Dissection of genetic diversity present in eggplant populations using simple sequence repeat markers


  • Mahammed Faizan Department of Genetics and Plant Breeding, College of Horticulture, Mudigere, University of Agricultural and Horticultural Sciences, Shivamogga-577201, Karnataka, India
  • B. N. Harish Babu Zonal Agricultural and Horticultural Research Station, Hiriyur, University of Agricultural and Horticultural Sciences, Shivamogga-577201, Karnataka, India
  • B. Fakrudin Department of Biotechnology and Crop improvement, PG centre, GKVK, Bangalore University of Horticultural Sciences, Bagalkot, Karnataka-587104, India
  • D. Lakshmana Department of Genetics and Plant Breeding, College of Horticulture, Mudigere, University of Agricultural and Horticultural Sciences, Shivamogga-577201, Karnataka, India
  • M. Rakshith Department of Genetics and Plant Breeding, College of Horticulture, Mudigere, University of Agricultural and Horticultural Sciences, Shivamogga-577201, Karnataka, India




DNA, Genetic diversity, SSR markers, AMOVA, GenAlEx, PCA


Eggplant (Solanum melongena L.) is the third most important solanaceous vegetable and most diversified within species spread across the world-geographical area. A study was conducted to assess the genetic diversity among the selected fifty-four eggplant genotypes (sub-categorized into five sub-population) using twenty-three SSR markers. The Analysis of Molecular Variance among the five sub-population of eggplant revealed the existence of 90.67% variation within populations and 9.34% variation among populations. The SSR markers analysis revealed important locus-wise information like mean Observed-Heterozygosity (0.216), mean Expected-Heterozygosity (0.496), Shannon’s Information Index (0.879), mean number of different alleles (3.209), mean number of effective alleles (2.535), Fixation-Index (0.649). Further, Phylogenetic-analysis clearly categorize genetically distinct individuals in which the most diversified clusters was cluster-1 (C1) out of total of five clusters and especially, wild cultivars were grouped into cluster-5 (C5). The obtained results can be used in eggplant breeding and germplasm conservation in a resourceful manner.


Download data is not yet available.


Ali, Z., Xu, Z. L., Zhang, D. Y., He, X. L., Bahadur, S., & Yi, J. X. (2011). Molecular diversity analysis of eggplant (Solanum melongena) genetic resources. Genetics and Molecular Research, 10(2), 1141- 1155. https://doi.org/10.4238/vol10-2gmr1279

Behera, T. K., Sharma, P., Singh, B. K., Kumar, G., Kumar, R., Mohapatra, T., & Singh, N. K. (2005). Assessment of genetic diversity and species relationships in eggplant (Solanum melongena L.) using STMS markers. Scientia Horticulturae, 107(4), 352–357. https://doi.org/10.1016/j.scienta.2005.11.004

Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32(3), 314- 331.

Demir, K., Bakir, M., Sarikamis, G., & Acunalp, S. (2010). Genetic diversity of eggplant (Solanum melongena) germplasm from Turkey assessed by SSR and RAPD markers. Genetics and Molecular Research, 9(3), 1568–1576. https://doi.org/10.4238/vol9-3gmr878

Excoffier, L., & Lischer, H. E. (2010). Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10(3), 564-567. https://doi.org/10.1111/j.1755-0998.2010.02847.x

Faizan, M., Harish Babu, B. N., Lakshmana, D., Ganapathi, M., & Rakshith, M. (2021a). Investigation on response of growth and yield characters of eggplant over moistures stress and dissection of genetic parameters. International Journal of Chemical Studies, 9(5), 08-14.

Faizan, M., Harish Babu, B. N., Lakshmana, D., Ganapathi, M., & Rakshith, M. (2021b). Physiological and root growth response of eggplant genotypes upon drought stress and assessment of genetic parameters at different developmental stage. International Journal of Ecology and Environmental Sciences, 3(4), 22-33. https://doi.org/10.5281/zenodo.5588965

Ge, H., Liu, Y., Jiang, M., Zhang, J., Han, H., & Chen, H. (2013). Analysis of genetic diversity and structure of eggplant populations (Solanum melongena L.) in China using simple sequence repeat markers. Scientia Horticulturae, 162, 71–75. https://doi.org/10.1016/j.scienta.2013.08.004

Gramazio, P., Prohens, J., Borràs, D., Plazas, M., Herraiza, F. J., & Vilanova, S. (2017). Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants. Euphytica, 213, 264. https://doi.org/10.1007/s10681-017-2057-3

Hu, J., & Quiros, C. F. (1991). Identification of broccoli and cauliflower cultivars with RAPD markers. Plant Cell Reports, 10, 505-511. https://doi.org/10.1007/BF00234583

Hurtado, M., Vilanova, S., Plazas, M., Gramazio, P., Fonseka, H. H., Fonseka, R., & Prohen J. (2012). Diversity and relationships of eggplants from three geographically distant secondary centres of diversity. PLoS ONE, 7(7), 1-15. https://doi.org/10.1371/journal.pone.0041748

Isshiki, S. O., & Fujieda, K. (1994). Phylogeny of eggplant and related Solanum species constructed by allozyme variation. Scientia Horticulturae, 59(3- 4), 171-176. https://doi.org/10.1016/0304-4238(94)90010-8

Jellan, R. R., Saracanlao, E. T. M., Ocampo, A. O., Canama, S. J. B., Manaday, R. G. M., & Evelyn, F. D. (2016). SSR-based genetic relationship in eggplant (solanum melongena L) genotypes with varying morphological response to drought. Philippine Journal of Crop Science, 41(3), 57-64.

Liao, Y., Sun, B., Sun, G., Liu, H., Li, Z., Li, Z., Wang, G. & Chen, R. (2009). AFLP and SCAR markers associated with peel color in eggplant (Solanum melongena). Agricultural Sciences in China,8(12), 1466- 1474. https://doi.org/10.1016/S1671-2927(08)60360-0

Mikaela, A. B., Ocampo, E. T. M., Canama, A. O., & Delfin, E. F. (2017). Hybridity testing of eggplant F1 progenies derived from parents with varying response to drought using SSR markers. Philippine Journal of Science, 146(3), 277-286.

Miyatake, K., Shinmura, Y., Matsunaga, H., Fukuoka, H., & Saito, T. (2019). Construction of a core collection of eggplant (Solanum melongena L.) based on genome-wide SNP and SSR genotypes. Breeding Science, 69(3), 498-502. https://doi.org/10.1270/jsbbs.18202

Nunome, T., Negoro, S., Kono, I., Kanamori, H., Miyatake, K., Yamaguchi, H., Ohyama, A., & Fukuoka, H. (2009). Development of SSR markers derived from SSR-enriched genomic library of eggplant (Solanum melongena L.). Theoretical and Applied Genetics, 119, 1143-1153. https://doi.org/10.1007/s00122-009-1116-0

Nunome, T., Suwabe, K., Iketani, H., Hirai, M., & Wricke, G. (2003). Identification and characterization of microsatellites in eggplant. Plant Breeding, 122(3), 256-262. https://doi.org/10.1046/j.1439-0523.2003.00816.x

Peakall, R., & Smouse P. E. (2012). GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research: an update. Bioinformatics, 28(19), 2537-2539. https://doi.org/10.1093/bioinformatics/bts460

Somawathi, K. M., Rizliya, V., Wijesinghe, D. G. N. G., & Madhujith, W. M. T. (2014). Antioxidant Activity and Total Phenolic Content of Different Skin Coloured Brinjal (Solanum melongena). Tropical Agricultural Research, 26(1), 152-161. http://doi.org/10.4038/tar.v26i1.8080

Stagel, A., Portis, E., Toppino, L., Rotino, G. L., & Lanteri, S. (2008). Gene-based microsatellite development for mapping and phylogeny studies in eggplant. BMC Genomics, 9, 357. https://doi.org/10.1186/1471-2164-9-357

Tiwari, S. K., Karihaloo, J. L., Hameed, N., & Gaikwad, A. B. (2009). Molecular characterization of brinjal (Solanum melongena L) cultivars using RAPD and ISSR Markers. Journal of Plant Biochemistry and Biotechnology, 18, 189-195. https://doi.org/10.1007/BF03263318

Tumbilen, Y., Frary, A., Daunay, M. C., & Doğanlar S. (2011). Application of EST-SSRs to examine genetic diversity in eggplant and its close relatives. Turkish Journal of Biology, 35(2), 125-136. https://doi.org/10.3906/biy-0906-57

Vilanova, S., Hurtado, M., Cardona, A., Plazas, M., Gramazio, P., Herraiz, F. J., Andújar, I., & Prohens, J. (2014). Genetic diversity and relationships in local varieties of eggplant from different cultivar groups as assessed by genomic SSR markers. Notulae botanicae Horti Agrobotanici Cluj- Napoca, 42(1), 59-65. https://doi.org/10.15835/nbha4219414

Weijun. (1992). Inheritance of isozymes and morphological characters in the brinjal eggplant. Acta Genetica Sinica, 19, 423-429.

Yang, L., Wen, C., Zhao, H., Liu, Q., Yang, J., Liu, L., & Wang, Y. (2015). Development of polymorphic genic SSR markers by transcriptome sequencing in the welsh onion (Allium fistulosum L.). Applied Sciences, 5(4), 1050-1063. https://doi.org/10.3390/app5041050



How to Cite

Faizan, M., B. N. . Harish Babu, B. . Fakrudin, D. . Lakshmana, and M. . Rakshith. “Dissection of Genetic Diversity Present in Eggplant Populations Using Simple Sequence Repeat Markers”. Journal of Plant Stress Physiology, vol. 8, Oct. 2022, pp. 8-16, doi:10.25081/jpsp.2022.v8.7848.