Genetic Diversity of Indigofera tinctoria L. in Java and Madura Islands as Natural Batik Dye based on Inter-simple Sequence Repeat Markers

Muhammad Rifqi Hariri, Tatik Chikmawati, Alex Hartana


Indigo leaves (Indigofera tinctoria L.) are utilized as a source of batik dye in Java and Madura islands, Indonesia. Batik makers from the islands collect indigo leaves from wild plants. Continuous collection of wild plants from their natural habitat may decrease their diversity. The present research was conducted to analyze the genetic diversity and population structure of I. tinctoria L. from Java and Madura. 55 indigo accessions were collected from 10 locations in Java and Madura. The indigo DNA was extracted and amplified using 15 ISSR primers. A total of 123 bands showed 50-90% polymorphic loci. PCA and UPGMA were used to analyze the data. All indigo accessions were clustered into 4 groups at a 60% similarity coefficient: a group consisting of Madura accessions, a group consisting of East Java accessions, a group consisting of Central Java accessions, and a group consisting of West Java accessions. Accessions collected from the same or adjacent populations tended to show similar ISSR characteristics. The genetic diversity of indigo in Java and Madura islands is relatively high (%P = 68.3), but the diversity residing within each population is lower (37%) than that between populations (63%).


indigo; genetic diversity; polymorphic bands; population structure

Full Text:



Arsenault, N., Rose, C., Azulay, A. & Meyer, R., Explorers, Traders & Immigrants: Tracking The Cultural and Social Impacts of the Global Commodity Trade, Hemispheres, The International Outreach Consortium, pp. 86-89, 2008.

Food and Agriculture Organization of the United Nations, Non-wood Forest Products – Natural Colourants and Dyestuffs, FAO Corporate Document Repository, pp. 70-92, 1995.

Gao, X. & Schrire, B.D., Indigofera, Flora of China, 10, pp. 137-164, 2010.

Narain, P., Genetic Diversity – Conservation and Assessment, Curr Sci, 79(2), pp. 170-175, 2000.

Babić, M., Babić, V., Prodanović, S., Filipović, M. & Andjelković, V., Comparison of Morphological and Molecular Genetic Distances of Maize Inbreds, Genetika, 44(1), pp. 119-128, 2012.

Sadeghi A. & Cheghamirza, K., Application of RAPD and ISSR Marker System for Studying Genetic Diversity in Common Bean (Phaseolus vulgaris L.) Cultivars, Ann. Biol. Res., 3(7), pp. 3267-3273, 2012.

Zietkiewicz, E., Rafalski, A. & Labuda, D., Genome Fingerprinting by Simple Sequence Repeat (SSR)-anchored Polymerase Chain Reaction Amplification, Genomics, 20, pp. 176-183, 1994.

Widjaja, E.A. & Poerba, Y.S., Data Collection Guidelines on Flora Diversity, pp. 113-138, 2004. (Text in Indonesia)

Tiwari, K.L., Jadhav, S.K. & Gupta, S., Modified CTAB Technique for Isolation of DNA from Some Medicinal Plants, Res. J. Med. Plant., 6(1), pp. 65-73, 2012.

Bisoyi, M.K., Acharya, L., Mukherjee, A.K. & Panda, C.P., Study of Inter-specific Relationship in Six Species of Sesbania Scop. (Leguminosae) through RAPD and ISSR Markers, Int. J. Plant. Physiol. Biochem., 2(2), pp. 11-17, 2010.

Khajudparn P., Prajonhjai T., Poolsawat, O. & Tantasawat, P.A., Efficiency of ISSR Markers for Verification of F1 Hybrids in Mungbean (Vigna radiata), Genet. Mol. Res., 11(3), pp. 3329-3338, 2012.

Pardhe, D.D., & Satpute, R.A., A Comparative Analysis of Genetic Diversity in Genus Vigna savi Genotypes using ISSR, Int. J. Pharm. Tech. Res., 3(1), pp. 464-470, 2011.

Rohlf, F.J, NTSYSpc – Numerical Taxonomy and Mutivariate Analysis System Version 2.02, pp. 24-26, 1998.

Peakall, R. & Smouse, P.E., GenAlEx 6.5: Genetic Analysis in Excel. Population Genetic Software for Teaching and Research – An Update, Bioinformatics, 28, pp. 2537-2539, 2012.

Rahayu S.E., Hartana, A., Chikmawati, T., Genetic Diversity of Pandanus and Freycinetia from Java based on ISSR Marker, Floribunda, 3(4), pp. 95-103, 2007.

Sebola, R.J. & Balkwill, K., Calibration, Verification and Stepwise Analysis for Numerical Phenetics: Olinia (Oliniaceae) as An Example, J. Bot. South Afr., 88, pp. 42-55, 2013.

Amirmoradi, B., Talebi, R., Karami, E. & Shirvani, H., Evaluation of Genetic Diversity within and between Cicer Species using ISSR Molecular Markers, Int. J. Agr. Crop. Sci., 5(22), pp. 2683-2688, 2013.

Huang, Y., Zhang, C.Q. & Li, D.Z., Low Genetic Diversity and High Genetic Differentiation in the Critically Endangered Omphalogramma souliei (Primulaceae): Implications for Its Conservation, J. Syst. Evol., 47(2), pp. 103-109, 2009.

Persson, K. & von Bothmer, R., Assessing the Allozyme Variation in Cultivars and Swedish Landraces of Rye (Secale cereale L.), Hereditas, 132, pp. 7-17, 2000.

Wright, S.I., Kalisz, S. & Slotte, T., Evolutionary Consequences of Selffertilization in Plants, Proc. R. Soc. B, 280, pp. 01-33, 2013.

Lin, X.C., Lou, Y.F., Liu, J. & Peng, J.S., Crossbreeding of Phyllostachys species (Poaceae) and Identification of their Hybrids using ISSR Markers, Genet. Mol. Res., 9, pp. 1398-1404, 2010.

Indriani F.C., Sudjindro, A.N, Sugiharto & Soetopo, L., Genetic Diversity of Kenaf Germplasm (Hibiscus cannabinus L.) and Several Closely-related Species based on Isozyme Analysis, Agritek, 6(9), pp. 1793-1802, 2008. (Text in Indonesia)



  • There are currently no refbacks.

View my Stats

Creative Commons License
This work is licensed under a Creative Commons Attribution-NoDerivatives 4.0 International License.


ITB Journal Publisher, LPPM ITB, Center for Research and Community Services (CRCS) Building, 6th & 7th Floor, Jalan Ganesha 10, Bandung 40132, Indonesia, Phone: +62-22-86010080, Fax.: +62-22-86010051; E-mail: