SSR marker development in Abelmoschus esculentus (L.) Moench using transcriptome sequencing and genetic diversity studies


  • M Gayathri Centre for Post-graduate studies, Jain University, Bangalore Author
  • M Pitchaimuthu ICAR-Indian Institute of Horticultural Research, Bengaluru 560089 Author
  • Kundapura Ravishankar ICAR -Indian Institute of Horticultural Research, Bengaluru,560089 Author



Abelmoschus esculentus, transcriptome, RNA sequencing, microsatellite markers, NGS, Next Generation Sequencing


Okra [Abelmoschus esculentus (L.) Moench] also known as bhindi or lady’s finger is an important vegetable crop in India, West Africa, South Africa, Brazil, USA and Turkey. It belongs to the family Malvaceae. Okra is mainly grown in tropics and subtropics of the world. The studies regarding the molecular marker development are very limited; still there is no SSR development from comprehensive transcriptome data in this crop. This study presents the first comprehensive transcriptome data, using RNA from different parts of okra such as root, stem, leaf, bud, flower, different stages of developing pod and from twenty days old plantlets of heat, drought and salt stressed. A total of 10,492 SSRs were identified in this study. Among these tri repeats (2112) were found to be predominant followed by di (1285), tetra (149), penta (24) and hexa. Thirty four SSRs were standardized for PCR and screened for 36 okra genotypes and accessions. Among these 18 SSR primers were found to be highly polymorphic with the PIC values more than 0.5. And the overall results of analysis showed that expected heterozygosity ranged from 0.000 to 0.971 with a mean of 0.593; the values for observed heterozygosity ranged from 0.000 to 0.794 with the mean of 0.254; the number of allele per locus ranged from 1 to 30 and the Polymorphic Information Content (PIC) ranged from 0.000 to 0.940 with the mean value of 0.5546. The genic SSR markers developed will help in germplasm characterization mapping, genetic diversity studies, molecular assisted breeding and also in gene discovery.


Download data is not yet available.


Bertini, C. D., Schuster, I., Sediyama, T., Barros, E. G. and Moreira, M. A. 2006. Characterization and genetic diversity analysis of cotton cultivars using microsatellites. Genet. Mol. Biol, 29: 321–329.

Buschiazzo, E. and Gemmell, N. 2006. The rise fall and renaissance of microsatellites in eukaryotic genomes. BioEssays, 28: 1040– 1050.

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.

Chen, G., Yue, Y., Hua, Y., Hu, D., Shi, T., Chang, Z., Yang, X. and Wang, L. 2019. SSR marker development in Clerodendrum trichotomum using transcriptome sequencing. PloS one, 14(11): 0225451.

FAOSTAT. 2018. Production database from the food and agriculture organization of the United Nations. Retrieved from

Grabherr, M. G., Hass, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R. and Zeng, Q. D. 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol, 29.

Guo, L. N., Zhao, X. and Gao, X. F. 2016. De novo assembly and characterization of leaf transcriptome for the development of EST-SSR markers of the non-model species Indigofera szechuen sis. Biochem. Syst. Ecol, 68: 36–43.

John, Z., Yu, D. D., Fang-Russell, J., Mauricio, U. L. L. and Hinze, R. G. 2012. Development of a core set of SSR markers for the characterization of Gossypium germplasm. Euphytica, 187: 203–213.

Joshi, A. B. and Hardas, M. W. 1956. Alloploid Nature of Okra, Abelmoschus esculentus (L.) Monech. Nature, 178(4543): 1190-1190.

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.

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.

Niemandt, M., Roodt-Wilding, R., Tobutt, K. R. and Bester, C. 2018. Microsatellite marker applications in Cyclopia (Fabaceae) species. S.Afr. J. Bot, 116: 52–60.

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, Abelmoschus esculentus (L.) Moench using principal component analysis (PCA) and single linkage cluster analysis (SLCA). Afr. J. Biotechnol, 10:54.

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.

Pan, L., Fu, J., Zhang, R., Qin, Y., Lu, F. and Jia, L. 2017. Genetic diversity among germplasms of Pitaya based on SSR markers. Sci. Hortic, 225: 171–176.

Perrier, X., Flori, A. and Bonnot, F. 2003. Data analysis methods. Enfield. Sci. Publish. Montpellier. 43–76.

Priyavathi, P., Nagesh, S., Kavitha, V. V. K., Johnson, C. and Gopal, P. 2018. Comprehensive leaf transcriptome of a non-model plant, Abelmoschus esculentus for the functional genomics studies. J. Genet. Genome Res, 5: 036.

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.

Ravishankar, K. V., Lalitha, A. and Dinesh, M. R. 2000. Assessment of genetic relatedness among a few Indian mango varieties using RAPD marker. J. Hortic. Sci. Biotechnol, 75: 198–201.

Ravishankar, K. V., Megha, H. S., Rekha, A., Khadke, G. N. and Veerraju, C. H. 2015. Insights into Musa balbisiana and Musa acuminata species divergence and development of genic microsatellites by transcriptomics approach. Plant Gene, 4: 78–82.

Ravishankar, K. V., Muthaiah, G., Mottaiyan, P. and Gundale, S. K. 2018. Identification of novel microsatellite markers in okra (Abelmoschus esculentus (L.) Moench) through nextgeneration sequencing and their utilization in analysis of genetic relatedness studies and cross-species transferability. J. genet, 97(1): 39-47.

Ronoh, R., Linde, M., Winkelmann, T., Abukutsa- Onyango, M. and Dinssa-Debener, T. 2018. Development of next-generation sequencing (NGS)-based SSRs in African nightshades: Tools for analyzing genetic diversity for conservation and breeding. Sci. Hortic, 235: 152–159.

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. Biotechno, 8: 2476- 2482.

Schafleitner, R., Kumar, S., Lin, C. and Ebert, H. A. 2013. The okra (Abelmoschus esculentus) transcriptomes a source for gene sequence information and molecular markers for diversity analysis. Gene, 17: 27–36.

Schuelke, M. 2000. An economic method for the fluorescent labelled of PCR fragment. Nat. Biotechnol, 18: 233– 234.

Shi, D., Wang, J., Bai, Y. and Liu, Y. 2020. Transcriptome sequencing of okra (Abelmoschus esculentus L. Moench) uncovers differently expressed genes responding to drought stress. J. Plant Biochem. Biotechnol, 29(2): 155-170.

Sonah, H., Deshmukh, R. K., Sharma, A., Singh, V. P., Gupta, D. K. and Gacche, R. N. 2011. Genome wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium. PLoS One, 10:137.

Strickler, S. R., Bombarely, A. and Mueller, L. A. 2012. Designing a transcriptome nextgeneration sequencing project for a non-model plant species. Am. J. Bot, 99: 257–266.

Suping, F., Helin, T., You, C., Jingyi, W., Yeyuan, C., Guangming S., Junhu, He. and Yaoting, Wu. 2013. Development of pineapple microsatellite markers and germplasm genetic diversity analysis. Biomed. Res. Int, 1–11.

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.

Xu, M., Liu, X., Wang, J. W., Teng, S. Y., Shi, J. Q. and Li, Y. Y. 2017. Transcriptome sequencing and development of novel genic SSR markers for Dendrobium officinale. Mol. Breed, 37(2): 18.

Yoder, A. D., Poelstra, J., Tiley, G. P. and Williams, R. 2018. Neutral Theory is the Foundation of Conservation Genetics. Mol. Biol. Evol, 35(6): 1322–1326.

Yuan, C. Y., Wang, P., Chen, P. P., Xiao, W. J., Zhang, C., Hu, S., Zhou, P., Chang, H. P., He, Z., Hu, R., Lu, X. T., Ye, J. Z. and Guo, Z. H. 2015. Genetic diversity revealed by morphological traits and ISSR markers in 48 okras (Abelmoschus esculentus L.). Physiol. Mol. Biol. Plant, 21: 359–364.

Yuan, C. Y., Zhang, C., Wang, P., Hu, S., Chang, H. P., Xiao, W. J., Lu, X. T., Jiang, S. B., Ye, J. Z. and Guo, X. H. 2014. Genetic diversity analysis of okra (Abelmoschus esculentus L.) by inter-simple sequence repeat (ISSR) markers. Genet. Mol. Res, 13: 3165–3175.

Zhang, R., Zhu, A. D., Wang, X. J., Yu, J., Zhang, H. R. and Gao, J. S. 2010. Development of Juglans Regia SSR Markers by Data Mining of the EST Database. Plant Mol. Biol. Rep, 28(4): 646–653.

Zhang, S., Qiu, S., Zheng, Y., Zhang, S., Wu, S., He, Y. and Zheng, K. 2017. The purple transcriptome as a source for gene sequence information. J. Nucl. Agric. Sci, 31(4): 643-663.






Original Research Papers

How to Cite

Gayathri, M., Pitchaimuthu, M., & Ravishankar, K. (2021). SSR marker development in Abelmoschus esculentus (L.) Moench using transcriptome sequencing and genetic diversity studies. Journal of Horticultural Sciences, 16(2), 206-214.

Similar Articles

1-10 of 109

You may also start an advanced similarity search for this article.

Most read articles by the same author(s)