pp 1–9 | Cite as

Identification of elite Indian sugarcane varieties through DNA fingerprinting using genic microsatellite markers

  • Ram Baran SinghEmail author
  • Balwant Singh
  • R. K. Singh
Research Articles


Sugarcane is one of the important crops for sustainable economy and global energy security with high phenotypic polymorphism. Precise identification and characterization of plant genetic resources is one of the most essential aspects for breeding programs. Sugarcane popular hybrid varieties and genetic stocks routinely being used as a parent in hybridization program were included in the study. Molecular cataloguing was accomplished using a set of 70 primer pairs, of which ~ 39% were found to be robust polymorphic and unique in all the genotypes used. The number of DNA bands amplified by expressed sequenced tags derived simple sequence repeat (EST-SSR) primers ranged from 1 to 10 with an average of 5 bands per primer pair and their fragment size ranged between 50 and 1690 bp. Polymorphism information content (PIC) values were ranged from 0.17 to 1.00 with an average of 0.58. Unique DNA fingerprints of thirteen elite sugarcane varieties were generated with 27 polymorphic sugarcane specific EST-SSR markers. Analyses of DNA profiles produced by microsatellite markers showed the unique bands specific for individual variety. Generated DNA profiles would facilitate accurate variety identification in the perspective of protection of the breeder’s intellectual property rights, farmer’s rights and their purity testing. In addition, developed reliable DNA fingerprinting system will be able to track a potent parent genotype for breeding programs. The identified genotype specific and unique EST-SSR markers will be valuable for conservation and management of sugarcane genetic resources.


DNA fingerprinting EST-SSR markers Morpho-agronomical descriptors Variety identification Germplasm conservation and management Purity testing 



Authors are thankful to Director, Uttar Pradesh Council of Sugarcane Research (UPCSR), Shahjahanpur, (UP) India for providing necessary facilities to perform this study.

Author contributions

RBS conceived and designed the experiment, performed the experiments, and wrote the paper. BS was involved in acquisition and interpretation of data. RKS revised the paper.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest directly or indirectly and informed consent to publish this study and that the manuscript complies with the ethical standards of the journal.


  1. Anonymous (2006) Guidelines for the conduct of test for distinctiveness, uniformity and stability on sugarcane (Saccharum L.). Protection of Plant Varieties and Farmers’ Rights Authority (PPV & FRA), Government of India, New DelhiGoogle Scholar
  2. Anonymous (2012) Louisiana sugarcane variety identification guide. Louisiana State University Agricultural Center, Baton Rouge, pp 1–22Google Scholar
  3. Artschwager E, Brandes EW (1958) Sugarcane (Saccharum officinarum) origin, classification and descriptions of representative clones. Agriculture hand book no. 122. USDA, US Government Priority Office, WashingtonGoogle Scholar
  4. Cordeiro GM, Casu RE, McIntyre CL (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci 160:1115–1123CrossRefGoogle Scholar
  5. De Souza AC, Carvalho FP, Batista CF, Schwan RF, Dias DR (2013) Sugarcane bagasse hydrolysis using yeast cellulolytic enzymes. J Microbiol Biotechnol 23:1403–1412CrossRefGoogle Scholar
  6. Govindaraj P, Ramesh R, Appunu C, Swapna S, Priji PJ (2012) DNA fingerprinting of subtropical sugarcane (Saccharum spp) genotypes using sequence tagged microsatellites sites (STMS) markers. Plant Arch 12:347–352Google Scholar
  7. Hemaprabha G, Krishna JA, Vincy P, Priji P, Swapna S, Govindaraj P (2010) DNA fingerprinting for identification and protection of elite sugarcane (Saccharum spp.) varieties. Electron J Plant Breed 4:420–425Google Scholar
  8. Hoang NV, Furtado A, Botha FC, Simmons BA, Henry RJ (2015) Potential for genetic improvement of sugarcane as a source of biomass for biofuels. Front Bioeng Biotechnol 3:1–15CrossRefGoogle Scholar
  9. Hoisington D (1992) Laboratory protocol. CIMMYT Applied Molecular Genetics Laboratory, CIMMYT, MexicoGoogle Scholar
  10. Jannoo N, Forget L, Dookun A (2001) Contribution of microsatellites to sugarcane breeding program in Mauritius. Proc Int Soc Sugarcane Technol 24:637–639Google Scholar
  11. Korir NK, Han J, Shangguan L, Wang C, Kayesh E, Zhang Y, Fang J (2012) Plant variety and cultivar identification: advances and prospects. Crit Rev Biotechnol 33:111–125CrossRefGoogle Scholar
  12. LaBorde C, Legendre B, Bischoff K, Gravois K, Robert T (2008) Sugarcane variety identification Guide 2008. Louisiana State University Ag Center Publication, Baton RougeGoogle Scholar
  13. Piperidis G (2003) Progress towards evaluation of SSR as a tool for sugarcane variety identification. In: ISSCT IV. Molecular biology workshop, Montpellier, FranceGoogle Scholar
  14. Ruiz M, Aguiriano E, Giraldo P, Carrillo JM (2011) Genetic redundancy among durum wheat accessions as assessed by SSRs and endosperm proteins. Span J Agric Res 9:156–165CrossRefGoogle Scholar
  15. Silva DC, Dos Santos JM, de Souza Barbosa GV, Almeida C (2012) DNA fingerprinting based on simple sequence repeat (SSR) markers in sugarcane clones from the breeding program RIDESA. Afr J Biotechnol 11:4722–4728Google Scholar
  16. Singh RK, Singh RB, Singh SP, Sharma ML (2011) Identification of sugarcane microsatellites associated to sugar content in sugarcane and transferability to other cereal genomes. Euphytica 182:335–354CrossRefGoogle Scholar
  17. Singh RK, Singh RB, Singh SP, Mishra N, Rastogi J, Sharma ML, Kumar A (2013) Genetic diversity among Saccharum spontaneum clones and commercial hybrids through SSR markers. Sugar Tech 15:109–115CrossRefGoogle Scholar
  18. Singh RB, Srivastava S, Rastogi J, Gupta GN, Tiwari NN, Singh B, Singh RK (2014a) Molecular markers: exploited in crop improvement practices. Res Environ Life Sci 7:223–232Google Scholar
  19. Singh RB, Srivastva S, Verma AK, Singh B, Singh RK (2014b) Importance and progress of microsatellite markers in sugarcane (Saccharum spp. hybrids). J Sugarcane Technol 29:1–12Google Scholar
  20. Singh RB, Singh B, Singh RK (2015) Development of microsatellite (SSRs) markers and evaluation of genetic variability within sugarcane commercial varieties (Saccharum spp. hybrids). Int J Adv Res 3:700–708Google Scholar
  21. Singh RB, Singh B, Singh RK (2017) Study of genetic diversity of sugarcane (Saccharum) species and commercial varieties through TRAP molecular markers. Indian J Plant Physiol 22:332–338CrossRefGoogle Scholar
  22. Singh RB, Singh B, Singh RK (2018) Evaluation of Genetic diversity in Saccharum species clones and commercial varieties employing molecular (SSRs) and physiological markers. Indian J Plant Genet Resour 31:17–26CrossRefGoogle Scholar
  23. Singh RB, Singh B, Singh RK (2019a) Development of potential dbEST-derived microsatellite markers for genetic evaluation of sugarcane and related cereal grasses. Ind Crops Prod 128:38–47CrossRefGoogle Scholar
  24. Singh RB, Singh B, Singh RK (2019b) Cross-taxon transferability of sugarcane expressed sequence tags derived microsatellite (EST-SSR) markers across the related cereal grasses. J Plant Biochem Biotechnol 28(2):176–188CrossRefGoogle Scholar
  25. Swapna M, Sivaraju K, Sharma RK, Singh NK, Mohapatra T (2011) Single-strand conformational polymorphism of EST-SSRs: a potential tool for diversity analysis and varietal identification in sugarcane. Plant Mol Biol Rep 29:505–513CrossRefGoogle Scholar
  26. Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7:537–546Google Scholar
  27. Zhu YF, Qin GC, Hu J, Wang Y, Wang JC, Zhu SJ (2012) Fingerprinting and variety identification of rice (Oryza sativa L.) based on simple sequence repeat markers. Plant Omics 5:421Google Scholar

Copyright information

© Society for Plant Research 2019

Authors and Affiliations

  1. 1.I.K. Gujral Punjab Technical University (IKG PTU)KapurthalaIndia
  2. 2.Swami Satyanand College of Management and TechnologyAmritsarIndia
  3. 3.Sugarcane Research Institute (U.P. Council of Sugarcane Research)ShahjahanpurIndia
  4. 4.International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)HyderabadIndia

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