ISSR Fingerprints and ITS Restriction Cleavage Differs in Selected Native Chilli Pepper Genotypes

Jana Žiarovská; Lucia Urbanová; Silvia Farkasová; Eloy Fernandez Cusimamani

doi:10.2478/ahr-2026-0007

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ISSR Fingerprints and ITS Restriction Cleavage Differs in Selected Native Chilli Pepper Genotypes

Acta Horticulturae et Regiotecturae

Volume 29 (2026): Issue 1 (May 2026)

By: Jana Žiarovská, Lucia Urbanová, Silvia Farkasová and Eloy Fernandez Cusimamani

Open Access

|May 2026

Abstract

Chilli peppers (Capsicum spp.) belong to very popular and significant horticultural crops, evaluated for their culinary, nutritional, and pharmacological properties. Knowledge about their genetic diversity is important because of their breeding strategies. In this study, restriction profiles of ITS sequences of three different chilli species were analysed for their differences together with ISSR fingerprint profile. A total of eleven genotypes of native chilli peppers from Peru were used in this study. Three different restriction patterns were obtained. Individual species, Capsicum chinesis Jacq, Capsicum frutescens and Capsicum baccatum were distinguished by UPGMA analysis.

References

Albrecht, E., Zhang, D., Saftner, R.A., & Stommel, J.R. (2012). Genetic diversity and population structure of Capsicum baccatum genetic resources. Genetic Resources and Crop Evolution, 59, 517–538. https://doi.org/10.1007/s10722-011-9700-y
Search in Google Scholar Back to article
Alansi, S., Tarroum, M., Al-Qurainy, F., Khan, S., & Nadeem, M. (2016). Use of ISSR markers to assess the genetic diversity in wild medicinal Ziziphus spina-christi (L.) Willd. collected from different regions of Saudi Arabia. Biotechnology and Biotechnological Equipment, 30, 942–947. https://doi.org/10.1080/13102818.2016.1199287
Search in Google Scholar Back to article
Amiteye, S. (2021). Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon, 30, e08093. https://doi.10.1016/j.heliyon.2021.e08093
Search in Google Scholar Back to article
Csilléry, G. (2006). Pepper taxonomy and the botanical description of the species. Acta Agronomica Hungarica, 54, 151–166. https://doi.org/10.1556/AAgr.54.2006.2.5
Search in Google Scholar Back to article
da Costa, F.R., Pereira, T.N.S., Vitória, A.P., de Campos, K.P., Rodrigues, R., da Silva, D.H., & Pereira, M.G. (2006). Genetic diversity among Capsicum accessions using RAPD markers. Crop Breeding and Applied Biotechnology, 6, 18–23.
Search in Google Scholar Back to article
dos Santos Pessoa, A.M., do Rago, E.R., dos Santos, C.A., & do Rago, M.M. (2018). Genetic diversity among accessions of Capsicum annuum L. through morphoagronomic characters. Genetics and Molecular Research, 17, gmr16039883. https://doi.org/10.4238/gmr16039883
Search in Google Scholar Back to article
Gemmill, C.E.C., & Grierson, E.R.P. (2021). Inter-Simple Sequence Repeats (ISSR), Microsatellite-Primed Genomic Profiling Using Universal Primers. Methods of Molecular Biology, 2222, 49–262. https://doi.org.10.1007/978-1-0716-0997-2_14
Search in Google Scholar Back to article
Gu, X.Z., Cao, Y.C., Zhang, Z.H., Zhang, B.X., Zhao, H., Zhang, X.M., Wang, H.P., Li, X.X., & Wang, L.H. (2019). Genetic diversity and population structure analysis of Capsicum germplasm accessions. Journal of Integrative Agriculture, 18, 1312–1320. https://doi.org/10.1016/S2095-3119(18)62132-X
Search in Google Scholar Back to article
Gupta, M., Verma, B., Kumar, N., Chahota, R.K., Rathour, R., Sharma, S.K., Bhatia, S., & Sharma, T.R. (2012). Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers. Journal of Genetics, 91, 279–287. https://doi.org/10.1007/s12041-012-0180-4
Search in Google Scholar Back to article
Gupta, V., Jatav, P.K., Haq, S.U., Verma, K.S., Kaul, V.K., Kothari, S., & Kachhwaha, S. (2019). Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity. Journal of Genetics, 98,1–12. https://doi.org/10.1007/s12041-019-1095-0
Search in Google Scholar Back to article
Haq, S., Dubey, S., Dhingra, P. et al. (2022). Exploring the genetic makeup and population structure among Capsicum accessions for crop improvement and breeding curriculum insights. Journal of Genetic Engeneering and Biotechnology, 20, 116. https://doi.org/10.1186/s43141-022-00398-1
Search in Google Scholar Back to article
Hasan, M., Kulsum, M., Ullah, M., Hossain, M.M., & Mahmud, M.E. (2014). Genetic diversity of some chili (Capsicum annuum L.) genotypes. International Journal of Agricultural Research, Innovation and Technology, 4, 32–35. https://doi.org/10.3329/ijarit.v4i1.21088
Search in Google Scholar Back to article
Qin, C., Yu, C., Shen, Y., Fang, X., Chen, L., Min, J., Cheng, J., Zhao, S., Xu, & M., Luo, Y. (2014). Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proceedings of National Academy of Sciences, 111, 5135–5140. https://doi.org/10.1073/pnas.1400975111
Search in Google Scholar Back to article
Ibarra-Torres, P., Valadez-Moctezuma, E., Pérez-Grajales, M., Rodríguez-Campos, J., & Jaramillo-Flores, M.E. (2015). Inter-and intraspecific differentiation of Capsicum annuum and Capsicum pubescens using ISSR and SSR markers. Scientia Horticulturae, 181,137–146. https://doi.org/10.1016/jscienta.2014.10.054
Search in Google Scholar Back to article
Jha, T.B., & Bhowmick, B.K. (2021). Conservation of floral, fruit and chromosomal diversity: a review on diploid and polyploid Capsicum annuum complex in India. Molecular Biology Reports, 48, 5587–5605. https://doi.org/10.1007/s11033-021-06355-4
Search in Google Scholar Back to article
Kehie, M., Kumaria, S., Devi, K.S., & Tandon, P. (2015). Genetic diversity and molecular evolution of Naga King Chili inferred from internal transcribed spacer sequence of nuclear ribosomal DNA. Meta Gene, 2, 56–63. https://doi.org.10.1016/j.mgene.2015.11.006
Search in Google Scholar Back to article
Lozada, D.N., Bhatta, M., Coon, D., & Bosland, P.W. (2021). Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.). BMC Genomics, 17, 356. https://doi.org.10.1186/s12864-021-07662-7
Search in Google Scholar Back to article
Maharijaya, A., Vosman, B., Pelgrom, K., Wahyuni, Y., de Vos, R.C., & Voorrips, R.E. (2019). Genetic variation in phytochemicals in leaves of pepper (Capsicum) in relation to thrips resistance. Arthropod-Plant Interactions, 13, 1–9. https://doi.org/10.1007/s11829-018-9628-7
Search in Google Scholar Back to article
Meckelmann, S.W., Riegel, D.W., van Zonneveld, M.J., Ríos, L., Peña, K., Ugas, R., Quinonez, L., Mueller-Seitz, E., & Petz, M. (2013). Compositional Characterization of Native Peruvian Chilli Peppers (Capsicum spp.). Journal of Agriculture Food and Chemistry, 61, 2530–2537.
Search in Google Scholar Back to article
Milad, S.I., Wahba, L.E., & Barakat, M.N. (2011). Identification of RAPD and ISSR markers associated with flag leaf senescence under water-stressed conditions in wheat (Triticum aestivum L.). Australian Journal of Crop Science, 5, 337–343. https://doi.org/10.3316/informit.279862523722050
Search in Google Scholar Back to article
Naegele, R.P., Mitchell, J., & Hausbeck, M.K. (2016). Genetic diversity, population structure, and heritability of fruit traits in Capsicum annuum. Plos one, 11. https://doi.org/10.1371/journal.pone.0156969
Search in Google Scholar Back to article
Nilkanta, H., Amom, T., Tikendra, L., Rahaman, H., & Nongdam, P. (2017). ISSR marker based population genetic study of Melocanna baccifera (Roxb.) Kurz: a commercially important bamboo of Manipur, North-East India. Scientifica, 9. https://doi.org/10.1155/2017/3757238
Search in Google Scholar Back to article
Rai, V.P., Kumar, R., Kumar, S., Rai, A., Kumar, S., Singh, M., Singh, S.P., Rai, A.B., & Paliwal, R. (2013). Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers. Physiology and Molecular Biology of Plants, 19, 575–586. https://doi.org/10.1007/s12298-013-0185-3
Search in Google Scholar Back to article
Sharmin, A., Hoque, E., Haque, M., & Khatun, F. (2018). Molecular Diversity Analysis of Some Chilli (Capsicum spp.) Genotypes Using SSR Markers. American Journal of Plant Sciences, 9, 82464. https://doi.org.10.4236/ajps.2018.93029
Search in Google Scholar Back to article
Shiragaki, K., Yokoi, S., & Tezuka, T. (2020). Phylogenetic Analysis and Molecular Diversity of Capsicum Based on rDNAITS Region. Horticulturae, 6, 87. https://doi.org/10.3390/horticulturae6040087
Search in Google Scholar Back to article
Swamy, K.R.M. (2023). Origin, distribution, taxonomy, botanical description, genetic diversity and breeding of capsicum (Capsicum annuum L.). International Journal of Development Research, 13, 61956-61977.
Search in Google Scholar Back to article
White, T.J. et al. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR protocols a guide to methods and applications. Academic Press (pp. 315–322).
Search in Google Scholar Back to article
Zhao, F., Li, D., Tian, X., & Du, W. (2020). QTL mapping for the resistance to yellow rust race CYR34 in triticale. Chilean Journal of Agricultural Research, 80, 405–412. https://doi.org/10.4067/S0718-58392020000300405
Search in Google Scholar Back to article

Articles in this issue

DOI: https://doi.org/10.2478/ahr-2026-0007 | Journal eISSN: 1338-5259 | Journal ISSN: 1335-2563

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Language: English

Page range: 55 - 60

Submitted on: Feb 3, 2026

Accepted on: Mar 17, 2026

Published on: May 18, 2026

Published by: Slovak University of Agriculture in Nitra

In partnership with: Paradigm Publishing Services

Publication frequency: 2 issues per year

Keywords:

variability,

DNA markers,

chilli peppers

Related subjects:

Industrial chemistry,

Green and sustainable technology

© 2026 Jana Žiarovská, Lucia Urbanová, Silvia Farkasová, Eloy Fernandez Cusimamani, published by Slovak University of Agriculture in Nitra
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Volume 29 (2026): Issue 1 (May 2026)