Evaluation of Iranian pomegranate collection using simple sequence repeat and morphological traits


1 Department of Agricultural Science, Payame Noor University, Tehran, Iran.

2 Biotechnology Research and Development Center, Tarbiat Modares University,Tehran, Iran.

3 Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.

4 Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.


Pomegranate, Punica granatum L., is one of the oldest cultivated fruit species. This study used morphological data and a set of simple sequence repeat markers to investigategenetic diversity among 202 Iranian pomegranate accessions during the 2010 and 2011 growing seasons at Saveh Research Station, Saveh, Iran. Principal component analysis showed that leaf traits were predominant in the first and second component during both years, indicating that these traits are not only useful in assessing genetic diversity, but also for characterizing pomegranate germplasm. There was high correlation between the length of style and flower shape, implying that these traits are directly associated with tree performance. There was also close correlation between leaf length with leaf width, and total leaf length as well as and flower traits such as flower diameter and width. Twenty-three alleles (ranging from two to nine per locus) were detected using seven SSR markers with ABRII-MO26 showing the highest level of polymorphism. The average expected heterozygosity and mean PIC values were 0.36 and 0.34, respectively.Cluster analysis showed a simple matching coefficient ranging from 0.24 to 1 indicating high genetic diversity. Punica microsatellite markers and morphological characters revealed a relatively high genetic diversity among 202 pomegranate accessions. This great variation in the pomegranate collection of Saveh Research Station ensures the future of pomegranate breeding programs in Iran. Strategic research on the base collection and characterization of accessions provides useful information to breeding programs and will enhance the development of core collections.


Anarinco. 2006. Pomegranate history. Available at: www.anarainco.com/history.htm. (accessed on 1 September 2015).

Awamleh, H., D. Hassawi, H. Migdadi, and M. Brake.2009. Molecular characterization of pomegranate (Punica granatum L.) landraces grown in Jordan using amplified fragment length polymorphism markers. Biotechnol. 83: 316- 322.

Brown, A. H. D. 1989. Core collections: a practical approach to genetic resources management. Genome. 31(2): 818-824.

Chao, S., W. Zhang, J. Dubcovsky, and M. Sorrells. 2007. Evaluation of genetic diversity and genome-wide linkage disequilibrium among U. S. wheat (Triticum aestivum L.) germplasm representing different market classes. Crop Sci. 47: 1018–1030.

Chaudhari, S. M., and U. T.  Desai. 1993. Effects of plant growth regulators on flower sex in pomegranate (Punica granatume L.). Ind. J. Agric. Sci. 63(1): 34- 35.

Curro S., M. Carusa, G. Distefano, A. Gentile, S. Lamalfa. 2010. New microsatellite loci for pomegranate, Punica granatum (Lytraceae). Am. J. Bot. 97: 58- 60.

Devos, K. M. G., J. Bryan, A. J. Collins, P. Stephenson, and M. D. Gale. 1995. Application of two microsatellite sequences in wheat storage proteins as molecular markers. Theor. Appl. Genet. 90: 247–252.

Dicenta F., and J. E. Garcia. 1992. Phenotypical correlations among some traits in almond. J. Genet. Breed. 46: 241–246.

Durgac, C., M. Ozgan, O. Simsek, Y. A. Kacar, Y.  Kiyaga, S. Celebil, K. Gunduzl, and S, Serce. 2008. Molecular and pomological diversity among pomegranate (Punica granatum L.) cultivars in Eastern Mediterraneran region of Turkey. Afr. J. Biotechnol. 7: 1294- 1301.

Ebrahimi, S., B. E. Tabatabaei, and B. Sharifnabi. 2010. Microsatellite isolation and characterization in pomegranate (Punica granatum L.). Iranian J. Biotechnol. 8: 156-163.

El Sese, A. M. 1988. Physiological studies on flowering and fruiting habits of some pomegranate cultivars under assiut conditions. Assuit J. Agric. Sci. 19(4): 320- 336.

Ercisli, S., G. Agar, E. Orhan, A. Yildirim, and Y. Hizarci. 2007. Interspecific variability of RAPD and fatty acid composition of some pomegranate cultivars (Punica granatum L.) growing in Sothern Anatolia Region in Turkey. Biochem. Syst. Ecol. 35: 764- 769.

Excoffier, L., P. E. Smouse, and J. M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genet. 131: 479-491.

Hamrick, J. L., and M. J. Godt. 1990. Allozyme diversity in plant species. Pp. 43-63. In Brown A. H. D., M. T. Clegg, A. L. Kahle, S. WeiB (eds.). Plant population genetics, breeding, and genetic resources. Sunderland, MA.

Huff, D. R. 1997. RAPD characterization of heterogeneous perennial ryegrass cultivars. Crop Sci. 37: 557-564.

Jalikop, S. H., and P. Sampath Kumar. 1990. Use of a gene marker to study the mode of pollination in pomegranate (Punica granatum L.). J. Hort. Sci 65(2): 221- 223.

Jubrael, J. M. S., S. M. Udupa, and M. Baum. 2005. Assessment of AFLP- based genetic relationship among date palm (Phoenix dactylifera L.) varieties of Iraq. Am. Soc. Hort. 130: 442- 447.

Khadivi-Khub, A., Z. Zamani, and N. Bouzari. 2008. Evaluation of genetic diversity in some Iranian and foreign sweet cherry cultivars by using RAPD molecular markers and morphological traits. Hort. Environ. Biotechnol. 49: 188–196.

Kim. S. C., C. Lee Santoa, and A. Guerra. 2005. Genetic analysis and conservation of the endangered Canary Island woody sow-thistle, Sonchus gandogeri (Astoraceae). J. Plant Res. 118: 147- 153.

Kolliker. R., F. J. Stadelmann, B. Reidy, and J. Nosberger. 1998. Fertilization and defoliation frequency affect genetic diversity of Festuca pratensis Huds. in permanent grasslands. Mol. Ecol. 7: 1557-1567.

Liu, K., and S. V. Muse. 2005. Power Marker: An integrated analysis environment for genetic marker analysis. Bioinfo. 21: 2128–2129.

MAGRAMA. 2014. Available at http://www.magrama.es/ (accessed on 3 December 2015).

Manly, B. F. J. 1985. The Statistics of Natural Selection. Chapman & Hall, London. 484 pp.

Melgarejo, P., R. Martinez-Valero, J. M. Guillamon, M. Miro, and A. Amoros. 1997. Phenological stages of the pomegranate tree (Punica granatum L.). Ann. Appl. Biol. 130: 135-140.

Melgarejo, P., J. J. Martínez, F. Hernández, R. Martínez, P. Legua, R. Oncina, and A. Martinez-Murcia. 2009. Cultivar identification using 18S–28S rDNA intergenic spacer-RFLP in pomegranate (Punica granatum L.). Sci. Hort. 120(4): 500-503.

Noormohammadi, Z., F. Parvini, and M. Sheidai. 2010. Further study of morphological and molecular diversity in 18 pomegranate landraces of Iran. Gene Conserve. 38: 189-200.

Pirseyedi, S. M., S. Valizadehgan, M. Mardi, M. R. Ghaffari, P. Mahmoodi, M. Zahravi, M. Zeinalabedini, and S. M. Khayam-Nekoui. 2010. Isolation and characterization of novel microsatellite markers in pomegranate (Punica geranatum L.). Int. J. Mol. Sci. 11: 2010-2016.

Prasad, M., R. K. Varshney, J. K. Roy, H. S. Balyan, and P. K. Gupta. 2000. The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theor. Appl. Genet. 100: 584–592.

Rohlf, F. J. 2002. NTSYS- pc: numerical taxonomy and multivariate analysis system, version 1.60. Exeter Software, New York, USA.

Roldán-Ruiz, I., F. A. van Eeuwijk, T. J. Gilliand, P. Dubrcuit, C. Diumman, J. Lallemand, M. De Lose, and C. P. Baril. 2001. A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties. Theor. Appl. Genet. 103: 1138- 1150.

Salem, K. F. M., A. M. El-Zanaty, and R. M. Esmail. 2008. Assessing wheat (Triticum aestivum L.) genetic diversity using morphological characters and microsatallite markers. World J. Agric. Sci. 4(5): 538-544.

Sarkhosh, A., Z. Zamani, R. Fatahi, A. Ebadi. 2006. RAPD markers reveal polymorphism among some Iranian pomegranate (Punica granatum L.) landraces. Sci. Hort. 11: 24-29.

Schloetterer, C., B. Amos, and D. Tautz. 1991. Conservation of polymorphic simple sequence loci microsatellite DNA polymorphism divergence in in cetacean species. Nature (London). 354: 63-65.

Semagn, K. 2002. Genetic relationships among ten endod types as revealed by a combination of morphological, RAPD and AFLP markers. Hereditas. 137: 149-146.

Soriano, J. M., E. Zuriago, P. Rubio, G. Llacer, R. Infante, and M. Badens. 2011. Development and characterization of microsatellite markers in pomegranate (Punica granatum L.). Mol. Breed. 27: 119- 128.

Sorkheh. K., B. Shiran, T. M. Gradzeil, P. Epperson, P. Martinez-Gomez, and E. Asadi. 2007. Amplified fragment length polymorphism as a tool for molecular characterization of almond germplasm: genetic diversity among genotypes and related species of almond, and its relationships with agronomic traits. Euphytica. 156: 327-344.

Spagnoletti-Zeuli, P. L., and C. O. Qualset. 1993. Evaluation of five strategies for obtaining a core subset from a large genetic resources collection of durum wheat. Theor. Appl. Genet. 87: 295- 304.

Stover. E., and E. W. Mercure. 2007. The pomegranate: Anew look at the fruit of paradise. Hort Sci. 42: 1088- 1092.


Ubi, G. N., W. J. Kenworthy, J. M. Costa, P. B. Cregan, and J. Alvernaz. 2003. Genetic diversity of soybean cultivars from China, Japan, North America, and North American ancestral lines determined by amplified fragment length polymorphism. Crop Sci. 43: 1858-1867.

Van Hintum, T. J. L., A. H. D. Brown, C. Spillane, and T.  Hodgkin. 2000. Core collection of plant genetic resources. International Plant Genetic Resources Institute (IPGRI), Rome. 51 pp.

Wright, S. 1951. The genetical structure of populations. Ann. Eugen. 15: 323-354.

Yeh, F. C., R. C. Yang, T. B. J. Boyel, Z. H. Ye, and J. X. Mao.1997. POPGENE, the user friendly shareware for population genetic analysis. Molecular Biology and Biotechnology Center, University of Alberta, Edmonton, Canada.

Youn, Z., Y. Yin, L. Zhu, andY. Li. 2007. Population genetic diversity in chines pomegranate (Punica granatum L.) Cultivars revealed by fluorescent- AFLP marker. Genet. Genomics 34: 1061- 1071.

Zabeau Vos, P. 1993. Selective restriction fragment amplification: a general method for DNA fingerprinting. European Patent Application, Publicationi 0534858-A1, Office europeen des brevets, Paris.

Zamani, Z., A. Sarkhosh, R. Fatahi, and A. Ebadi. 2007. Genetic relationships among pomegranate genotypes studied by fruit characteristics and RAPD markers. J. Hort. Sci. Biotechnol. 82:11- 18.

Zhang, D., E. Germain, and S. Reynders-Aloisi. 2003. Development of amplified fragment polymorphism markers for variety identification in rose. Acta Hort. 508: 115-120.