Skip to main content
SpringerLink
Log in

Genetic characterization of Iranian grapes (Vitis vinifera L.) and their relationships with Italian ecotypes

  • Published:
Agroforestry Systems Aims and scope Submit manuscript

Abstract

Grapevine (Vitis vinifera L.) is one of the oldest and most important fruit crops in the world. Iran is considered as one of the regions where grapevine plants have been used and taken into cultivation. In the present study, 12 simple sequence repeat (SSR) markers were used to evaluate the genetic diversity among Iranian grape cultivars and their relationships with Italian ones. The observed number of alleles (N) per locus varied from 6 to 20 and also the number of effective alleles (Ne) ranged from 1.34 to 2.00 among cultivars, indicating that the SSRs were highly informative. The polymorphism information content (PIC) values ranged from 0.49 to 0.87 and classified the six loci as highly informative markers (PIC > 0.70). The mean observed heterozygosity (Ho) was higher (0.85) than the mean expected heterozygosity (He) (0.43), demonstrating a random union of gametes in the population. Genetic similarity among cultivars ranged from 0.14 to 0.93, indicating high genetic variation among them. UPGMA and Bayesian clustering analyses revealed high genetic variation among studied cultivars and grouped them into two main clusters. The present findings might render striking information in breeding management strategies for genetic conservation and cultivar improvement.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Adam-Blondon AF, Roux C, Claux D, Butterlin G, Merdinoglu D, This P (2004) Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics. Theor Appl Genet 109:1017–1027

    Article  CAS  PubMed  Google Scholar 

  • Agar G, Yildirim N, Ercisli S, Ergul l, Yuksel C (2012) Determination of genetic diversity of Vitis vinifera cv. Kabarcik populations from the Coruh Valley using SSR markers. Biochem Genet 50:476–483

    Article  CAS  PubMed  Google Scholar 

  • Arnold C, Gillet F, Cobat JM (1998) Situation de la vigne sauvage (Vitis vinifera subsp. sylvestris) en Europe. Vitis 37:159–170

    Google Scholar 

  • Bandelj D, Jaksˇe J, Javornik B (2004) Assessment of genetic variability of olive varieties by microsatellite and AFLP markers. Euphytica 136:93–102

    Article  CAS  Google Scholar 

  • Beridze T, Pipia I, Beck J, Hsu SC, Gamkrelidze M, Gognashvili M, Tabidze V, This P, Bacilieri R, Gotsiridze V, Glonti M, Schaal B (2011) Plastid DNA sequence diversity in a worldwide set of grapevine cultivars (Vitis vinifera L. subsp. sativa). Bull Georgian Natl Acad Sci 5:98–103

    CAS  Google Scholar 

  • Bikash D, Ranvir S, Kumar S (2008) Fruit based agro-forestry system for uplands. Horticulture and AgroForestry Research Programme. ICAR Research Complex for Eastern Region Ranchi, Jharkhand, India, pp 341–345

  • Borrego J, Rodriguez I, Andres MT, Martin J, Chavez J, Cabello F, Ibanez J (2001) Characterization of the most important Spanish grape varieties through isoenzyme and microsatellite analysis. Proc Int Symp Mol Markers Acta Hortic 546:371–375

    CAS  Google Scholar 

  • Boz Y, Bakir M, Celikkol BP (2011) Genetic characterization of grape (Vitis vinifera L.) germplasm from Southeast Anatolia by SSR markers. Vitis. 50(3):99–106

    Google Scholar 

  • Buteler MI, Jarret RL, LaBonte DR (1999) Sequence characterization of microsatellites in diploid and polyploid Ipomea. Theor Appl Genet 99:123–132

    Article  CAS  Google Scholar 

  • Commbe BG (1992) Research on development and ripening of the grape berry. Am J Enol Viticult 43:101–110

    Google Scholar 

  • Crespan M (2003) The parentage of Muscat of Hamburg. Vitis 42:193–197

    CAS  Google Scholar 

  • Crespan M, Milani N (2001) The muscats: a molecular analysis of synonyms, homonyms and genetic relationships within a large family of grapevine cultivars. Vitis 40:23–30

    CAS  Google Scholar 

  • Dalbo MA, Ye GN, Weeden NF, Steinkellner H, Sefc KM, Reisch BI (2000) A gene controlling sex in grapevine placed on a molecular marker based genetic map. Genome 43:333–340

    Article  CAS  PubMed  Google Scholar 

  • Doliguez A, Bouquet A, Danglot Y, Lahogue F, Riaz S, Meredith CP, Edwards KJ, This P (2002) Genetic mapping of grapevine (Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight. Theor Appl Genet 105:780–795

    Article  CAS  Google Scholar 

  • Doulati-Baneh H, Mohammadi SA, Labra M (2013) Genetic structure and diversity analysis in Vitis vinifera L. cultivars from Iran using SSR markers. Sci Hortic 160:29–36

    Article  CAS  Google Scholar 

  • Dzhambazova T, Tsvetkov I, Atanassov I (2009) Genetic diversity in native Bulgarian grapevine germplasm (Vitis vinifera L.) based on nuclear and chloroplast microsatellite polymorphisms. Vitis. 48(3):115–121

    CAS  Google Scholar 

  • Ekhvaia J, Gurushidze M, Blattner FR, Akhalkatsi M (2014) Genetic diversity of Vitis vinifera in Georgia: relationships between local cultivars and wild grapevine, V. vinifera L. subsp. sylvestris. Genet Resour Crop Evol 61:1507–1521

    Article  Google Scholar 

  • Ergul A, Kazan K, Aras S, Cevik V, Celik H, Soylemezoglu G (2006) AFLP analysis of genetic variation within the two economically important Anatolian grapevine (Vitis vinifera L.) varietal groups. Genome 49:467–495

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Eyduran SP, Ercisli S, Akin M, Eyduran E (2016) Genetic characterization of autochthonous grapevine cultivars from Eastern Turkey by simple sequence repeats (SSRs). Biotechnol Biotechnol Equip 30:26–31

    Article  CAS  Google Scholar 

  • Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7:574–578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Frank T, Botta R, Thomas MR (2002) Chimerism in grapevine: implications for cultivar identity, ancestry and genetic improvement. Theor Appl Genet 204:192–199

    Article  Google Scholar 

  • Gago P, Santiago JL, Boso S, Alonso-Villaverde V, Grando S, Martinez C (2009) Biodiversity and characterization of twenty-two Vitis vinifera L. cultivars in the Northwestern Iberian Peninsula. Am J Enol Viticult 60:293–301

    CAS  Google Scholar 

  • GENRES-081 (2001) Primary and secondary descriptors list for grapevine cultivars and species (Vitis L.) Institut für Rebenzüchtung Geilweilerhof, Siebeldingen. http://www.genres.de/vitis/

  • Gheorghe RN, Popescu CF, Pamfil D (2010) Genetic diversity of some Romanian grapevine cultivars as revealed by microsatellite markers. Rom Biotechnol Lett 15(2):26–31

    CAS  Google Scholar 

  • Gismondi A, Canini A (2013) Microsatellite analysis of Latial Olea europaea L. cultivars. Plant Biosyst 147(3):686–691

    Article  Google Scholar 

  • Gismondi A, Fanali F, Martìnez-Labarga JM, Grilli Caiola M, Canini A (2013) Crocus sativus L. genomics and different DNA barcode applications. Plant Syst Evol 299(10):1859–1863

    Article  CAS  Google Scholar 

  • Gismondi A, Impei S, Di Marco G, Crespan M, Leonardi D, Canini A (2014) Detection of new genetic profiles and allelic variants in improperly classified grapevine accessions. Genome 57:111–118

    Article  CAS  PubMed  Google Scholar 

  • Godarzian P, Erfanifard SY, Sadeghi H (2013) Detection and classification of available agroforestry systems in Fars province (case study: Kazerun city). Sus Agric Prod Sci 23:56–70

    Google Scholar 

  • Goudarzian P, Yazdani MR (2015) Climate diversity in line with agroforestry systems: studying technicalities of agroforestry systems and allied components in two diverse climatic regions (Warm climate vs. cold climate) (Case study: Kazeroun and Sepidan in Fars Province, I.R.Iran). Desert 20:157–166

    Google Scholar 

  • Grassi F, Labra M, Imazio S, Ocete R, Failla O, Scienza A, Sala F (2006) Phylogeographical structure and conservation genetics of wild grapevine. Conserv Genet 7:837–845

    Article  Google Scholar 

  • Haidari M, Lotfalian M, Tashakori M, Valipour A (2016) Investigating the local utilization of forest in north Zagros (Case study: Baneh Region) Iranian Journal of. Forest 8:313–331

    Google Scholar 

  • Hocquigny S, Pelsy F, Dumas V, Kindt S, Heloir MC, Merdinoglu D (2004) Diversification within grapevine cultivars goes through chimeric states. Genome 47:579–589

    Article  CAS  PubMed  Google Scholar 

  • Huglin P (1988) Biologie et e`cologie de la vigne, 2nd edn. Tec and Doc, Bordeaux

    Google Scholar 

  • Hvarleva T, Rusanov K, Lefort F et al (2004) Genotyping of Bulgarian Vitis vinifera L. cultivars by microsatellite analysis. Vitis. 43:27–34

    CAS  Google Scholar 

  • Ibanez J, Andres MT, Molino A, Borrego J (2003) Genetic study of key Spanish grapevine varieties using microsatellite analysis. Am J Enol Viticult 54(1):22–30

    CAS  Google Scholar 

  • Imazio S, Maghradze D, De Lorenzis G, Bacilieri R, Laucou V, This P, Scienza A, Kaill O (2013) From the cradle of grapevine domestication: molecular overview and description of Georgian grapevine (Vitis vinifera L.) germplasm. Tree Genet Genomes 9:641–658

    Article  Google Scholar 

  • Khadivi-Khub A, Salimpour A, Rasouli M (2014) Analysis of grape germplasm from Iran based on fruit characteristics. Braz J Bot 37:105–113

    Article  Google Scholar 

  • Lefort F, Roubelakis-Angelakis KA (2001) Genetic comparison of Greek cultivars of Vitis vinifera L. by nuclear microsatellite profiling. Am J Ecol Vitic 52(2):101–108

    Google Scholar 

  • Lopes MS, Sefc KM, Dias EE, Steinkellner H, Machado MLD, Machado AD (1999) The use of microsatellites for germplasm management in a Portuguese grapevine collection. Theor Appl Genet 99(3–4):733–739

    Article  CAS  PubMed  Google Scholar 

  • Lopes MS, Mendonca D, Rodrigues dos Santos M, Eiras-Dias JE, da Camara Machado A (2009) New insights on the genetic basis of Portuguese grapevine and on grapevine domestication. Genome 52:790–800

    Article  CAS  PubMed  Google Scholar 

  • Mantel N (1967) The detection of disease clustering and generalized regression approach. Cancer Res 27:209–220

    CAS  Google Scholar 

  • Martin JP, Borrego J, Cabello F, Ortiz JM (2003) Characterization of Spanish grapevine cultivar diversity using sequence-tagged microsatellite site markers. Genome 46:10–18

    Article  CAS  PubMed  Google Scholar 

  • Martin JP, Santiago PC, Leel F, Martinez MC, Ortiz JM (2006) Determination of relationships among autochthonous grapevine varieties (Vitis vinifera L.) in the Northwest of the Iberian Peninsula by using microsatellite markers. Genet Resour Crop Evol 53:1255–1261

    Article  CAS  Google Scholar 

  • Matinkhah SH, Shamekhi T, Khajedin G, Jafari M, Jalalian A (2003) Developing a method for diagnosis and characterization of traditional agroforestry systems in Iran (Case Study: Kohkiloieh and Boyerahmad Province). Iran J Natural Res 56:213–229

    Google Scholar 

  • McGovern PE (2003) Ancient wine. Princeton University Press, Princeton

    Google Scholar 

  • Mcgovern PE, Glusker DL, Exner LJ, Voigt MM (1996) Neolithic resinated wine. Nature 381:480–481

    Article  CAS  Google Scholar 

  • Moreno-Sanz P, Dolores Loureiro M, Suárez B (2011) Microsatellite characterization of grapevine (Vitis vinifera L.) genetic diversity in Asturias (Northern Spain). Sci Hortic 129:433–440

    Article  CAS  Google Scholar 

  • Nunez Y, Fresno J, Torres V, Ponz F, Gallego FJ (2004) Practical use of microsatellite markers to manage Vitis vinifera germplasm: molecular identification of grapevine samples collected blindly in D.O. ‘‘El Bierzo’’ (Spain). J Hortic Sci Biotech 79(3):437–440

    Article  CAS  Google Scholar 

  • Olmo HP (1976) Grapes. In: Simmonds NW (ed) Evolution of crop plants. Longman, London, pp 294–298

    Google Scholar 

  • PapannA N, Rao V, Murthy S, Simon L (2009) Microsatellite-based genetic diversity assessment in grape (Vitis vinifera L.) germplasm and its relationship with agronomic traits. Int J Fruit Sci 9:92–105

    Article  Google Scholar 

  • Pavlicek A, Hrda S, Flegr J (1999) FreeTree—freeware program for construction of phylogenetic trees on the basis of distance data and bootstrap/jackknife analysis of the tree robustness. Folia Biol 45:97–99

    CAS  Google Scholar 

  • Peakall R, Smouse PE (2006) genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6(1):288–295

    Article  Google Scholar 

  • Pipia I, Gogniashvili M, Tabidze V, Beridze T, Gamkrelidze M, Gotsiridze V, Melyan G, Musayev M, Salimov V, Beck J, Schaal B (2012) Plastid DNA sequence diversity in wild grapevine samples (Vitis vinifera subsp. sylvestris) from the Caucasus region. Vitis 51:119–124

    CAS  Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Riaz S, Garrison KE, Dangl GS, Boursiquot JM, Meredith CP (2002) Genetic divergence and chimerism within ancient asexually propagated winegrape cultivars. J Am Soc Hort Sci 127:508–514

    Article  CAS  Google Scholar 

  • Riaz S, Dangl GS, Edwards KJ, Meredith CP (2004) A microsatellite marker based framework map of Vitis vinifera L. Theor Appl Genet 108:864–872

    Article  CAS  PubMed  Google Scholar 

  • Rohlf FJ (2000) NTSYS-pc numerical taxonomy and multivariate analysis system. Version 2.1. Exeter Software, Setauket

  • Romesburg HC (1990) Cluster analysis for researchers. Krieger Publishing, Malabar

    Google Scholar 

  • Santana JC, Hidalgo E, De Lucas AU, Recio P, Ortiz JM, Martin JP, Yuste J, Arranz C, Rubio JA (2008) Identification and relationships of accessions grown in the grapevine (Vitis vinifera L.) Germplasm Bank of Castilla y Leon (Spain) and the varieties authorized in the VQPRD areas of the region by SSR-marker analysis. Genet Resour Crop Evol 55:573–583

    Article  Google Scholar 

  • Sefc KM, Lefort F, Gando MS, Scott KD, Steinkeller H, Thomas MR (2001) Microsatellite markers for grapevine: a state of the art. In: Roubelakis-Angelakis KA (ed) Molecular biology and biotechnology of the grapevine. Kluwer Academic Publishers, Amsterdam, pp 433–463

    Chapter  Google Scholar 

  • Sefc KM, Steinkellner H, Lefort F, Botta R, Da Camara Machado A, Borrego J, Maletic E, Glo¨ssl H (2003) Evaluation of the genetic contribution of local wild vines to European grapevine cultivars. Am J Enol Viticul 54:15–21

    Google Scholar 

  • Selli F, Bakir M, Inan G, Aygun H, Boz Y, Yasasin AS, Ozer C, Akman B, Soylemezoglu G, Kazan K, Ergul A (2007) Simple sequence repeat-based assessment of genetic diversity in ‘Dimrit’ and ‘Germe’ grapevine accessions from Turkey. Vitis 46:182–187

    CAS  Google Scholar 

  • Shahabian M, Mostashari M, Malakouti MJ (2001) Effect of different methods of fertilisation on grape yield in Qazvin. In: Horst WJ (ed) Plant Nutrition. Developments in Plant and Soil Sciences, vol 92. Springer, Dordrecht, pp 790–791

    Google Scholar 

  • Snoussi H, Harbi Ben Slimane M, Ruiz-Garcia L, Zapataer JM, Arroyo-Garcia R (2004) Genetic relationships among cultivated and wild grapevine accessions from Tunisia. Genome 47:1211–1219

    Article  CAS  PubMed  Google Scholar 

  • Stajner N, Korosec-Koruza Rusjan D (2008) Microsatellite genotyping of old Slovenian grapevine varieties (Vitis vinifera L.) of the Primorje (coastal) winegrowing region. Vitis 47(4):201–204

    Google Scholar 

  • Stajner N, Rusjan D, Korosec-Koruza Z (2011) Genetic characterization of old Slovenian grapevine varieties of Vitis vinifera L. by microsatellite genotyping. Am J Enol Vitic 62(2):250–255

    Article  Google Scholar 

  • Stajner N, Tomic L, Ivanisevic D (2014) Microsatellite inferred genetic diversity and structure of Western Balkan grapevines (Vitis vinifera L.). Tree Genet Genomes 10:127–140

    Article  Google Scholar 

  • Tangolar SG, Soydam S, Bakir M, Karaagac E, Tangolar S, Ergul A (2009) Genetic analysis of grapevine cultivars from the eastern Mediterranean region of Turkey, based on SSR markers. Tarim Bilim Derg 15(1):1–8

    Article  Google Scholar 

  • This P, Jung A, Boccacci P, Borrego J, Botta R, Costantini L, Maul E (2004) Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theor Appl Genet 109(7):1448–1458

    Article  CAS  PubMed  Google Scholar 

  • This P, Lacombe T, Tomas M (2006) Historical origins and genetic diversity of wine grapes. Trends Genet 22:511–519

    Article  CAS  PubMed  Google Scholar 

  • Tomic L, Stajner N, Jovanovic-Cvetkovic T (2012) Identity and genetic relatedness of Bosnia and Herzegovina grapevine germplasm. Sci Hortic 143:122–126

    Article  CAS  Google Scholar 

  • Vafaee Y, Ghaderi N, Khadivi A (2017) Morphological variation and marker-fruit trait associations in a collection of grape (Vitis vinifera L.). Sci Hortic 225:771–782

    Article  Google Scholar 

  • Vavilov NI (1931) Dikie rodichi plodovikh dereviev Aziatskoi chasti SSSR I Kvakaza I problema proiskhozhdenia plodovikh dereveiev (Wild progenitors of the fruit trees of Turkestan and the Caucasus and the problem of the origin of the fruit trees). Bull App Bot Genet Plant Breed 26:85–134 (in Russian)

    Google Scholar 

  • Vignani R, Scali M, Masi E, Cresti M (2002) Genomic variability in Vitis vinifera L. ‘Sangiovese’ assessed by microsatellite and non-radioactive AFLP test. Electron J Biotech 5:1–11

    Article  Google Scholar 

  • White E, Sahota R, Edes S (2002) Rapid microsatellite analysis using discontinuous polyacrylamide gel electrophoresis. Genome 45:1107–1109

    Article  CAS  PubMed  Google Scholar 

  • Zecca G, Grassi F (2013) RPB2 gene reveals phylodemographic signal in wild and domesticated grapevine (Vitis vinifera). J Syst Evol 51:205–211

    Article  Google Scholar 

  • Zohary D, Hopf M (2000) Domestication of plants in the Old World. University Press, Oxford

    Google Scholar 

  • Zulini L, Russo M, Peterlunger E (2002) Genotyping wine and table grape cultivars from Apulia (Southern Italy) using microsatellite markers. Vitis 41:183–187

    CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to thank Arak University in Iran and University of Rome ‘‘Tor Vergata’’ in Italy for funding this research work.

Author information

Authors and Affiliations

  1. Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, 38156-8-8349, Iran

    Ali Khadivi

  2. Department of Biology, University of Rome ‘‘Tor Vergata’’, Via della Ricerca Scientifica 1, Rome, 00133, Italy

    Angelo Gismondi & Antonella Canini

Authors
  1. Ali Khadivi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Angelo Gismondi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Antonella Canini
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ali Khadivi.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Khadivi, A., Gismondi, A. & Canini, A. Genetic characterization of Iranian grapes (Vitis vinifera L.) and their relationships with Italian ecotypes. Agroforest Syst 93, 435–447 (2019). https://doi.org/10.1007/s10457-017-0134-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10457-017-0134-1

Keywords

Search

Navigation