Evaluation of the genetic diversity of pomegranate accessions from Turkey using new microsatellite markers

Evaluation of the genetic diversity of pomegranate accessions from Turkey using new microsatellite markers

Turkey has many valuable genetic resources for pomegranate; however, there have not been many studies on the identificationand characterization of these important genetic resources. New microsatellite markers were used to characterize a set of 78 pomegranateaccessions from Turkey. Using six SSR primers, a total of 41 alleles were characterized with an average of 4.6 alleles per locus andmean probability of identity (PI) value of 0.366. These data indicated a high level of polymorphism in pomegranate germplasm. Fivesynonymous groups could be detected among 30 accessions. This microsatellite-based key is a first step towards a database for markerassisted identification of pomegranate accessions in Turkey. The present study provides essential information to devise a pomegranatecore germplasm collection without duplication of plant material, to sustainably manage pomegranate breeding programs, and toestablish conservation strategies for preserving local pomegranate genetic resources.

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  • Alamuti MK, Zeinalabedini M, Derazmahalleh MM, Shojaie TR, Irandoost HP, Zahravi M, Vazifehshenas M, Ebrahimi MA, Nekouei SMK, Salekdeh GH et al. (2012). Extensive genetic diversity in Iranian pomegranate (Punica granatum L.) germplasm revealed by microsatellite markers. Sci Hortic 146: 104-114.
  • Bashalkhanov S, Pandey M, Rajora OP (2009). A simple method for estimation genetic diversity in large populations from finite sample sizes. BMC Genetics 84: 1-10.
  • Bellini E, Giordani E (1998). Descriptor List for Pomegranate (Punica granatum L.). Project on “Minor Fruit Tree Species Conservation”: RESGEN29. Florence, Italy: Horticulture Department, University of Florence.
  • Ben-Simhon Z, Judeinstein S, Trainin T, Harel-Beja R, Bar-Ya’akov I, Borochov-Neori H, Holland H (2015). A “white” anthocyaninless pomegranate (Punica granatum L.) caused by an insertion in the coding region of the leucoanthocyanidin dioxygenase (LDOX; ANS) gene. PLoS One 10: e0142777.
  • Berinyuy JE, Fontem DA, Focho DA, Schippers RR (2002). Morphological diversity of Solanum scabrum accessions in Cameroon. Plant Genet Res News 131: 42-48.
  • Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, CavalliSforza LL (1994). High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455-457.
  • Boz Y, Bakir M, Çelikkol BP, Kazan K, Yilmaz F, Çakir B, Aslantaş S, Söylemezoğlu G, Yaşasin AS, Özer C et al. (2011). Genetic characterization of grape (Vitis vinifera L.) germplasm from Southeast Anatolia by SSR markers. Vitis 50: 99-106.
  • Caliskan O, Bayazit S (2012). Phytochemical and antioxidant attributes of autochthonous Turkish pomegranates. Sci Hortic 147: 81-88.
  • Caliskan O, Bayazit S (2013). Morpho-pomological and chemical diversity of pomegranate accessions grown in eastern Mediterranean region of Turkey. J Agr Sci Tech 15: 1449-1460.
  • Caliskan O, Polat AA, Celikkol P, Bakir M (2012). Molecular characterization of autochthonous Turkish fig accessions. Span J Agric Res 10: 130-140.
  • Currὸ S, Caruso M, Distefano G, Gentile A, La Malfa S (2010). New microsatellite loci for pomegranate, Punica granatum (Lythraceae). Am J Bot 97: 58-60.
  • Drogoudi PD, Tsipouridis C, Michailidis Z (2005). Physical and chemical characteristics of pomegranates. Hort Sci 40: 1200- 1203.
  • Ebrahimi S, Sayed-Tabatabaei BE, Sharifnabi B (2010) Microsatellite isolation and characterization in pomegranate (Punica granatum L.). Iran J Biotechnol 8: 156-163.
  • Ellegren H (2004). Microsatellites: simple sequences with complex evaluation. Nature Rev Genet 5: 435-445.
  • Ercisli S (2009). Apricot culture in Turkey. Sci Res Essays 4: 715-719.
  • Ercisli S, Gadze J, Agar G, Yildirim N, Hizarci Y (2011a). Genetic relationships among wild pomegranate (Punica granatum) genotypes from Coruh Valley in Turkey. Genet Mol Res 10: 459-464.
  • Ercisli S, Kafkas E, Orhan E, Kafkas S, Dogan Y, Esitken A (2011b). Genetic characterization of pomegranate (Punica granatum L.) genotypes by AFLP markers. Biol Res 44: 345-350.
  • Ergül A, Bakır M (2013). Development of genomic SSRs markers of pomegranate (Punica granatum L.). In: National Agriculture Symposium; 26–29 October; Antalya, Turkey (in Turkish).
  • Ergül A, Marasali B, Ağaoğlu YS (2002). Molecular discrimination and identification of some Turkish grape cultivars (Vitis vinifera L.) by RAPD markers. Vitis 41: 159-160.
  • Erturk Y, Ercisli S, Haznedar A, Cakmakci R (2010). Effects of plant growth promoting rhizobacteria (PGPR) on rooting and root growth of kiwifruit (Actinidia deliciosa) stem cuttings. Biol Res 43: 91-98.
  • Ferrara G, Cavoski I, Pacifico A, Tedone L, Mondelli D (2011). Morpho-pomological and chemical characterization of pomegranates (Punica granatum L.) genotypes in Apulia region, Southeastern Italy. Sci Hortic 130: 599-606.
  • Ferrara G, Gianaspro A, Mazzeo A, Giove SL, Stella Matarrese AM, Pacucci C, Punzi R, Trani A, Gambacorta G, Blanco A et al. (2014) Characterization of pomegranate (Punica granatum L.) genotypes collected in Puglia region, Southeastern Italy. Sci Hortic 178: 70-78.
  • Gil MI, Tomas-Barberan FA, Hess-Pierce B, Holcroft DM, Kader AA (2000). Antioxidant activity of pomegranate juice and its relationship with phenolic composition and processing. J Agric Food Chem 48: 4581-4589.
  • Hasnaoui N, Buonamici A, Sebastiani F, Mars M, Zhang D, Vendramin GG (2012). Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers (SSR). Gene 493: 105-112.
  • Hasnaoui N, Buonamici A, Sebastiani F, Mars Trifi M, Vendramin GG (2010). Development and characterization of SSR markers for pomegranate (Punica granatum L.) using an enriched library. Conservation Genet Resour 2: 283-285.
  • Hedrick PW (1999). Perspective: Highly variable loci and their interpretation in evolution and conservation. Evolution 53: 313-318.
  • Holland D, Hatib K, Bar-Ya’akov I (2009). Pomegranate: botany, horticulture, breeding. Hort Rev 35: 127-191.
  • Hricova A, Fejer J, Libiakova G, Szabova M, Gazo J, Gajdosova A (2016). Characterization of phenotypic and nutritional properties of valuable Amaranthus cruentus L. mutants. Turk J Agric For 40: 761-771.
  • Jbir R, Zehdi S, Hasnaoui N, Salhi-Hannachi A, Mars M (2012). Microsatellite polymorphism in Tunisian pomegranates (Punica granatum L.): cultivar genotyping and identification. Biochem System Ecol 44: 27-35.
  • Lefort F, Lally M, Thompson D, Douglas GC (1998). Morphological traits, microsatellite fingerprinting and genetic relatedness of a stand of elite oaks (Q. robur L.) at Tullynally, Ireland. Silvae Genet 47: 5-6.
  • Levin GM (2006). Pomegranate Roads: A Soviet Botanist’s Exile from Eden. 1st ed. Forestville, CA, USA: Floreant Press.
  • Mena P, Garcia-Viguera C, Navarro-Rico J, Moreno D, Bartual J, Saura D, Marti N (2011). Phytochemical characterization for industrial use of pomegranate (Punica granatum L.) cultivars grown in Spain. J Sci Food Agric 91: 1893-1906.
  • Minch E, Ruiz-Linares A, Goldstein DB, Feldman M, Cavalli-Sforza LL (1995). Microsat (Version 1.5d): A Computer Program for Calculating Various Statistics on Microsatellite Allele Data. Palo Alto, CA, USA: Stanford, CA, USA.
  • Moslemi M, Zahravi M, Khaniki GB (2010). Genetic diversity and population genetic structure of pomegranate (Punica granatum L.) in Iran using AFLP markers. Sci Hortic 126: 441-447.
  • Nafees M, Jaskani MJ, Ahmed S, Awan FS (2015). Morpho-molecular characterization and phylogenetic relationship in pomegranate germplasm of Pakistan. Pak J Agri Sci 52: 97-106.
  • Nemati Z, Tehranifar A, Farsi M, Mirshamsi Kakhki A, Nemati H, Khayat M (2012). Evaluation of genetic diversity of Iranian pomegranate cultivars using fruit morphological characteristics and AFLP markers. Not Bot Hortic Agrobo 40: 261-268.
  • Okatan V, Akca Y, Ercisli S, Gozlekci S (2015). Genotype selection for physico-chemical fruit traits in pomegranate (Punica granatum L.) in Turkey. Acta Scientiarum Polonorum Hortorum Cultus 14: 123-132.
  • Onur C (1982). Akdeniz Bölgesi narlarının seleksiyonu. PhD, Çukurova University, Adana, Turkey (in Turkish).
  • Ophir R, Sherman A, Rubinstein M, Eshed R, Schwager MS, HarelBeja R, Bar-Yáakov I, Holland D (2014). Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity. PLOS One 9: e88998.
  • Orhan E, Ercisli S, Esitken A, Sengul M (2014). Molecular and morphological characterization of pomegranate (Punica granatum L.) genotypes sampled from Coruh valley in Turkey. Genet Mol Res 13: 6375-6382.
  • Özgüven AI, Yılmaz M, Yılmaz C (2011). The fruit traits of some pomegranate cultivars in Adana ecological conditions. Acta Hortic 890: 197-200.
  • Paetkau D, Calvert W, Stirling I, Strobeck C (1995). Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol 4: 347-354.
  • Parvaresh M, Talebi M, Sayed-Tabatabaei BE (2012). Molecular diversity and genetic relationship of pomegranate (Punica granatum L.) genotypes using microsatellite markers. Sci Hortic 138: 244-252.
  • Pirseyedi SM, Valizadehghan S, Mardi M, Ghaffari MR, Mahmoodi M, Zahravi M, Zeinalabedini M, Nekoui SMK (2010). Isolation and characterization of novel microsatellite markers in pomegranate (Punica granatum L.). Int J Mol Sci 11: 2010-2016.
  • Poyrazoğlu E, Gökmen V, Artık N (2002). Organic acids and phenolic compounds in pomegranates (Punica granatum L.) grown in Turkey. J Food Comp Anal 15: 567-575.
  • Ranade SA, Rana TS, Narzary D (2009). SPAR profiles and genetic diversity amongst pomegranate (Punica granatum L.) genotypes. Physiol Mol Biol Plants 15: 61-70.
  • Rohlf FJ (1998). NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.0, User’s Guide. Setauket, NY, USA: Exeter Software.
  • Sánchez-Pérez R, Ruiz D, Dicenta F, Egea J, Martínez-Gómez P (2005). Application of simple sequence repeat (SSR) markers in apricot breeding: molecular characterization, protection, and genetic relationships. Sci Hortic 103: 305-315.
  • Sarıdaş MA, Kafkas NE, Zarifikhosroshahi M, Bozhaydar O, Paydaş Kargı S (2016). Quality traits of green plums (Prunus cerasifera Ehrh.) at different maturity stages. Turk J Agric For 40: 655- 663.
  • Sarkhosh A, Zamani Z, Fatahi R, Ebadi A (2006). RAPD markers reveal polymorphism among some Iranian pomegranate (Punica granatum L.) genotypes. Sci Hortic 111: 24-29.
  • Seeram NP, Henning SM, Zhang Y, Suchard M, Li Z, Heber D (2006). Pomegranate juice ellagitannin metabolites are present in human plasma and some persist in urine for up to 48 hours. J Nutr 136: 2481-5.
  • Sneath PHA, Sokal RR (1973). Numerical Taxonomy. San Francisco, CA, USA: Freeman.
  • Soleimani MH, Talebi M, Sayed-Tabatabaei BE (2012). Use of SRAP markers to assess genetic diversity and population structure of wild, cultivated, and ornamental pomegranates (Punica granatum L.) in different regions of Iran. Plant Syst Evol 298: 1141-1149.
  • Soriano JM, Zuriaga E, Rubio P, Llácer G, Infante R, Badenes M L (2011). Development and characterization of microsatellite markers in pomegranate (Punica granatum L.). Mol Breed 27: 119-128.
  • Varshney RK, Graner A, Sorrells ME (2005). Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23: 48-55.
  • Yamamoto T, Saito T, Kotobuki K, Matsuta N, Hayashi T, Kimura T, van de Weg WE, Liebhard R, Gessler C (2003). Genetic linkage maps of Japanese and European pears aligned to the apple consensus map. In: Eucarpia Symposium in Fruit Breeding and Genetics; 1–5 September 2003; Angers, France.
  • Yazıcı K, Şahin A (2016). Characterization of pomegranate (Punica granatum L.) hybrids and their potential use in further breeding. Turk J Agric For 40: 813-824.
  • Zaouay F, Mars M (2011). Diversity among Tunisian pomegranate (Punica granatum) cultivars as assessed by pomological and chemical traits. International Journal of Fruit Science 11: 151- 166.
  • Zhao LH (2011). Population genetics structure of pomegranate Punica granatum L. revealed by ISSR markers in China. Northern Hortic 10: 038.