Genetic Diversity of Bread Wheat (Triticum aestivum L.) Genotypes Using RAPD and ISSR Molecular Markers

Document Type: Research Article


1 Department of Genetics, Tabriz Branch, Islamic Azad University, Tabriz, Iran

2 Department of Molecular and Cell Biology, Marand Branch, Islamic Azad University, Marand, Iran

3 Department of Plant Biology, Marand Branch, Islamic Azad University, Marand, Iran



The importance of grain cultivation especially wheat is obvious in terms of providing human and animal food and its impact on the economy of human societies. The reduction of genetic diversity in cultivars prevents increasing yields in line with rising demand and consumption. Therefore, it is necessary to improve the compatibility of them and increase their genetic extent. In the current, the genetic diversity of Iranian wheat genotypes was investigated at the DNA level using RAPD and ISSR markers. 17 RAPD primers and 16 ISSR primers generated 86 (86/99= %86.86) and 56 (56/64= %57.5) polymorphic bands respectively. The cluster analysis based on UPGMA and dendrogram plotted using NTSYSpc 2.02 software revealed three main clusters. The highest genetic distance was between CD-89-2 and CD-89-7 genotypes and the minimum genetic distance was between CD-89-2 and CD-89-3 genotypes. Based on Nei's genetic distance matrix, the mean number of effective bands, the Shannon index, and polymorphism content were 1.381, 0.332, and % 87.12, respectively. Our results showed that RAPD and ISSR analysis are suitable methods to study genetic diversity and relationships among T. aestivum genotypes.


Abdellatif KF, AbuZeid HM. 2011. Assessment of genetic diversity of Mediterranean bread wheat using randomly amplified polymorphic DNA (RAPD) markers. J Genet Eng Biotechnol 9: 157-163.

Aghazadeh Gholaki R, Ghareiazi B, Nematzadeh GH A, Babaeian NA. 2003. Classification of some Iranian Rice germplasms by use of RAPD marker. Iranian J Agri Sci 34: 757-767.

Allard RW. 1996. Genetic basis of the evolution of adaptedness in plants. Euphytica 92:1-11.

Arekesh Salmani N. 2014. Quantitative and qualitative comparison of fatty acids and proteins of 6 Iranian wheat cultivars. MSc Thesis. Marand Branch, Islamic Azad University, Marand, Iran.

Barakat MN, Al-Doss AA, Elshafei AA, Moustafa KA. 2011. Identification of new microsatellite marker linked to the grain filling rate as indicator for heat tolerance genes in F2 wheat population. Aust J Crop Sci 5(2):104-110.

Barbosa-Nato JF, Sorrells ME Ciser G. 1996. Prediction of heterosis in wheat using coefficient of parentage and RFLP-based estimates of genetic relationship. Genome 39: 1142-1149.

Bedo Z, Szunics L, Lang L, Szunics Lu, Veisz O, Karsai I, Vida GY, Szücs P, Juhasz A, Gal M, Bencze SZ, Megyeri M, Puskas K, Horvath CS. 2000. Genetic diversity in durum wheat. Annl Wheat News Items from Hungary 46.

Blair MW, Panaud O, Mccouch SR. 1999. Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.). Theor Appl Genet 98: 780-792.

Cao W, Hucl P, Scoles G, Chibbar RN, Fox PN, Skovmand B. 2002. Cultivar identification and pedigree assessment of common wheat based on RAPD analysis. Wheat Inf Serv 95: 29-35.

Casaoli M, Mattion C, Cherubini M, Villani F. 2001. A genetic linkage map of European chestnut (Castanea sativa Mill.) based on RAPD, ISSR and isozyme markers. Theor Appl Genet 102: 1190-1199.

Cekic C, Battey NH, Wilkinson MJ. 2001. The potential of ISSR-PCR primer-pair combinations for genetic. Theor Appl Genet 103: 540-546.

Das S, Misra RC. 2010. Assessment of genetic diversity among finger millet genotypes using RAPD markers. Indian J Agr Res 44:112-118.

Doyle JJ, Doyle JL. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochem Bull 19: 11-15.

Eid M. 2019. RAPD fingerprinting and genetic relationships of some wheat genotypes. Int J Genet Genom 7(1):1-11.

FAO. 2006. World agriculture: Towards 2030/2050. Interim Report. Global Perspective Studies Unit, FAO, Rome, Italy.

Fazeli F, Chafgamirza k. 2011. Genetic variation in Iranian chickpea (Cicer arietinum L. Kabuli type) based on agronomic traits and RAPD marker. Seed Plant Improv J 27:555-579.

Golkar P, Arzani A, Rezaei AM. 2011. Genetic variation in safflower (Carthamus tinctorious L.) for seed quality-related traits and inter-simple sequence repeat (ISSR) markers. Int J Mol Sci 12: 2664-2677.

Gupta PK, Balyan HS, Parsad M, Varshney RK, Roy JK. 2000. Molecular markers for gene tagging and genetic diversity studies at meerut. Annl Wheat News L, Items from India 46.

Habash DZ, Kehel Z, Nachit M. 2009. Genomic approaches for designing durum wheat ready for climate change with a focus on drought. J Exp Bot 60(10): 2805-2815.

Hatari Z, Zamani Z, Nazeri V, Tabrizi L. 2013. Evaluation of genetic diversity in the medicinal plant Kakooti (Ziziphora tenuior L.) using morphological characteristics and RAPD markers. Mod Genet J l8:19-28.

Ijaz S, Khan IA. 2009. Molecular characterization of wheat germplasm using microsatellite markers. Genet Mol Res 8(3): 809-815.

Jedari Kouhi B, Garoosi GA, Hosseini R .2011. Investigation on genetic variation in seedless grapevine cultivars using RAPD molecular marker. J Cell Tissue 2: 99-106 (In Persian).

Johanson GK, Ganga G, Varma R, Sandeep, Sasikumar B, Saji KV. 2005. Identification of hybrids in black pepper (Piper nigrum L.) using male parent specific, RAPD markers. Curr Sci 88:216-218.

Khodadadi M, Fotokian MH, Miransari M. 2011. Genetic diversity of wheat (Triticum aestivum L.) genotypes based on cluster and principal component analyses for breeding strategies. Aust J Crop Sci 5(1): 17-24.

Khodadost, A, Yousefzadeh H, Amirchakhmaghi N, Abdollahi H, Hosseinzadeh Colagar A. 2016. Genetic diversity of Malus orientalis in hyrcanian forest using ISSR-PCR markers. J Mol Cell Res 29(4): 359-369. (In Persian)

Koohgard M, Shiran B, Mirakhorli N. 2012. Study of genetic diversity between and within populations of Fritillaria imperialis in Zagrose regions using RAPD marker. Mod Genet J 7: 353-362.

Kumar A, Sengar R S, Rao V P, Shukla G, Dixit R, Singh R. 2017. Assessment of genetic diversity in bread wheat (Triticum aestivum L.) using RAPD markers. J App Nat Sci 9(3): 1751-1755.

Malik TA, Price A, Wright D. 1996. Identification of wheat genotypes by random amplified polyorphic DNA technique. In: Agricultural Biotechnology, Proc 1st Biotech. Symp Univ Agri Faisalabad, Pakistan 81-87.

Martin JP, Sanchez-Yelamo MD. 2000. Genetic relationships among species of the genus Diplotaxis (Brassicaceae) using inter-simple sequence repeat markers. Theor Appl Genet 101: 1234-1241.

Muthusamy S, Kanagarajan S, Ponnusamy S. 2008. Efficiency of RAPD and ISSR markers system in accessing genetic variation of rice bean (Vigna umbellata) landraces. Electron J Biotechn 11(3): 1-10.

Najaphy A, Parchin RA, Farshadfar E. 2012. Comparison of phenotypic and molecular characterizations of some important wheat cultivars and advanced breeding lines. Aust J Crop Sci 6: 326-332.

Prevost D, Bordeleau LM, Antoun H. 1987. Symbiotic efectivness indigenous artic rhizoba on temperate forage legume sainfoin (Onobrychis viciifolia). Plant Soil 104:63-69.

Rana RM, Bilal M, Rehman SU, Iqbal F, Nawaz Shah MK. 2013. Synthetic wheat; a new hope for the hungry world. Asian J Agric Bio 1:91-94.

Rolf FJ, NTSYSpc. 1998. Numerical Taxonomy and Multivariate Analysis System, version 2.02c, Exeter Software, New York.

Roy JK, Lakshmikumaran MS, Balyan HS, Gupta PK. 2004. AFLP-based genetic diversity and its comparison with diversity based on SSR, SAMPL, and phenotypic traits in bread wheat. Biochem Genet 42: 43–59.

Patra AP, Mukherjee AK, Acharya L. 2011. Comparative study of RAPD and ISSR markers to assess the genetic diversity of Betel Vine (Piper betle L.) in Orissa, India. Am J Biochem Mol Biol 1: 200-211.

Sarabi B, Hassandokht MR, Hassani ME, Masoumi TR, Rich T. 2010. Evaluation of genetic diversity among some Iranian wild asparagus populations using morphologicalncharacteristics and RAPD markers. Sci Hortic 126(1): 1-7.

Shirmohammadi S, Sabouri H, Ahangar L, Ebadi AA, Sajadi J. 2018. Genetic diversity and association analysis of rice genotypes for grain physical quality using iPBS, IRAP, and ISSR markers. J Genet Resour 4(2): 122-129.

Sivaprakash KR, Prasanth SR, Mohanty BP, Parida A. 2004. Genetic diversity of black gram landraces as evaluated by AFLP markers. Curr Sci 86(10): 1411-1415.

Sofalian O, Chaparzadeh N, Javanmard A, Hejazi, MS. 2008. Study the genetic diversity of wheat landraces from northwest of Iran based on ISSR molecular markers. Int J Agri Biol 10: 465-468.

Tahir NA. 2008. Assesment of genetic diversity among wheat varieties in sulaimanyah using random amplified polymorphic DNA (RAPD) analysis. Jordan J Biol Sci 1(4):159-164.

Tanyolac B. 2003. Inter-simple sequence repeat (ISSR) and RAPD variation among wild barely (Hordeum vulgare subsp. spontaneum) populations from west Turkey. Genet Resour Crop Ev 50(6): 611-614.

Terzopoulos PJ, Bebeli PJ. 2008. Genetic diversity analysis of Mediterranean faba bean (Vicia faba L.) with ISSR markers. Field Crops Res 108: 39-44.

Varshney RK, Graner A, Sorrell AE. 2005. Genetic microsatellite markers in plants: features and applications. Trends Biotechnol 23: 48-55.

Welsh J. 1990. Mcclelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18: 7213-7218.

Yavari AR, Nazeri V, Sefidkon F, Zamani Z, Hassani ME. 2012. Evaluation of genetic diversity among and within some endemic populations of Thymus migricus Klokov & Desj.-Shost using RAPD molecular markers. Iranian J Med Arom Plants 28: 35-47.

Yu LX and Nguyen NT. 1994. Genetic variation detected with RAPD markers among upland and lowland rice cultivars (Oryza sativa L.). Theor Appl Genet 87(6): 668-672.

Zietkiewicz E, Rafalski A, Labuda D. 1994. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20: 176-183.