Molecular characters of melon (Cucumis melo L. ‘Kinaya’) using inter simple sequence repeat

  • Budi Setiadi Daryono Faculty of Biology, Universitas Gadjah Mada
  • Puti Hana Ramadhani Faculty of Biology, Universitas Gadjah Mada
  • Esty Nidianti Faculty of Biology, Universitas Gadjah Mada


Cultivar ‘Kinaya’ is a melon produced from breeding between ‘Sonya’ and ‘Kinanti’. This study on phenotypic and molecular characters is carried out to support ‘Kinaya’ as a superior cultivar. Our study aimed to analyze the genetic variation of the melon ‘Kinaya Bulat Kuning’ and ‘Kinaya Kuning Lonjong’ and its parental ‘Sonya’ and ‘Kinanti’. The research was conducted in the Greenhouse of Mutihan, D.I.Yogyakarta, and the Laboratory of Genetics and Breeding, Faculty of Biology, Universitas Gadjah Mada. Quantitative characters were determined by morphometric comparisons, fruit weights, and the number of seeds. Qualitative characters included fruit color, fruit skin color, aroma, texture, and taste. The molecular characterization method was inter simple sequence repeat (ISSR) and included DNA isolation, spectrophotometry, amplification of DNA target using PCR, and visualization of DNA target. Molecular characters were analyzed using spectrophotometry and visualization of DNA bands by electrophoresis using the MVSP 3.1 program. PCR used four random primers such as UBC 807, 809, 810, and 812, which obtained 11 polymorphic and 12 monomorphic DNA bands with a polymorphism rate of 47.8%. It is known that the cultivar ‘Kinaya’ has a similarity of 72% with its inductees ‘Sonya’ and ‘Kinanti’.


Ahmed OB, Asghar AH, Elhassan MM. 2014. Comparison of three DNA extraction methods for polymerase chain reaction (PCR) analysis of bacterial genomic DNA. African Journal of Microbiology Research. vol 8(6): 598–602. doi:

Ajuru MG, Okoli BE. 2013. The morphological characterization of the melon species in the family Cucurbitaceae Juss., and their utilization in Nigeria. International Journal of Modern Botany. vol 3(2): 15–19. doi:

Akash M, Awad N, Kasrawi M. 2018. Genetic diversity among snake melon landraces (Cucumis melo var. flexuosus) using molecular descriptors. Plant Biosystems-An International Journal Dealing with all Aspects of Plant Biology. vol 154(2): 206–212. doi:

Aristya GR, Maulina NTA, Arif MF, Kasiamdari RS, Widiastuti A. 2019. Detection and analysis of delayed-ripening genes in the growth of strawberries (Fragaria× ananassa) treated 1-naphtaleneacetic acid. Journal of Physics: Conference Series. vol 1374: 1–10. doi:

Boyd M, Panoyan MA, Michael P, Nkongolo KK. 2019. Development and characterization of species-diagnostic ISSR and SCAR DNA markers for differentiating red maple (Acer rubrum) and silver maple (A. saccharinum). Genome. vol 62(8): 527–535. doi:

Dangi B, Khurana-Kaul V, Kothari SL, Kachhwaha S. 2014. Micropropagation of Terminalia bellerica from nodal explants of mature tree and assessment of genetic fidelity using ISSR and RAPD markers. Physiology and Molecular Biology of Plants. vol 20(4): 509–516. doi:

Daryono BS, Subiastuti AS, Fatmadanni A, Sartika D. 2019. Phenotypic and genetic stability of new Indonesian melon cultivar (Cucumis melo L.‘Melonia’) based on ISSR markers. Biodiversitas Journal of Biological Diversity. vol 20(4): 1069–1075. doi:

Devarumath RM, Kalwade SB, Kawar PG, Sushir KV. 2012. Assessment of genetic diversity in sugarcane germplasm using ISSR and SSR markers. Sugar Tech. vol 14(4): 334–344. doi:

Flores-León A, García-Martínez S, González V, Garcés-Claver A, Martí R, Julián C, Sifres A, Pérez-de-Castro A, Díez MJ, López C, Ferriol M, Gisbert C, Ruiz JJ, Cebolla-Cornejo J, Picó B. 2021. Grafting snake melon [Cucumis melo L. subsp. melo var. flexuosus (L.) Naudin] in organic farming: Effects on agronomic performance; resistance to pathogens; sugar, acid, and VOC profiles; and consumer acceptance. Frontiers in Plant Science. vol 12: 1–22. doi:

Gebrehiwet M, Haileselassie T, Gadissa F, Tesfaye K. 2019. Genetic diversity analysis in Plectranthus edulis (Vatke) Agnew populations collected from diverse geographic regions in Ethiopia using inter-simple sequence repeats (ISSRs) DNA marker system. Journal of Biological Research-Thessaloniki. vol 26(1): 1–11. doi:

Gómez-García R, Campos DA, Aguilar CN, Madureira AR, Pintado M. 2020. Valorization of melon fruit (Cucumis melo L.) by-products: Phytochemical and biofunctional properties with emphasis on recent trends and advances. Trends in Food Science & Technology. vol 99: 507–19. doi:

Granier C, Vile D. 2014. Phenotyping and beyond: modelling the relationships between traits. Current Opinion in Plant Biology. vol 18: 96–102. doi:

Guliyev N, Sharifova S, Ojaghi J, Abbasov M, Akparov Z. 2018. Genetic diversity among melon (Cucumis melo L.) accessions revealed by morphological traits and ISSR markers. Turkish Journal of Agriculture and Forestry. vol 42(6): 393–401.

Healey A, Furtado A, Cooper T, Henry RJ. 2014. Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods. vol 10(1): 1–8. doi:

Ittiyavirah SP, George A, Santhosh AM, Kurian ST, Pappachan P, Jacob G. 2013. Studies of cytotoxic potential of Cucumis melo Linn fruit aqueous extract in prostate cancer cell lines PC-3 using MTT and neutral red assay. Iranian Journal of Pharmacology and Therapeutics. vol 12(1): 24–30.

Liu W, Fu R, Li Q, Li J, Wang L, Ren Z. 2013. Genome-wide identification and expression profile of homeodomain-leucine zipper Class I gene family in Cucumis sativus. Gene. vol 531(2): 279–287. doi:

Lucas MS, Carvalho CD, Hypolito GB, Côrtes MC. 2019. Optimized protocol to isolate high quality genomic DNA from different tissues of a palm species. Hoehnea. vol 46(2): 1–10. doi:

Mohamed FH, Abo-Zeid AA, El-Hamed KEA, Elwan MW, Salam MMA. 2020. Genetic diversity in Egyptian snake melon accessions as revealed by inter simple sequence repeat (ISSR) markers. Catrina The International Journal of Environmental Sciences. vol 22(1): 71–76. doi:

Nadeem MA, Nawaz MA, Shahid MQ, Doğan Y, Comertpay G, Yıldız M, Hatipoğlu R, Ahmad F, Alsaleh A, Labhane N, Özkan H. Chung G, Baloch FS. 2017. DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnology & Biotechnological Equipment. vol 32(2): 261–285. doi:

Nanda S, Kar B, Nayak S, Jha S, Joshi RK. 2013. Development of an ISSR based STS marker for sex identification in pointed gourd (Trichosanthes dioica Roxb.). Scientia Horticulturae. vol 150: 11–15. doi:

Ng WL, Tan SG. 2015. Inter-simple sequence repeat (ISSR) markers: are we doing it right. ASM Science Journal. vol 9(1): 30–39.

Paris HS, Amar Z, Lev E. 2012. Medieval emergence of sweet melons, Cucumis melo (Cucurbitaceae). Annals of Botany. vol 110(1): 23–33. doi:

Pellicer J, Hidalgo O, Dodsworth S, Leitch IJ. 2018. Genome size diversity and its impact on the evolution of land plants. Genes. vol 9(2): 1–14. doi:

Pitrat M. 2016. Melon genetic resources: phenotypic diversity and horticultural taxonomy. Genetics and genomics of Cucurbitaceae. New York: Springer. pp 25–60.

Poverenov E, Danino S, Horev B, Granit R, Vinokur Y, Rodov V. 2014. Layer-by-layer electrostatic deposition of edible coating on fresh cut melon model: Anticipated and unexpected effects of alginate–chitosan combination. Food and Bioprocess Technology. vol 7(5): 1424–1432. doi:

Ragupathya S, Fallera AC, Shanmughanandhan D, Kesanakurti P, Shaanker U, Ravikanth G, Sathishkumar R, Mathivanan N, Song J, Han J, Newmaster S. 2019. Exploring DNA quantity and quality from raw materials to botanical extracts. Heliyon. vol 5(6): 1–7. doi:

Raji OH, Orelaja OT. 2014. Nutritional composition and oil characteristics of golden melon (Cucumis melo) seeds. Food Science and Quality Management. vol 27: 18–21.

Rohela GK, Jogam P, Bylla P, Reuben C. 2019. Indirect regeneration and assessment of genetic fidelity of acclimated plantlets by SCoT, ISSR, and RAPD markers in Rauwolfia tetraphylla L.: An endangered medicinal plant. BioMed Research International. vol 2019: 1–15. doi:

Sangamithra A, Ragavi P. 2020. Post-harvest attributes of muskmelon (Cucumis melo): A mini review on the potential of value addition. Current Nutrition & Food Science. vol 16(6): 854–859. doi:

Shahid M, Srivastava M, Kumar V, Singh A, Pandey S. 2014. Genetic determination of potential Trichoderma species using ISSR (Microsatellite) marker in Uttar Pradesh. Microbial & Biochemical Technology. vol 6(3): 174–178. doi:

Shin AY, Koo N, Kim S, Sim YM, Choi D, Kim YM, Kwon SY. 2019. Draft genome sequences of two oriental melons, Cucumis melo L. var. makuwa. Scientific Data. vol 6(1): 1–8. doi:

Singh AK, Kumar S, Singh H, Rai VP, Singh BD, Pandey S. 2015. Genetic diversity in Indian snapmelon (Cucumis melo var. 'momordica') accessions revealed by ISSR markers. Plant Omics. vol 8(1): 9–16.

Son JH, Park KC, Lee SI, Kim JH, Kim NS. 2012. Species relationships among Allium species by ISSR analysis. Horticulture, Environment, and Biotechnology. vol 53(3): 256–262. doi:

Sultana RS, Rahman MM. 2014. Melon crops improvement through biotechnological techniques for the changing climatic conditions of the 21st century. International Journal of Genetics and Genomics. vol 2(3): 30–41. doi:

Tahseen RA, Amein KA, Samak DH, El-Sayed YS, Nasr SM. 2018. Verifying parentage and genetic variability among Arabian horse using ISSR markers. Alexandria Journal for Veterinary Sciences. vol 59(1): 125–133. doi:

Wang XM. 2011. Inter-simple sequence repeats (ISSR) molecular fingerprinting markers for authenticating the genuine species of rhubarb. Journal of Medicinal Plants Research. vol 5(5): 758–764. doi:

Research Articles
Abstract viewed = 231 times