Genetic diversity analysis of Valencia and Navel group sweet orange cultivars by SSR markers

Year 2015, Volume: 32 Issue: 1, 47 - 62, 16.01.2015

İlknur Polat

https://doi.org/10.16882/derim.2015.93793

Cited By: 3

Abstract

Sweet orange [Citrus sinensis (L.) Osbeck] fruit is one of the main citrus fruits, Navel and Valencia group sweet orange being the most representative and recognizable species of this species. The aims of this study were to determine genetic relationships and diversity of 84 Navel and 36 Valencia groups of sweet orange using SSR (simple sequence repeat) molecular markers. Twenty-six SSR primers were tested on these accessions. Seven SSR primers produced thirteen polymorphic fragments, eight SSR primers produced monomorphic fragments, and eleven SSR primers produced no scorable fragments. Thirteen SSR primers produced a total of 29 fragments and 13 of them were polymorphic. The number of average polymorphic fragments per primer was 1.93. The mean polymorphism information content (PIC) and marker index (MI) are 0.16 and 11.74, respectively. The Dice’s similarity coefficient among Navel and Valencia group sweet oranges ranged from 0.42 to 1.00 and matrix correlation (r) was 0.79. In the cluster analysis, Navel group sweet oranges were indicated as a separate group from Valencia group sweet oranges. ‘Antalya (40)’ was most distinct accessions from the others.

Keywords

Citrus sinensis L.; Genetic diversity; Genetic resources; SSR

Valencia ve Navel grup portakal çeşitlerinin SSR markörleri yardımıyla genetik çeşitlilik analizi

Abstract

Portakal [Citrus sinensis (L.) Osbeck] turunçgil yetiştiriciliği içerisinde en önemli türü oluşturur, Navel ve Valencia grubu portakallar ise portakallar içerisinde en fazla yetiştirilenlerdir.  Çalışmanın amacı, 84 adet Navel ve 36 adet Valencia grubu portakalın SSR (simple sequence repeat) moleküler markırı kullanarak genetik akrabalıklarını ve farklılıklarını belirlemektir. Kullanılan 26 SSR primerinden 13 tanesi polimorfik, 8 tanesi monomorfik bant sağlarken, 11 primerden değerlendirilebilecek bant elde edilememiştir. Polimorfizm sağlayan 13 SSR primerinden toplam 29 bant elde edilmiş ve bunların 13 adeti polimorfizm sağlamıştır. Her bir primere düşen ortalama polimorfik bant sayısı 1.93’tür. Ortalama PIC (polymorphism information content) ve MI (marker index) değerleri sırasıyla 0.16 ve 11.74’dür. Navel ve Valencia grubu portakallarında Dice’ın benzerlik indisi (Dice’s similarity coefficient) 0.42 ile 1.00 arasında değişim göstermiştir, matriks korelasyon (r=matrix correlation) ise 0.79’dur. Kümeleme analizinde (cluster analysis) ise, Navel grubu portakallar Valencia grubu portakallardan ayrılmıştır. ‘Antalya (40)’ tüm portakal grupları içerisinde en uzak bireyi oluşturmuştur.

Keywords

Citrus sinensis L.; Genetik farklılık; Genetik kaynak; SSR

References

• Abouzied, H.M., Eldemery, S.M.M., & Abdellatif, K.F. (2013). SSR- Based genetic diversity assessment in tetraploid and hexaploid wheat populations. British Biotechnology Journal, 3(3):390-404.
• Agarwal, M., Neeta, S., & Harish, P. (2008). Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports, 27:617–631.
• Ahmad, R., Struss, D., & Southwick, S.M. (2003). Development and characterization of microsatellite markers in Citrus. Journal of American Society Horticultural Science, 128(4):584-590.
• Al-Mouei, R., & Choumane, W. (2014). Assessment of genetic variability within the genus Citrus in Syria using SSR markers. American Journal of Experimental Agriculture, 4(8): 939-950.
• Amar, M.H., Biswas, M.K., Zhang, Z., & Guo, W.W. (2011). Exploitation of SSR, SRAP and CAPS-SNP markers for genetic diversity of Citrus germplasm collection. Scientia Horticulturae, 128:220–227.
• Anonymous (2012). Bati Akdeniz Agricultural Research Institute, Portakal. Available at [http://www.batem.gov.tr/urunler/meyvelerimiz/portakal/portakal.htm]. Accessed: 23 December 2012.
• Anonymous (2013). UCR Citrus variety collection. Available at [http://www.citrusvariety.ucr.edu/citrus/navelina.html].Accessed:9 September 2013.
• Arumuganathan, K. & Earle, E. (1991). Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter, 9: 208-218.
• Baig, M.N.R, Grewal, S., & Dhillon, S. (2009). Molecular characterization and genetic diversity analysis of citrus cultivars by RAPD markers. Turkish Journal of Agriculture Forestry, 33:375-384.
• Barkley, N.A., Roose, M.L., Krueger, R.R., & Federici, C.T. (2006). Assessing genetic diversity and population structure in a Citrus germplasm collection utilizing Simple Sequence Repeat Markers (SSRs). Theoretical and Applied Genetics, 112:1519–1531.
• Biswas, M.K., Chai, L., Amar, M.H., Zhang, X., & Deng, X.X. (2011). Comparative analysis of genetic diversity in Citrus germplasm collection using AFLP, SSAP, SAMPL and SSR markers. Scientia Horticulturae, 129: 798–803.
• Campos, E.T., Espinosa, M.A.G., Warburton, M.L., Varela, A.S., & Monter, A.V. (2005). Characterization of mandarin (Citrus spp.) using morphological and AFLP markers. Interciencia, 30(11): 687-693.
• Cristofani-Yaly, M., Novelli, V.M., Bastianel, M., & Machado, M.A. (2011). Transferability and level of heterozygosity of microsatellite markers in Citrus species. Plant Molecular Biology Reports, 29:418–423.
• Davies, F. and Albrigo, L.G. (1994). Citrus. CAB International, Wallingford, Oxon, UK, 254p.
• De Pasquale, F., Siragusa, M., Abbate, L., Tusa, N., De Pasquale, C., & Alonzo, G. (2006). Characterization of five sour orange clones through molecular markers and leaf essential oils analysis. Scientia Horticulturae, 109: 54–59.
• Dice, L.R. (1945). Measures of the amount of ecologic association between species. Ecology, 26:297–302.
• El-Mouei, R., Choumane,W., & Dway, F. (2011). Molecular characterization and genetic diversity in genus Citrus in Syria. International Journal of Agriculture and Biology, 13: 351–356.
• Elmeer, K., & Almalki, A. (2011). DNA Finger printing of Prosopis cineraria and Prosopis juliflora using ISSR and RAPD techniques. American Journal of Plant Sciences 2:527-534.
• Fu, C.H., Guo, W.W., Liu, J.H., & Deng, X.X. (2003). Regeneration of Citrus sinensis (+) Clausena lansium intergeneric triploid and tetraploid somatic hybrids and their identification by molecular markers. In Vitro Cellular & Developmental Biololgy Plant, 39:360–364.
• Garcίa-Lor, A., Luro, F., Navarro, L., & Ollitrault, P. (2012). Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies. Molecular Genetic Genomics, 287:77–94.
• Goswami, B.R., Kamdar, J.H., & Bera, S.K. (2013). Molecular diversity and association of simple sequence repeat markers with kernel mass in cultivated groundnut (Arachis hypogaea L.). Australian Journal of Crop Science, 7(8):1152-1159.
• Hammer, R., Harper, D.A.T, & Ryan, P.D. (2001). PAST: Paleontological statistics software package for education and data analysis. Palaeontol Electronica, 4(1):9 pp.
• Hildebrand, C.E., Torney, D.C., & Wagner, R.P. (1992). Mapping the genome. informativeness of polymorphic DNA markers. Los Alamos Science, 20:100-102.
• Hodgson, R.W. (1967). Horticultural varieties of citrus. In: Reuther W, Webber HJ and Batchelor LD (eds) The Citrus Industry. University of California, Berkeley, v. I, pp 431-589.
• Jannati, M., Fotouhi, R., Abad, A.P., & Salehi, Z. (2009). Genetic diversity analysis of Iranian citrus varieties using micro satellite (SSR) based markers. Journal of Horticulture and Forestry, 1(7):120-125.
• Kacar, Y., Uzun, A., Polat, I., Yesiloglu,T., Yilmaz, B., Gulsen, O., Tuzcu, O., Kamiloglu,M., Kurt, S., & Seday, U. (2013). Molecular characterization and genetic diversity analysis of mandarin genotypes by SSR and SRAP markers. Journal of Food, Agriculture & Environment, 11(1):516-521.
• Kadve, S., Yadav, M., & Tiwari, A. (2012). Genetic analysis on hibiscus species by using RAPD markers. International Journal of Biomedical and Advance Research, 03(06):473-485.
• Király, I., Redeczki, R., Erdélyi, É., & Tóth, M. (2012). Morphological and molecular (SSR) analysis of old apple cultivars. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 40(1):269-275.
• Liou, P.C., Gmitter, F.G., & Moore, G.A. 1996. Characterization of the Citrus genome through analysis of restriction fragment length polymorphisms. Theoretical and Applied Genetics, 92(3-4):425-435.
• Machado, M.A., Coletta, H.D., Targon, M.L.P.N., & Pompeu, J. (1996). Genetic relationship of Mediterranean mandarins (Citrus deliciosa Tenore) using RAPD markers. Euphytica, 92: 3, 321-326.
• Malik, S.K., Rohini, M.R., Kumar, S., Choudhary, R., Pal, D., & Chaudhury, R. (2012). Assessment of Genetic Diversity in Sweet Orange [Citrus sinensis (L.) Osbeck] Cultivars of India Using Morphological and RAPD Markers. Agricultural Research, 1(4):317–324.
• Nicolosi, E., Deng, Z.N., Gentile, A., La Malfa, S., Continella, G., & Tribulato, E. (2000). Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theoretical and Applied Genetics, 100:1155-1166.
• Novelli, V.M. Cristofani, M. Souza, A.A. & Machado, M.A. (2006). Development and characterization of polymorphic microsatellite markers for the sweet orange (Citrus sinensis L. Osbeck). Genetics and Molecular Biology. 29: 90-96.
• Oliveira, A.C., Garcia, A.N., Cristofani, M., & Machado, M.A. (2002). Identification of citrus hybrids through the combination of leaf apex morphology and SSR markers. Euphytica, 128: 397–403.
• Polat, I. (2009). Üç Yapraklı (Poncirus trifoliata L. Raf.) ve Üç Yapraklı Melezleri Grubu Turunçgillerin Genetik Akrabalık ve Farklılıklarının SSR Moleküler Markırlarla Tanımlanması. Derim, 26: 2, 30-41.
• Polat, I., Kacar, Y.A., Yesiloglu, T., Uzun, A., Tuzcu, O., Gulsen, O., Incesu, M., Kafa, G., Turgutoglu, E., & Anil, S. (2012). Molecular characterization of sour orange (Citrus aurantium) accessions and their relatives using SSR and SRAP markers. Genetics and Molecular Research, 11(3):3267-3276.
• Polat, I. (2014). Bazı Citrus ve Akrabalarının Genetik Farklılık ve Yakınlıklarının SSR Moleküler Belirteçlerle Belirlenmesi. Akdeniz Üniversitesi Ziraat Fakültesi Dergisi, 27(2): 99-106.
• Powell, W., Machray, G.C., & Provan, J. (1996). Polymorphism revealed by simple sequence repeats. Trends in Plant Science, 1:215–222.
• Rahman, N.M., & Nito, N. (1994). Use of glutamate-oxaloacetate transaminase isozymes for detection of hybrids among genera of the true citrus-fruit trees. Scientia Horticulturae, 58(3):197-206.
• -
• Roose, M.L. (2009). Use of Molecular Markers to Understand Phylogeny and Genetic Diversity of Citrus. PCR Primers for Citrus Germplasm Characterization. Available at [http://www.plantbiology.ucr.edu/faculty/roose.html]. Accessed: 9 January 2011.
• Ryan, P.D., Harper, D.A.T., & Whalley, J.S. (1995). PALSTAT, Statistics for palaeontologists. Chapman & Hall (now Kluwer Academic Publishers).
• Smith, J.S.C., Chin, E.C.L., Shu, H., Smith, O.S., Wall, S.J., Senior, M.L., Mitchel, S.E., Kresorich, S., & Tiegle, J. (1997). An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPs and pedigree. Theoretical and Applied Genetics, 95:163–173.
• Sun, X., Mu, Q., Jiang, D., Wang, C., Wang, X.C., & Fang, J.G. (2012). A new strategy employed for identification of sweet orange cultivars with RAPD markers. Genetics and Molecular Research, 11(3):2071-2080.
• TUIK (2013). Turkish Statistical Institute. www.tuik.gov.tr. Accessed: 06 April 2015.
• Uzun, A., Yesiloglu, T., Aka-Kacar, Y., Tuzcu, O., & Gulsen, O. (2009). Genetic diversity and relationships within Citrus and related genera based on sequence related amplified polymorphism markers (SRAPs). Scientia Horticulture, 121: 306-312.
• Uzun, A., Yesiloglu, T., Polat, I., Aka-Kacar, Y., Gulsen, O., Yildirim, B., Tuzcu, O., Tepe, S., Canan, I., & Anil, S. (2011). Evaluation of Genetic Diversity in Lemons and Some of Their Relatives Based on SRAP and SSR Markers. Plant Molecular Biology Reports, 29: 693–701.
• Zaragoza, S., & Alonso, E. (1975). El manchado de la corteza de los agrios. Estudio preliminar de la variedad Navelate: manchas pre-recolección. Comúnicaciones INIA., Seri4 Protección Vegetal, no: 4, pp.32.