashi, S., T. Furukawa, T. Asano, and Y. Terajima. 2005. Very close relationship of the chloroplast genomes among Saccharum species. Theoretical and Applied Genetics 110: 1523–1529.

    Article  CAS  PubMed  Google Scholar 

  • Tambarussi, E.V., D.M. Melotto-Passarin, S.G. Gonzalez, J.B. Brigati, F.A. de Jesus, A.L. Barbosa, K. Dressano, and H. Carrer. 2009. In silico analysis of simple sequence repeats from chloroplast genomes of Solanaceae species. Crop Breeding and Applied Biotechnology 9: 344–352.

    Article  CAS  Google Scholar 

  • Walbot, V. 1998. Preparation of DNA from rice seedlings. Rice Genetics Newsletters 5: 149–151.

    Google Scholar 

  • Zhu, J.R., H. Zhou, Y. Pan, and X. Lu. 2014. Genetic variability among the chloroplast genomes of sugarcane (Saccharum spp.) and its wild progenitor species Saccharum spontaneum L. Genetics and Molecular Research 13(2): 3037–3047.

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Biotechnology Laboratory, Sugarcane Breeding Institute, Coimbatore, 641007, India

    Punnya Raj, A. Selvi, P. T. Prathima & N. V. Nair

Authors
  1. Punnya Raj
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. Selvi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. P. T. Prathima
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. N. V. Nair
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Punnya Raj.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Raj, P., Selvi, A., Prathima, P.T. et al. Analysis of Genetic Diversity of Saccharum Complex Using Chloroplast Microsatellite Markers. Sugar Tech 18, 141–148 (2016). https://doi.org/10.1007/s12355-015-0382-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12355-015-0382-1

Keywords

Search

Navigation