Iranian Journal of Horticultural Science

Iranian Journal of Horticultural Science

Evaluation of genetic diversity in local cultivars and genotypes of grape (Vitis vinifera) using ISSR Markers

Document Type : Full Paper

Authors
Mitra Razi 1
Mohammad Amiri 2
Reza Darvishzadeh 3
Hamed Doulati Baneh 4
Pedro Martinez Gomez 5
1 Former Ph.D. Student, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
2 Professor, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
3 Professor, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran
4 Associate Professor, Department of Horticulture Research, Agricultural and Natural Resources Research and Education Center of West Azarbaijan, Organization for Research, Education and Extension of Agriculture, Urmia, Iran
5 Professor, Research Center of CEBAS, Spain
10.22059/ijhs.2018.253391.1411
Abstract
Grape (Vitis vinifera L.)  is an important fruit crop and widely cultivated because of its nutritional and economical values. For getting new cultivars with higher yield and better quality, it is essential to characterize the cultivars. Some wild species faced to genetic erosion, so determination of genetic diversity of grape cultivars and genotypes is an important task for improving breeding programs in the future. In this research genetic diversity among 75 cultivars and wild genotypes (Vitis vinifera L.) of grape with 17 ISSR primers was investigated. 132 bands were produced by 17 primer pairs, out of which 75 bands (57/58%) were polymorphic. The polymorphic bands ranged from 2 in locus UBC873 to 7 in locus UBC836. Effective number of allele (Ne), varied from 1.72 in locus UBC880 to 1.18 in UBC873. To identify the high informative retrotransposon primer combination, the amount of PIC were estimated for each primer which ranged from 0.14 for locus UBC873 to 0.42 for locus UBC880 with an average value of 0.32. Cluster analysis using Dice similarity coefficients and complete algorithm put the 75 studied genotypes in four different groups. The most genetic similarity (0.73) was observed between Jig Jiga and Black Seedless and also between Alphonse Lavallee and Black Seedless and the least genetic similarity (0.11) observed between Dastarchin and Lal Seyah. The maximum Nei genetic distance was belong to Foreign and Wild populations. The AMOVA result indicated that the within and among population diversity were 61% and 39% respectively.
Keywords
Cluster Analysis
genomic diversity
Molecular markers
Subjects
  1. Ammiraju, J. S. S., Dholakia, B. B., Santra, D. K., Singh, H., Lagu, M. D., Tamhankar, S. A., Dhaliwal, H. S., Rao, V. S. & Ranjekar, P. K. (2001). Identification of inter simple sequence repeat (ISSR) markers associated with seed size in wheat. Theoretical and Applied Genetics, 102(5), 726-732.
  2. Argade, N., Tamhankar, S., Karibasappa, G., Patil, S. & Rao, V. (2009). DNA profiling and assessment of genetic relationships among important seedless grape (Vitis vinifera) varieties in India, using ISSR markers. Journal of Plant Biochemistry and Biotechnology, 18(1), 45-51.
  3. Askari, N., Mohammad, A. M. & Baghizadeh, A. (2011). ISSR markers for assessing DNA polymorphism and genetic characterization of cattle, goat and sheep populations. Iranian Journal of Biotechnology, 9, 222-229.
  4. Bowers, J. E. & Meredith, C. P. (1996). Genetic similarities among wine grape cultivars revealed by restriction fragment-length polymorphism (RFLP) analysis. Journal of the American Society for Horticultural Science, 121(4), 620-624.
  5. Cervera, M. T., Cabezas, J., Sancha, J., De Toda, F. M. & Martinez-Zapater, J. (1998). Application of AFLPs to the characterization of grapevine Vitis vinifera L. genetic resources. A case study with accessions from Rioja (Spain). Theoretical and Applied Genetics, 97(1-2), 51-59.
  6. Choudhary, R., Zagade, V., Khalakar, G. & Singh, N. (2014). ISSR based genotypic differentiation of grape (Vitis vinifera L.). Bioscan-an International Quarterly Journal of Life Sciences, 9(2), 823.
  7. Dhanorkar, V., Tamhankar, S., Patil, S. & Rao, V. (2005). ISSR-PCR for assessment of genetic relationships among grape varieties cultivated in India. Vitis, 44(3), 127.
  8. Doulati Baneh, H.‚ Grassi, F.‚ Mohammadi, S. A.‚ Nazemieh, A.‚ De Mattia, F.‚ Imazio, S. & Labra, M. (2007a). The use of AFLP and morphological markers to study Iranian grapevine germplasm to avoid genetic erosion. Journal of Horticultural Science and Biotechnology, 82, 745-752.
  9. Doulati Baneh, H., Mohammadi, S. A., Labra, M., Nazemieh, A., De Mattia, F. & Mardi, M. (2007b). Chloroplast microsatellite markers to assess genetic diversity in wild and cultivated grapevines of Iran. Pakistan Journal of Biological Science, 10, 1855-1859.
  10. Doulati Baneh, H., Nazemia, A., Mohammadi, S., Hassani, G. & Hanareh, M. (2010). Identification and evaluation of west Azarbaijan grape cultivars by ampelography and ampelometery. Plant Production Technology, 10(1), 13-24. (in Farsi)
  11. Doulati-Baneh, H., Mohammadi, S. & Labra, M. (2013). Genetic structure and diversity analysis in Vitis vinifera L. cultivars from Iran using SSR markers. Scientia Horticulturae, 160, 29-3.
  12. Doyle, J. J. & Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19, 11-15.
  13. Ferguson, A., Taggart, J., Prodöhl, P., McMeel, O., Thompson, C., Stone, C., McGinnity, P. & Hynes, R. (1995). The application of molecular markers to the study and conservation of fish populations, with special reference to Salmo. Journal of Fish Biology, 47(sA), 103-126.
  14. Ghasemi, M., Baghizadeh, A. & Abadi, M. (2010). Determination of genetic polymorphism in Kerman Holstein and Jersey cattle population using ISSR markers. Australian Journal of Basic and Applied Sciences, 4(12), 5758-5760.
  15. Grando, M. S. & Frisinghelli, C. (1998). Grape microsatellite markers: Sizing of DNA alleles and genotype analysis of some grapevine cultivars. Vitis, 37(2), 79-82.
  16. Hassan, N. A., El-Homosany, A., Gomma, A. H. & Shaheen, M. (2011). Morphological and ISSR polymorphisms in some Egyptian grapes (Vitis vinefera L.) collection. World Applied Sciences Journal, 15(10), 1369-1375.
  17. Herrera, R., Cares, V., Wilkinson, M. & Caligari, P. (2002). Characterisation of genetic variation between Vitis vinifera cultivars from central Chile using RAPD and Inter Simple Sequence Repeat markers. Euphytica, 124(1), 139-145.
  18. Jing, Z. & Wang, X. (2013). Genetic relationship between Chinese wild Vitis species and American and European cultivars based on ISSR markers. Biochemical Systematics and Ecology, 46, 120-126.
  19. Karami, M. J. (1996). Identification of grapevines of Kurdistan state. M.Sc. thesis, Faculty of Agriculture Tabriz University, Iran. (in Farsi)
  20. Keshavarz Khoob, M., Gharanjik, S., Masoumiasl, A. & Abdollahi, M. B. (2016). Evaluation of diversity and genetic relationships among some grapevine cultivars using ISSR markers. Journal of Agricultural Biotechnology, 7 (4), 129-141. (in Farsi)
  21. Kocsis, M., Jaromi, L., Putnoky, P., Kozma, P. & Borhidi, A. (2005). Genetic diversity among twelve grape cultivars indigenous to the Carpathian Basin revealed by RAPD markers. Vitis,44(2), 87-91.
  22. Martinez, L., Cavagnaro, P., Masuelli, R. & Zuniga, M. (2006). SSR-based assessment of genetic diversity in South American Vitis vinifera varieties. Plant Science,170(6), 1036-1044.
  23. McGovern, P. E. (2003). Ancient Wine: the Search for the Origin of Viniculture. Princeton University Press, Princeton and Oxford, UK.
  24. Peakall, R. & Smouse, P. E. (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Resources,6(1), 288-295.
  25. Ratnaparkhe, M., Tekeoglu, M. & Muehlbauer, F. (1998). Inter-simple-sequence-repeat (ISSR) polymorphisms are useful for finding markers associated with disease resistance gene clusters. Theoretical and Applied Genetics, 97(4), 515-519.
  26. Reddy, M. P., Sarla, N. & Siddiq, E. (2002). Inter simple sequence repeat (ISSR) polymorphism and its application in plant breeding. Euphytica, 128(1), 9-17.
  27. Reif, J. C., Gumpert, F. M., Fischer, S. & Melchinger, A. E. (2007). Impact of interpopulation divergence on additive and dominance variance in hybrid populations. Genetics, 176, 1931-1934.
  28. Rohlf, F. (2000). NTSYS-PC numerical taxonomy and multivariate system, version 2.1 Applied Biostatistics Inc. New York.
  29. Sabeti, H. (1976). Forests, Trees and Shrubs of Iran. Agriculture and Natural Resources Research Organization Press, Tehran, Iran. (in Farsi)
  30. Shannon, C. (1948). A mathematical theory of communication. The Bell System Technical Journal, 27, 379-423.
  31. Sicard, D., Nanni, L., Porfiri, O., Bulfon, D. & Papa, R. (2005). Genetic diversity of Phaseolus vulgaris L. and P. coccineus L. landraces in central Italy. Plant Breeding, 124(5), 464-472.
  32. Solomon, K., Labuschagne, M. & Viljoen, C. (2007). Estimates of heterosis and association of genetic distance with heterosis in durum wheat under different moisture regimes. The Journal of Agricultural Science, 145(3), 239-248.
  33. Tamhankar, S., Argade, N., More, M., Dhanorkar, V., Patil, S., Rao, V., Karibasappa, G & Agrawal, D. (2008). DNA profiling of the grape varieties grown in India using ISSR markers. Acta Horticulturae.
  34. Tsumura, Y., Ohba, K. & Strauss, S. (1996). Diversity and inheritance of inter-simple sequence repeat polymorphisms in Douglas-fir (Pseudotsuga menziesii) and sugi (Cryptomeria japonica). Theoretical and Applied Genetics,92(1), 40-45.
  35. Wang, G., Mahalingam, R. & Knap, H. (1998). (CA) and (GA) anchored simple sequence repeats (ASSRs) generated polymorphism in soybean, Glycine max (L.) Merr. Theoretical and Applied Genetics, 96(8), 1086-1096.
  36. Williams, J. G., Kubelik, A. R., Livak, K. J., Rafalski, J. A. & Tingey, S. V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18(22), 6531-6535.
  37. Zahedi, B. (1996). Identification of grapevines of Lorestan state. M.Sc. Thesis, Faculty of Agriculture Tehran University, Iran. (in Farsi)
  38. Zamani, P., Akhondi, M., Mohammadabadi, M. R., Saki, A. A., Ershadi, A., Banabazi, M. H. & Abdolmohammadi, A. R. (2011). Genetic variation of Mehraban sheep using two intersimple sequence repeat (ISSR) markers. African Journal of Biotechnology, 10(10), 1812-1817.
  39. Zamani, P., Akhondi, M. & Mohammadabadi, M. (2015). Associations of Inter-Simple Sequence Repeat loci with predicted breeding values of body weight in sheep. Small Ruminant Research, 132, 123-127.
  40. Zietkiewicz, E., Rafalski, A. & Labuda, D. (1994). Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics, 20(2), 176-183.
Iranian Journal of Horticultural Science
Volume 50, Issue 1
Spring 2019
Pages 197-207

  • Receive Date 26 February 2018
  • Revise Date 10 April 2018
  • Accept Date 05 May 2018