Genetic diversity of native Cucumis melo L. accessions from Iran and Iraq revealed by SCoT and ISSR markers

genetic-diversity-of-native-cucumis-melo-l.-accessions-from-iran-and-iraq-revealed-by-scot-and-issr-markers
Genetic diversity of native Cucumis melo L. accessions from Iran and Iraq revealed by SCoT and ISSR markers

References

  1. Ebadi, A., Ghaderi, N. & Vafaee, Y. Genetic diversity of Iranian and some European grapes as revealed by nuclear and chloroplast microsatellite and SNP molecular markers. J. Hortic. Sci. Biotechnol. 94, 599–610 (2019).

    Google Scholar 

  2. Govindaraj, M., Vetriventhan, M. & Srinivasan, M. Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genet. Res. Int. 2015, 431487 (2015).

    Google Scholar 

  3. Houmanat, K. et al. Molecular diversity of walnut (Juglans regia L) among two major areas in Morocco in contrast with foreign varieties. Int. J. Fruit Sci. 21, 180–192 (2021).

    Google Scholar 

  4. Rao, B. R. Genetic diversity, genetic erosion, conservation of genetic resources, and cultivation of medicinal plants. In: Genetic Diversity and Erosion in Plants: Case Histories Vol. 8 (ed Ahuja MR) 357–392 (Springer, 2015).

  5. Huang, W. et al. Effects of environmental factors on genetic diversity of Caragana microphylla in Horqin Sandy Land, northeast China. Ecol. Evol. 6, 8256–8266 (2016).

    Google Scholar 

  6. Ghanbari Moheb Seraj, R. et al. Metabolomics analysis of milk thistle lipids to identify drought-tolerant genes. Sci. Rep. 12, 12827 (2022).

    Google Scholar 

  7. Hasanpour, K. et al. Identification of drought-tolerant hub genes in Iranian KC-2226 genotype of Aegilops tauschii using transcriptomic analysis. Sci. Rep. 13, 9499 (2023).

    Google Scholar 

  8. Azad, M. et al. Identification of responsive genes to multiple abiotic stresses in rice (Oryza sativa): A meta-analysis of transcriptomics data. Sci. Rep. 14, 5463 (2024).

    Google Scholar 

  9. Pradeep Reddy, M., Sarla, N. & Siddiq, E. A. Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica 128, 9–17 (2002).

    Google Scholar 

  10. Grover, A. & Sharma, P. C. Development and use of molecular markers: past and present. Crit. Rev. Biotechnol. 36, 290–302 (2016).

    Google Scholar 

  11. Coşkun, Ö. F., Toprak, S. & Mavi, K. Genetic diversity and association mapping for salinity tolerance in watermelon (Citrullus Lanatus L.). J. Crop Health 77(2), 73 (2025).

    Google Scholar 

  12. Erkek, B. et al. Natural diversity of Crataegus monogyna Jacq. in Northeastern Türkiye encompassing morphological, biochemical, and molecular features. Horticulturae 11(3), 238 (2025).

    Google Scholar 

  13. Toprak, S., Coşkun, Ö. F. & Mavi, K. Çerezlik karpuz genotiplerinin ISSR tekniği ile moleküler karakterizasyonu. Erciyes Tarım ve Hayvan Bilimleri Dergisi 6(1), 51–58 (2023).

    Google Scholar 

  14. Collard, B. C. Y. & Mackill, D. J. Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Mol. Biol. Rep. 27, 86–93 (2009).

    Google Scholar 

  15. Jedrzejczyk, I. Genome size and SCoT markers as tools for identification and genetic diversity assessment in Echinacea genus. Ind. Crops Prod. 144, 112055 (2020).

    Google Scholar 

  16. Abulela, H. A. et al. Evaluation of the morpho-physiological traits and the genetic diversity of some Egyptian bread wheat cultivars under salt stress conditions. Cereal Res. Commun. 50, 733–753 (2022).

    Google Scholar 

  17. Mulpuri, S., Muddanuru, T. & Francis, G. Start codon targeted (SCoT) polymorphism in toxic and non-toxic accessions of Jatropha curcas L. and development of a codominant SCAR marker. Plant Sci. 207, 117–127 (2013).

    Google Scholar 

  18. Gupta, P. K. & Rustgi, S. Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct. Integr. Genomics 4, 139–162 (2004).

    Google Scholar 

  19. Xanthopoulou, A. et al. Comparative analysis of genetic diversity in Greek Genebank collection of summer squash (Cucurbita pepo) landraces using start codon targeted (SCoT) polymorphism and ISSR markers. Aust. J. Crop Sci. 9, 14–21 (2015).

    Google Scholar 

  20. Tyagi, R. et al. Genetic diversity and population structure detection in sponge gourd (Luffa cylindrica) using ISSR, SCoT and morphological markers. Physiol. Mol. Biol. Plants 26, 119–131 (2020).

    Google Scholar 

  21. Kumar, J. & Agrawal, V. Assessment of genetic diversity, population structure and sex identification in dioecious crop, Trichosanthes dioica employing ISSR SCoT and SRAP markers. Heliyon 5, e01346 (2019).

    Google Scholar 

  22. Gogoi, B., Wann, S. B. & Saikia, S. P. Comparative assessment of ISSR, RAPD, and SCoT markers for genetic diversity in Clerodendrum species of North East India. Mol. Biol. Rep. 47, 7365–7377 (2020).

    Google Scholar 

  23. Abouseada, H. H. et al. Genetic diversity analysis in wheat cultivars using SCoT and ISSR markers, chloroplast DNA barcoding and grain SEM. BMC Plant Biol. 23, 193 (2023).

    Google Scholar 

  24. Jahangir, M. & Nasernakhaei, F. Molecular characterization of Cressa cretica L. Using SCoT and ISSR markers. J. Genet. Resour. 11, 126–131 (2025).

    Google Scholar 

  25. Nasri, F., Zakizadeh, H., Vafaee, Y. & Mozafari, A. A. Callus induction and plant regeneration of Chrysanthemum morifolium and C coccineum via direct and indirect organogenesis and genetic fidelity analysis using IRAP, ISSR and SCoT molecular markers. J. Ornam. Plants 8, 265–284 (2018).

    Google Scholar 

  26. Elgohary, M. E. et al. Integrating SCoT, CBDP, and ISSR molecular markers for genetic diversity assessment and taxonomic authentication of some Asteraceae species in Egypt. Genet. Resour. Crop Evol. (2025).

  27. Baghizadeh, A. & Dehghan, E. Efficacy of SCoT and ISSR markers in assessment of genetic diversity in some Iranian pistachio (Pistacia vera L) cultivars. Pistachio Health J. 1, 37–43 (2018).

    Google Scholar 

  28. Keshavarzi, M., Tabaripour, R. & Ullah, F. Assessment of SCoT and ISSR molecular markers in genetic diversity of rigid ryegrass (Lolium rigidum Gaud) in Iran. BMC Genet. 23, 12 (2022).

    Google Scholar 

  29. Kirkbride, J. H. Biosystematic Monograph of the Genus Cucumis (Cucurbitaceae): Botanical Identification of Cucumbers and Melons (Parkway Publishers, 1993).

    Google Scholar 

  30. Bates, D., Merrick, L. & Robinson, R. Minor cucurbits: Benincasa, Lagenaria, Luffa, Sechium, and other genera (Cucurbitaceae). in Evolution of Crop Plants (eds. Smartt, J. & Simmonds, N. W.) 105–111 (Longman, 1995).

  31. Mccreight, J. D., Nerson, H. & Grumet, R. Melon: Cucumis melo L. In: Genetic Improvement of Vegetable Crops (eds. Kalloo, G. & Bergh, B. O.) 267–294 (Pergamon Press, 1993).

  32. Sabato, D., Esteras, C., Grillo, O., Pico, B. & Bacchetta, G. Seeds morpho-colourimetric analysis as complementary method to molecular characterization of melon diversity. Sci. Hortic. 192, 441–452 (2015).

    Google Scholar 

  33. Rad, N. Assessment of genetic diversity among melon accessions using graphical principal component and cluster analysis. Iraqi J. Agric. Sci. 49, 1–12 (2018).

    Google Scholar 

  34. Ghorbani, E., Motallebi-Azar, A. & Bolandnazar, S. Agro-Morphological Variation in Some Iranian Melon (Cucumis melo L) genotypes revealed by multivariate analysis. Indian J. Agric. Res. 54, 161–167 (2020).

    Google Scholar 

  35. Danesh, M., Lotfi, M. & Azizinia, S. Genetic diversity of Iranian melon cultigens revealed by AFLP markers. Biharean Biol. 9, 1–6 (2015).

    Google Scholar 

  36. Dastranji, N. et al. Assessment of genetic diversity of some of Iranian snake melon (Cucumis melo var. flexuosus) accessions using morphological markers. Plant Prod. 39, 15–26 (2016).

    Google Scholar 

  37. Al-Juboori, A. W. A., Ismail, E. N. & Alwan, K. A. Molecular and morphological indicators (Qutha) Cucumis melo planted in Iraq. Iraqi J. Agric. Sci. 50, 835–841 (2018).

    Google Scholar 

  38. Maleki, M., Shojaeiyan, A. & Monfared, S. R. Population structure, morphological and genetic diversity within and among melon (Cucumis melo L) landraces in Iran. J. Genet. Eng. Biotechnol. 16, 599–606 (2018).

    Google Scholar 

  39. Al Khazraji, H. A., Abd, A. M. & Abdulla, A. A. The determination of the genetic distance of various snake melon Cucumis melo var flexuosus cultivars using inter simple sequence repeat technique (ISSR). Basrah J. Agric. Sci. 34, 111–123 (2021).

    Google Scholar 

  40. Al-Juboori, A. W. A. & Ismail, E. N. Genetic diversity and morphological markers of Cucumis melo L. in Iraq. Iraqi J. Agric. Sci. 50, 835–841 (2018).

    Google Scholar 

  41. Aziz, R. R. & Tahir, N. A. R. Genetic diversity and structure analysis of melon (Cucumis melo L.) genotypes using URP, SRAP, and CDDP markers. Genet. Resour. Crop Evol. 70, 799–813 (2023).

    Google Scholar 

  42. Murray, M. G. & Thompson, W. F. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res. 8, 4321–4325 (1980).

    Google Scholar 

  43. Gholami, S. et al. Molecular characterization of endangered Iranian terrestrial orchids using ISSR markers and association with floral and tuber-related phenotypic traits. Physiol. Mol. Biol. Plants 27, 53–68 (2021).

    Google Scholar 

  44. Gholami, S. et al. Exploring genetic variations in threatened medicinal orchids using start codon targeted (SCoT) polymorphism and marker-association with seed morphometric traits. Physiol. Mol. Biol. Plants 27, 769–785 (2021).

    Google Scholar 

  45. Rahmani, M.-S. et al. Genetic differentiation in Quercus infectoria from northwest of Iran revealed by different nuclear markers. Tree Genet. Genomes 11, 1–9 (2015).

    Google Scholar 

  46. Peakall, R. & Smouse, P. E. GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6, 288–295 (2006).

    Google Scholar 

  47. Hammer, Ø., Harper, D. A. T. & Ryan, P. D. PAST: Paleontological Statistics software package for education and data analysis. Palaeontol. Electron. 4, 1–9 (2001).

    Google Scholar 

  48. Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).

    Google Scholar 

  49. Falush, D., Stephens, M. & Pritchard, J. K. Inference of population structure using multilocus genotype data: Dominant markers and null alleles. Mol. Ecol. Notes 7, 574–578 (2007).

    Google Scholar 

  50. Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611–2620 (2005).

    Google Scholar 

  51. Earl, D. A. & VonHoldt, B. M. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359–361 (2012).

    Google Scholar 

  52. Gorji, A. M., Poczai, P., Polgar, Z. & Taller, J. Efficiency of arbitrarily amplified dominant markers (SCoT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato. Am. J. Potato Res. 88, 226–237 (2011).

    Google Scholar 

  53. Tahir, N. et al. Assessment of genetic variation and population structure in Iraqi barley accessions using ISSR, CDDP, and SCoT markers. Biol. Life Sci. Forum 11, 4 (2023).

    Google Scholar 

  54. Jing, Z. et al. Genetic diversity and relationships between and within persimmon (Diospyros L) wild species and cultivated varieties by SRAP markers. Plant Syst. Evol. 299, 1485–1492 (2013).

    Google Scholar 

  55. Agarwal, A. et al. Assessment of genetic diversity in 29 rose germplasms using SCoT marker. J. King Saud Univ. Sci. 31, 780–788 (2019).

    Google Scholar 

  56. Gupta, P. et al. DNA fingerprinting and genetic relationships similarities among the accessions/species of Ocimum using SCoT and ISSR markers system. Mol. Biotechnol. 63, 446–457 (2021).

    Google Scholar 

  57. Kumar, A. et al. Estimation of genetic diversity utilizing gene-targeted SCoT markers and morpho-chemotypic analyses in Senna alexandrina Mill. (Senna). Ecol. Genet. Genom. 31, 100252 (2024).

    Google Scholar 

  58. Goswami, B., Gadi, B. & Rao, S. R. Morphological and molecular markers based assessment of genetic diversity of a valuable endemic plant Lasiurus sindicus Henr in the arid region of Rajasthan India. Arid Land Res. Manag. 36, 298–313 (2022).

    Google Scholar 

  59. Amom, T. et al. Efficiency of RAPD, ISSR, iPBS, SCoT and phytochemical markers in the genetic relationship study of five native and economical important bamboos of North-East India. Phytochemistry 174, 112330 (2020).

    Google Scholar 

  60. Bidyananda, N. et al. Plant genetic diversity studies: Insights from DNA marker analyses. Int. J. Plant Biol. 15, 607–640 (2024).

    Google Scholar 

  61. Paris, H. S. et al. Genetic relationships in Cucurbita pepo (pumpkin, squash, gourd) as viewed with high frequency oligonucleotide–targeting active gene (HFO–TAG) markers. Genet. Resour. Crop Evol. 62, 1095–1111 (2015).

    Google Scholar 

  62. Pandey, A. et al. Genetic diversity and population structure of watermelon (Citrullus sp) genotypes. 3 Biotech 9, 1–14 (2019).

    Google Scholar 

  63. Amom, T. et al. Conservation strategies for endemic Dendrocalamus manipureanus: A study on genetic diversity and population structure based on molecular and phytochemical markers. S. Afr. J. Bot. 152, 106–123 (2023).

    Google Scholar 

  64. Tiwari, G. et al. Study of arbitrarily amplified (RAPD and ISSR) and gene targeted (SCoT and CBDP) markers for genetic diversity and population structure in Kalmegh [Andrographis paniculata (Burm f) Nees]. Ind. Crops Prod. 86, 1–11 (2016).

    Google Scholar 

  65. Hromadová, Z. et al. Efficiency of RAPD and SCoT markers in the genetic diversity assessment of the common bean. Plants 12, 2763 (2023).

    Google Scholar 

  66. Dadras, A. Evaluation of genetic diversity of tobacco (Nicotiana tabacum L.) cultivars using AFLP molecular marker. MSc Thesis, Shahid Bahonar University of Kerman (2012).

  67. Mansoory, A. et al. Evaluation of genetic diversity in three Diospyros species, collected from different regions in Iran, using ISSR and SCoT molecular markers. Int. J. Fruit Sci. 22, 235–248 (2022).

    Google Scholar 

  68. Sayed Ibrahim, A. et al. Physiological, biochemical, and molecular characterization of some cucumber (Cucumis sativus L) genotypes. Int. J. Veg. Sci. 30, 673–694 (2024).

    Google Scholar 

  69. Khodaee, L. et al. Assessment of genetic diversity among Iranian Aegilops triuncialis accessions using ISSR, SCoT, and CBDP markers. J. Genet. Eng. Biotechnol. 19, 5 (2021).

    Google Scholar 

  70. Tanaka, K. et al. Melon diversity on the silk road by molecular phylogenetic analysis in Kazakhstan melons. Breed. Sci. 73, 219–229 (2023).

    Google Scholar 

  71. Yermagambetova, M. et al. Conspectus of the genus Juniperus L growing in Kazakhstan. Proc. Appl. Bot. Genet. Breed. 183, 161–170 (2022).

    Google Scholar 

  72. Whitaker, T. W. & Davis, G. N. Cucurbits: Botany, Cultivation and Utilization (Leonard Hill Books Limited, 1962).

    Google Scholar 

  73. Cao, Y.-N. et al. Inferring spatial patterns and drivers of population divergence of Neolitsea sericea (Lauraceae), based on molecular phylogeography and landscape genomics. Mol. Phylogenet. Evol. 126, 162–172 (2018).

    Google Scholar 

  74. Dilipan, E. & Nisha, A. J. Assessing salinity tolerance and genetic variation in mung bean (Vigna radiata) through CAAT box and SCoT marker analysis. Ecol. Genet. Genom. 32, 100266 (2024).

    Google Scholar 

  75. Patel, S. et al. Deciphering the genetic architecture of resistance to Corynespora cassiicola in soybean (Glycine max L.) by integrating genome-wide association mapping and RNA-Seq analysis. Front. Plant Sci. 14, 1255763 (2023).

    Google Scholar 

  76. Jahantigh, M. & Jahantigh, M. Effect of clay-pot irrigation on Citrullus colocynthis plant growth for arid land restoration (A case study: Southeast of Iran). Sustainability 15, 16267 (2023).

    Google Scholar 

Download references