Novel EST-SSR marker development and validation in black pepper cultivars and varieties

Sherin Jose, R. Sujatha, K.P. Deeshma


Expressed Sequence Tags-Simple Sequence Repeat (EST-SSR) markers are more preferred because it is more efficient, fast and low cost. The main objective of the study was to develop new EST-SSR markers in black pepper. Sixty eight unigene sequences containing 70 SSRs were detected from 1048 unigenes using MIcroSAtellite (MISA) identification tool. Sixty two mononucleotides, two dinucleotides and six trinucleotides were the repeat motifs obtained. Nine primer pairs were designed for eight unigene sequences. Primers were screened using DNA isolated from Panniyur-1 variety at different annealing temperature. Primers which are clear and unambiguous were selected for validation in 35 black pepper varieties and cultivars. In total, 18 alleles were obtained from five EST-SSR markers with an average of 3.6.


Black pepper, Cultivars, EST-SSR markers, Genotypes

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Doyle, J. J. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19: 11-15.

Farooq, S. and Azam, F. 2002. Molecular markers in plant breeding-I: Concepts and characterization. Pak. J. Biol. Sci. 5(10): 1135-1140.

George, K. J., Ganga, G., Varam, R. S., Sasikumar, B., and Saji, K. V. 2005. Identification of hybrids in black pepper (Piper nigrum L.) using male parent specific RAPD markers. Curr. Sci. 88(2): 216-218.

Hou, B., Feng, S., and Wu, Y. 2017. Systemic Identification of Hevea brasiliensis EST-SSR Markers and Primer Screening. J. nucleic acids 2017. Available:

Jagtap, A. B., Sujatha, R., Nazeem, P. A., Meena, O. P., and Pathania, S. 2016. Morpho-molecular characterization of putative interspecific crosses in black pepper (Piper nigrum L. and Piper colubrinum). Plant Omics J. 9(1): 73-80.

Jiang, Y. and Liu, J.P. 2011. Analysis of genetic diversity of Piper spp. in Hainan Island (China) using inter-simple sequence repeat ISSR markers. Afr. J. Biotechnol. 10(66): 14731-14737.

Joy, N., Abraham, Z., and Soniya, E. V. 2007. A preliminary assessment of genetic relationship among agronomically important cultivars of black pepper. BMC Genet. 8: 42-48.

Joy, N., Prasanth, V. P., and Soniya, E. V. 2011. Microsatellite based analysis of genetic diversity of popular black pepper genotypes in South India. Genetica 139(8): 1033-1044.

Litt, M. and Luty, J. A. 1989. A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am. J. Hum. Genet. 44: 397- 401.

Menezes, I. C., Cidade, F. W., Souza, A. P., and Sampaio, I. C. 2009. Isolation and characterization of microsatellite loci in the black pepper, Piper nigrum L. (piperaceae). Conserv. Genet. Resour. 1(1): 209-212.

Parida, S. K., Kalia, S. K., Sunita, K., Dalal, V., Hemaprabha, G., Selvi, A., Pandit, A., Singh, A., Gaikwad, K., Sharma, T. R., Srivastava, P. S., Singh, N. K., and Mohapatra, T. 2009. Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor. Appl. Genet. 118: 327-338.

Pradeepkumar, T., Karihaloo, J. L., Archak, S. and Baldev, A. 2003. Analysis of genetic diversity in Piper nigrum L. using RAPD markers. Genetic Resources Crop Evol. 50(5): 469-475.

Sen, S., Skaria, R., and Muneer, P. M. A. 2010. Genetic diversity analysis in Piper species (Piperaceae) using RAPD markers. Mol. Biotechnol. 46: 72-79.

Sheeja, T. E., Uma, G., Sasikumar, B., Saji, K. V., and Rahul, P. R. 2013. Genetic diversity study in Piper spp. using inters simple sequence repeat (ISSR) markers. J. Spices aromat. crop 22(2): 111-119.

Zhou, M. L., Xia, Z. Q., Chen, J. R., and Wang, W. Q. 2012. Analysis of SSR information and annotation in EST resource of Castor Bean (Ricinus communis). Chinese J. Trop. Crop 33(12): 2138–2143.


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