Identification of novel microsatellite markers in okra (Abelmoschus esculentus (L.) Moench) through next-generation sequencing and their utilization in analysis of genetic relatedness studies and cross-species transferability

  • Kundapura V. Ravishankar
  • Gayathri Muthaiah
  • Pitchaimuthu Mottaiyan
  • Santhosh-kumar Gundale
Online Resources


Abelmoschus esculentusL. (Malvaceae), populary known as okra, is one of the important pod vegetable crops in tropics and subtropics. To develop the microsatellite markers, we have partially sequenced genomic DNA using Roche 454 Titanium pyrosequencing technology. A total of 979,806 bp data from 61,722 reads were obtained. These reads were assembled into 3735 contigs of which 2708 had microsatellites. Primers were designed for 402 microsatellites, from which 50 randomly selected SSR primers were standardized for amplification of okra DNA. Genetic analysis was done by employing 29 genotypes. Polymorphic information content (PIC) across all 50 loci ranged from 0.000 to 0.865 with a mean value of 0.519. The observed and expected heterozygosity ranged from 0.000 to 0.750 and 0.000 to 0.972, respectively. Alleles per locus ranged from 1 to 27. This is the first report on the development of genomic SSR markers in okra using next-generation sequencing technology. We have also...


microsatellite markers transferability polymorphic information content Abelmaschus esculentus 



Authors acknowledge the financial support through institute project from ICAR-Indian Institute of Horticultural Research, Bengaluru.


  1. Aladele S. E., Ariyo O. J. and Lapena R. 2008 Genetic relationships among West African okra (Abelmoschuscaillei) and Asian genotypes (Abelmoschu sesculentus) using RAPD. Afr. J. Biotechnol. 7, 1426–1431.Google Scholar
  2. Andre G., Emese M., Nicolas P., Stephanie F., Thibaut M. and Jean F. M. 2011 Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12, 245.CrossRefGoogle Scholar
  3. Bertini C. D., Schuster I., Sediyama T., de Barros E. G. and Moreira M. A. 2006 Characterization and genetic diversity analysis of cotton cultivars using microsatellites. Genet. Mol. Biol. 29, 321–329.CrossRefGoogle Scholar
  4. Buschiazzo E. and Gemmell N. 2006 The rise fall and renaissance of microsatellites in eukaryotic genomes. BioEssays. 28, 1040–1050.Google Scholar
  5. Chakravarthi B. K. and Naravaneni R. 2006 SSR Marker based DNA fingerprinting and diversity study in rice (Oriza sativa L.). Afr. J. Biotechnol. 5, 684–688.Google Scholar
  6. Fan Q., Chen S., Li M., He S., Zhou R. and Liao W. 2013 Development and characterization of microsatellite markers from the transcriptome of Firmiana danxiaensis (Malvaceaes.l.). Appl. Plant Sci. 28, 12–16.Google Scholar
  7. Gilles A., Meglé Cz E., Pech N., Ferreira S., Malausa T., and Martin J. F. 2011 Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12, 245.Google Scholar
  8. Gulsen O., Karagul S. and Abak K. 2007 Diversity and relationships among Turkish okra germplasm by SRAP and phenotypic marker polymorphism. Biologia 62, 41–45.CrossRefGoogle Scholar
  9. Huang and Anup M. 1999 CAP3: A DNA sequence assembly programe. Genome Res. 9, 868–877.Google Scholar
  10. John Z., Yu D. D., Fang, Russell J., Mauricio U. L. L., Hinze R. G. et al. 2012 Development of a core set of SSR markers for the characterization of Gossypium germplasm. Euphytica 187, 203–213.CrossRefGoogle Scholar
  11. Joshi A. B. and Hardas M. W. 1956 Alloploid nature of okra, Abelmoschu sesculentus (L.) Moench. Nature 178, 1190.CrossRefGoogle Scholar
  12. Ju M. M., Ma H. C., Xin P. Y., Zhou Z. L. and Tian B. 2015 Development and characterization of EST-SSR markers in Bomba xceiba (Malvaceae). Appl. Plant Sci. 3, 1–4.CrossRefGoogle Scholar
  13. Kalinowski S. T., Taper M. L. and Marshall T. C. 2007 Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol. 16, 1099–1006.CrossRefPubMedGoogle Scholar
  14. Muhammad S., Bahaeldeen B. M., Muhammad A. A., Agung N. P., Kamran S. B., Ahmad A. S. and Tayyab H. 2013 Genetic diversity assessment of cotton (Gossypium hirsutum L.) genotypes from pakistan using simple sequence repeat markers. Aust. J. Crop Sci. 7, 261–267.Google Scholar
  15. Nwangburuka C. C., Kehinde O. B., Ojo D. K., Denton O. A. and Popoola A. R. 2011 Morphological classification of genetic diversity in cultivated okra, Abelmoschu sesculentus (L.) Moench using principal component analysis (PCA) and single linkage cluster analysis (SLCA). Afr. J. Biotechnol. 10, 54.Google Scholar
  16. Oetting W. S., Lee H. K., Flanders D. J. and Wiesner G. L. 1995 Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers. Genomics 30, 450–458.CrossRefPubMedGoogle Scholar
  17. Perrier X., Flori A. and Bonnot F. 2003 Data analysis methods. Enfield. Sci. Publish. Montpellier. 43–76.Google Scholar
  18. Phuekvilai P. and Wolff K. 2013 Characterization of microsatellite loci in Tiliap latyphyllos (Malvaceae) and cross-amplification in related species. Appl. Plant Sci. 1.
  19. Prakash K., Pitchaimuthu M. and Ravishankar K. V. 2011 Assessment of genetic relatedness among okra genotypes (Abelmoschu sesculentus L. Moench) using RAPD markers. Electron. J. Plant Breed. 2, 80–86.Google Scholar
  20. Ramya P. and Bhat K. V. 2012 Analysis of phylogenetic relationships in Abelmoschus species (Malvaceae) using ribosomal and chloroplast intergenic spacers. Indian J. Genet. Plant Breed. 72, 445–453.Google Scholar
  21. Ravishankar K. V., Dinesh M. R., Nischita P. and Sandya B. S. 2015 Development and characterization of microsatellite markers in mango (Mangifera indica) using next-generation sequencing technology and their transferability across species. Mol. Breed. 35, 1–13.CrossRefGoogle Scholar
  22. Ravishankar K. V., Lalitha A. and Dinesh M. R. 2000 Assesment of genetic relatedness among a few Indian mango varieties using RAPD marker. J. Hortic. Sci. Biotechnol. 75, 198–201.CrossRefGoogle Scholar
  23. Rymer P. D., Harris S. and Boshier D. 2014 Isolation and characterization of microsatellite markers for the neotropical tree Pachir aquinata (Malvaceae). Conserv. Genet. Resour. 6, 375–382.CrossRefGoogle Scholar
  24. Sawadogo M., Ouedraogojt B. D., Ouedraogo M., Gowdabs B. C. and Timko M. 2009 The use of cross species SSR primers to study genetic diversity of okra from Burkina Faso. Afr. J. Biotechnol. 8, 2476–2482.Google Scholar
  25. Schafleitner R., Kumar S., Lin C. Y., Hegde S. G. and Ebert A. 2013 The okra (Abelmoschu sesculentus) transcriptome as a source for gene sequence information and molecular markers for diversity analysis. Gene 517, 27–36.CrossRefPubMedGoogle Scholar
  26. Schuelke M. 2000 An economic method for the fluorescent labeled of PCR fragment. Nat. Biotechnol. 18, 233–234.CrossRefPubMedGoogle Scholar
  27. Seo K. I., Lee G., Park S. K., Yoon M. S., Ma K. H., Lee J. R. et al. 2012 Genome shotgun sequencing and development of microsatellite markers for gerbera (Gerbera hybrid H.) by 454 GS-FLX. Afr. J. Biotechnol. 11, 7388–7396.CrossRefGoogle Scholar
  28. Sonah H., Deshmukh R. K., Sharma A., Singh V. P., Gupta D. K., Gacche R. N. et al. 2011 Genome wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium. PLoS One 10, 137.Google Scholar
  29. Sunday E., Aladele O. J. Ariyo L. and Robert D. L. 2008 Genetic relationship among West African Okra (Abelmo schuscaillei) and Asian genotypes (Abelmo schusesculentus) using RAPD. Afri. J. Biotechnol. 7, 1426–1431.Google Scholar
  30. Suping F., Helin T., You C., Jingyi W., Yeyuan C., Guangming S. et al. 2013 Development of pineapple microsatellite markers and germplasm genetic diversity analysis. Biomed. Res. Int. 1–11.
  31. Untergasser A., Cutcutache J., Koressaar T., Ye J., Faircloth B. C., Remm M. and Rozen S. G 2012 Rozen.Primer3 - new capabilities and interfaces. Nucleic. Acids. Res. 40, 15.Google Scholar
  32. Wang S., Xiaokun L., Jianwei L., Juan H., Gang C., Xinxin X. et al. 2013 Effects of controlled-release urea application on the growth, yield and nitrogen recovery efficiency of cotton. Agric. Sci. 4, 3–38.Google Scholar
  33. Yuan C. Y., Wang P., Chen P. P., Xiao W. J., Zhang C., Hu S. et al. 2015 Genetic diversity revealed by morphological traits and ISSR markers in 48 okras (Abelmoschus escullentus L.). Physiol. Mol. Biol. Plant. 21, 359–364.CrossRefGoogle Scholar
  34. Yuan C. Y., Zhang C., Wang P., Hu S., Chang H. P., Xiao W. J. et al. 2014 Genetic diversity analysis of okra (Abelmoschus esculentus L.) by inter-simple sequence repeat (ISSR) markers. Genet. Mol. Res. 13, 3165–3175.CrossRefPubMedGoogle Scholar

Copyright information

© Indian Academy of Sciences 2018

Authors and Affiliations

  • Kundapura V. Ravishankar
    • 1
  • Gayathri Muthaiah
    • 1
  • Pitchaimuthu Mottaiyan
    • 1
  • Santhosh-kumar Gundale
    • 1
  1. 1.Division of Biotechnology and Division of Vegetable CropsICAR-Indian Institute of Horticultural ResearchBengaluruIndia

Personalised recommendations