Characterization of strawberry (Fragaria × ananassa Duch.) cultivars using SCoT, ISSR and IRAP markers


Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran.


Genetic relationship of 36 strawberry cultivars was analyzed using three molecular marker systems; inter simple sequence repeats (ISSR), inter-retrotransposon amplified polymorphism (IRAP) and start codon targeted (SCoT) polymorphism. SCoT, IRAP and ISSR primers generated 238, 113 and 122 bands, respectively, of which 85.2, 91.5 and 89.35% were polymorphic. IRAPs with the highest values of expected heterozygosity (He), Shanonn index (I) and resolution power (Rp) were more powerful compared with SCoT and ISSR. However, the highest value of marker index was calculated for ISSRs. The genetic relationships were estimated using Dice similarity coefficient between different pairs of cultivars which varied from 0.577 to 0.901 for SCoT, 0.547 to 0.918 for IRAP, and 0.531 to 0.983 for ISSR. The UPGMA dendrograms using the SCoT and ISSR data classified cultivars into four major clusters; whereas based on the IRAP and combined data, the cultivars were divided into three major clusters. Approximately 50% of the cultivars with affiliation to pedigree and geographic origins were assigned to their major clusters. The results demonstrated that SCoT, ISSR and IRAP marker systems are useful for identification and genetic diversity analysis of strawberry cultivars.


AiFen, T., Zhong Hua, L., JianMin Q., Dong Xin, Z., Tao, W. and Shun Hui, C. 2009. Comparison and analysis of IRAP and ISSR molecular methods used for assessment of genetic diversity in tobacco. J. Wuhan Bot. Res. 27(6): 589-594.
Alavikia, S. S., Mohammadi, S. A.,  Aharizad, S. and Moghaddam, M. 2008. Analysis of genetic diversity and phylogenetic relationships in Crocus genus of Iran using inter-retrotransposon amplified polymorphism. Biotechnol. Biotechnol. Equip. 22: 795-800.
Arnau, G., Lallemand, J. and Bourgoin, M. 2002. Fast and reliable strawberry cultivar identification using inter simple sequence repeat (ISSR) amplification. Euphytica 129: 69-79.
Carvalho, A., Guedes‐Pinto, H., Martins‐Lopes, P. and Lima‐Brito, J. 2010. Genetic variability of Old Portuguese bread wheat cultivars assayed by IRAP and REMAP markers. Ann. Appl. Biol. 156(3): 337-345.
Collard, B. C. Y., and Mackill, D. J. 2009. 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.
Debnath, S. C., and Ricard, E. 2009. ISSR, anthocyanin content and antioxidant activity analyses to characterize strawberry genotypes. J. Appl. Hortic. 11(2): 83-89.
Degani, C., Rowland, L. J.,  Saunders, J. A.,  Hokanson, S. C.,  Ogden, E. L.,  Golan-Goldhirsh, A. and Galletta G. J., 2001. A comparison of genetic relationship measures in strawberry (Fragaria× ananassa Duch.) based on AFLPs, RAPDs, and pedigree data. Euphytica 117(1): 1-12.
Dong, Q., Wang, X., Zhao, M., Song, C. N, Ge, A. J. and Wang, J. 2011. Development of EST-derived SSR markers and their application in strawberry genetic diversity analysis. Sci. Agric. Sintica. 44: 3603-3612.
Doyle, J., and Doyle, J. L. 1990.  Isolation of plant DNA from fresh tissue. Focus 12: 13–15.
Eshghi, S., Abdi, G.,  Tafazoli, E. and Yavari, S. 2007.Strawberry research and biotechnology in Iran. Middle East Russ. J. Plant Sci. Biotech. 1(2): 39-41.
Fernandez, M., Figueiras, A. and Benito, C.  2002. The use of ISSR and RAPD markers for detecting DNA polymorphism, genotype identification and genetic diversity among barley cultivars with known origin. Theor. App. Genet.104: 845-851.
Giampieri, F., Tulipani, S., Alvarez-Suarez, J. M.,  Quiles, J. L.,  Mezzetti, B.  and Battino, M. 2012. The strawberry: composition, nutritional quality, and impact on human health. Nutrition 28: 9-19.
Hussein, T. S., Tawfik, A. A. and Khalifa, M. A. 2008. Molecular identification and genetic relatioships of six strawberry varieties using ISSR markers. Int. J. Agri. Biol. 10: 677-680.
Kalendar, R., Grob, T., Regina, M., Suoniemi, A. and Schulman, A. 1999. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor. Appl. Genet. 98: 704-711.
Kuras, A., Korbin, M.  and Zurawicz, E. 2004. Comparison of RAPD and ISSR techniques for determination of strawberry (Fragaria ananassa Duch) relationship. Plant Cell Tissue Organ Cult. 79: 189- 193.
Lim, S., Lee, J., Lee, H. J., Park, K. H.,  Kim, D. S.,  Min, S. R.,  Jang, W. S.,  Kim, T. and Kim, H. R. 2017. The genetic diversity among strawberry resources based on SSRs. Sci. Agric. 74(3): 226-234.
Luo, C., He, X., Chen, H., Ou, S. J.  and Gao, M. P. 2010. Analysis of diversity among mango cultivars using start codon targeted (SCoT) markers. Biochem. Syst. Ecol. 38 (6): 1176-1184.
Mahjbi, A., Baraket, G.,  Queslati, A., and Salhi-Hannachi, A. 2015. Start codon targeted (SCoT) markers provide new insights into the genetic diversity and characterization of Tunisian citrus species. Biochem. Syst. Ecol. 61: 300-308.
Manbari, Y., Karami, E., Etminan, A. and Talebi, R. 2012. Characterization of genetic variation between local and exotic Iranian strawberry (Fragaria× ananassa Duch.) cultivars using amplified fragment length polymorphism (AFLP) markers. Int. J. Biosci. 2(12): 159-167.
Meng, F., Liu, L., Peng, M., Wang, Z., Wang, C. and Zhao, Y. 2015. Genetic diversity and population structure analysis in wild strawberry (Fragaria nubicola L.) from Motuo in Tibet Plateau based on simple sequence repeats (SSRs). Biochem. Syst. Ecol. 63: 113-118.
Morales, R. F. G.,  Resende, J. T. V., Faria, M. V., Andrade, M. C., Resendae, L. V.,     Delatorre, C. A., and Silva, P. R. 2011. Genetic similarity among strawberry cultivars assessed by RAPD and ISSR markers. Sci. Agric. 68(6): 665- 670.
Mousapour Gorji, A., Poczai, P., Polger, Z. and Taller, J. 2011. Efficiency of arbitrary dominant markers (SCoT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato. Am. J. Pot. Res. 88: 226- 237.
Nagy, S., Poczai, P., Cernak, I., Mousapour Gorji, A., Hegedus, G. and Taller, J. 2012. PICcalc: An online program to calculate polymorphic information content for molecular genetic studies. Biochem. Genet. 50: 670- 672.
Nair, A. S., Teo, C. H.,  Schwarzacher, T.  and Harrison, P. H. 2005. Genome classification of banana cultivars from South India using IRAP markers. Euphytica 144(3): 285-290.
Nunes, C. F., Ferreira, J. L.,  Generose, A. L.,  Dias, M. S. C., Pasaqual, M. and Cancado, G. M. A. 2013. The genetic diversity of strawberry (Fragaria ananassa Duch.) hybrids based on ISSR markers. Acta. Sci. Agron. 35(4): 443-452. 
Peakall, R., and Smouse, P. E. 2012. Genalex 6.5. Genetic analysis in Excel. Population genetic software for teaching and research- an update. Bioinformatics bioinformatics/bts460.
Peng, M., Zong, X., Wang, C. and Meng, F. 2015. Genetic diversity of strawberry (Fragaria ananassa Duch.) from the Motuo county of the Tibet Plateau determined by AFLP markers. Biotechnol. Biotechnol. Equip. 29(5): 876-881.
Prevost, A. and Wilkinson, M. 1999. A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theo. Appl. Genet. 98: 107-112.
Rugienius, R., Siksnianiene, J. B.,  Freroks, B.,  Staniene, G., Stepalaitiene, I., Haimi, P. and Stanys, V. 2015. Characterization of strawberry (Fragaria × annanassa Duch) cultivars and hybrid using SSR and AFLP markers. Zemblirbyste Agric. 102 (2): 177-184.
Powell, W., Margenta, M., Andre, C., Hanfrey, M., Vogel, J.,  Tingey, S. and Rafalsky, A. 1996. The utility of RFLP, RAPD, AFLP and SSR (microsatellite) marker for germplasm analysis. Mol. Breed. 2: 225-238.
Rahmani, M. S., Alikhani, L., Shabanian, N., Badakhshan, H. and Khadivi-Khub, A. 2014. Genetic variability and structure of Quercus brantii assessed by ISSR, IRAP and SCoT markers. Gene 552: 176-183.
Rahmani, M. S., Shabanian, N., Khadivi-Khub, A.,  Woeste, K., Badakhshan, H. and Alikhani, L. 2015. Population structure and genotypic variation of Crataegus pontica inferred by molecular markers. Gene 572(1): 123-129.
Sanchez-Sevilla, J. F., Horvath, A., Botella, M. A., Gaston, A., Folta, K., Kilian, A., Denoyes, B. and Amaya, I. 2015. Diversity Arrays Technology (DArT) marker platforms for diversity analysis and linkage mapping in a complex crop, the octaploid cultivated strawberry (Fragaria × annassa). PLoS One 10 (12). prone 0144960 
Tehranifar, A., and Sarsaefi, M. 2002. Strawberry growing in Iran. Acta. Hortic. 567: 547-549.
Wang, S. Y. and Lin, H. S. 2000. Antioxidant activity in fruits and leaves of blackberry, raspberry, and strawberry varies with cultivar and developmental stage. J. Agric. Food. Chem. 48(2): 140-146.