A new set of mulberry-specific SSR markers for application in cultivar identification and DUS testing

  • Marian Vincent Pinto
  • H. S. Poornima
  • V. Sivaprasad
  • V. Girish Naik
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The monophagous domesticated silkworm Bombyx mori derives all its nutritional requirement from the mulberry (Morus spp.) leaves. Therefore, mulberry has a key role in sustainably improving the quality and yield of silk. Lack of codominant markers for use in genetic mapping has constrained the efforts in marker-assisted breeding for targeted trait improvement. Currently, a total of 443 (160 genomic and 283 genic) mulberry-specific simple sequence repeat (SSR) markers are available for genome analysis (Aggarwal et al.2004; Tani et al.2005; Zhao et al.2005; Gao 2013; Mathithumilan et al.2013; Thumilan et al.2016). The draft genome sequence of Morus notabilis was made available to the mulberry research community by He et al. (2013). Krishnan et al. (2014a) mined SSRs available in the genome sequence and archived them in the MulSatDB. In this study, we report the development and validation of 24 primer pairs for the SSRs archived in MulSatDB. We have used these markers to...


mulberry simple sequence repeats genotyping genetic analysis cultivar identification DUS testing 



This study was funded by the Department of Biotechnology, Ministry of Science and Technology, Govt. of India, New Delhi grant no. BT/PR5811/PDB/19/238/2012 sanctioned to VGN. MVP was supported with Senior Research Fellowship by the Council of Scientific and Industrial Research, New Delhi. The authors gratefully acknowledge the help received from Mr M. S. Rukmangada, CSRTI, Mysuru during genomic DNA extraction and QC. The authors also thank Prof. H. S. Prakash, Department of Studies in Biotechnology, University of Mysore, Mysuru for extending the NanoDrop 2000C facility.


  1. Aggarwal R. K., Udaykumar D., Hendre P. S., Sarkar A. and Singh, L. I. 2004 Isolation and characterization of six novel microsatellite markers for mulberry (Morus indica). Mol. Ecol. Notes 4, 477–479.CrossRefGoogle Scholar
  2. Akagi H., Yokozeki Y., Inagaki A. and Fujimura T. 1997 Highly polymorphic microsatellites of rice consist of AT repeats, and a classification of closely related cultivars with these microsatellite loci. Theor. Appl. Genet. 94, 61–67.CrossRefPubMedGoogle Scholar
  3. Gao L. 2013 Development of EST-SSR primers in mulberry. J. Southern Agri. 44, 1254–1257.Google Scholar
  4. Gray E. 1990 Evidence of phenotypic plasticity in mulberry (Morus L.). Castanea 55, 272–281.Google Scholar
  5. Gray E. and Call N. M. 1994 Effects of induced plant injury on leaf lobation in red mulberry (Morus rubra L.). Castanea 59, 167–175.Google Scholar
  6. He N., Zhang C., Qi X., Zhao S., Tao Y., Yang G. et al. 2013 Draft genome sequence of the mulberry tree Morus notabilis. Nat. Commun. 4, 2445.CrossRefPubMedPubMedCentralGoogle Scholar
  7. Jombart T. 2008 adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405.CrossRefPubMedGoogle Scholar
  8. Jombart T., Devillard S. and Balloux F. 2010 Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 11, 94.CrossRefPubMedPubMedCentralGoogle Scholar
  9. Jones C. J., Edwards K. J., Castaglione S., Winfield M. O., Sala F., van de Wiel C. et al. 1997 Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Mol. Breed. 3, 381–390.CrossRefGoogle Scholar
  10. Kibbe W. A. 2007 OligoCalc: an online oligonucleotide pro-perties calculator. Nucleic Acids Res. 35, W43–W46.CrossRefPubMedPubMedCentralGoogle Scholar
  11. Krishnan R. R. 2014 Development of panel of diverse germplasm and core subset of mulberry (Morus spp.) by microsatellite marker aided analysis. Ph.D. Thesis, University of Mysore, Mysuru.Google Scholar
  12. Krishnan R. R., Sumathy R., Bindroo B. B. and Naik V. G. 2014a MulSatDB: a first online database for mulberry microsatellites. Trees 28, 1793–1799.CrossRefGoogle Scholar
  13. Krishnan R. R., Naik V. G., Ramesh S. R. and Qadri S. M. H. 2014b Microsatellite marker analysis reveals the events of the introduction and spread of cultivated mulberry in the Indian subcontinent. Plant Genet. Resour. 12, 129–139.CrossRefGoogle Scholar
  14. Martins W. S., Lucas D. C. S., Neves K. D. S. and Bertioli D. J. 2009 WebSat – a web software for microsatellite marker development. Bioinformation 3, 282–283.CrossRefPubMedPubMedCentralGoogle Scholar
  15. Mathithumilan B., Kadam N. N., Biradar J., Reddy S. H., Ankaiah M., Narayanan M. J. et al. 2013 Development and characterization of microsatellite markers for Morus spp. and assessment of their transferability to other closely related species. BMC Plant Biol. 13, 194.CrossRefPubMedPubMedCentralGoogle Scholar
  16. Pinto M. V., Naik V. G. and Qadri S. M. H. 2012 Genetic variability studies in mulberry using microsatellite markers. J. Sericult. Technol. 3, 38–43.Google Scholar
  17. Powell W., Morgante M., Andre C., Hanafey M., Vogel J., Tingey, S. et al. 1996 The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breed. 2, 225–238.CrossRefGoogle Scholar
  18. Prevost A. and Wilkinson M. J. 1999 A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor. Appl. Genet. 98, 107–112.CrossRefGoogle Scholar
  19. Sambrook J. and Russell D. W. 2001 Molecular cloning: a laboratory manual, 3rd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.Google Scholar
  20. Sanguinetti C. J., Dias N. E. and Simpson A. J. 1994 Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. Biotechniques 17, 914–921.PubMedGoogle Scholar
  21. Tani N., Kawahara T. and Yoshimaru H. 2005 Development and diversity of microsatellite markers for endangered species, Morus boninensis Koidz., to establish conservation program. Mol. Ecol. Notes 5, 398–400.CrossRefGoogle Scholar
  22. Thumilan B. M., Sajeevan R. S., Biradar J., Madhuri T., Nataraja K. N. and Sreeman S. M. 2016 Development and characterization of genic SSR markers from Indian mulberry transcriptome and their transferability to related species of Moraceae. PLoS One 11, e0162909.CrossRefGoogle Scholar
  23. Vijayan K., Raju P. J., Tikader A. and Saratchnadra B. 2014 Biotechnology of mulberry (Morus L.) – a review. Emir. J. Food Agric. 26, 472–496.CrossRefGoogle Scholar
  24. Zhao W., Miao X., Jia S., Pan Y. and Huang Y. 2005 Isolation and characterization of microsatellite loci from the mulberry, Morus L. Plant Sci. 168, 519–525.CrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 2018

Authors and Affiliations

  • Marian Vincent Pinto
    • 1
  • H. S. Poornima
    • 1
  • V. Sivaprasad
    • 1
  • V. Girish Naik
    • 1
    • 2
  1. 1.Molecular Biology Laboratory-1Central Sericultural Research and Training InstituteMysuruIndia
  2. 2.Regional Sericultural Research StationChamarajanagarIndia

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