Yıldız Aka KAÇAR, TURGUT YEŞİLOĞLU, Bilge YILDIRIM, ÖZHAN ŞİMŞEK, MERAL İNCESU, Müge KAMİLOĞLU, Önder TUZCU

Bazı turunçgil anaçlarının SSR Markırları ile moleküler tanımlanması

Bu araştırmada, turunçgillerde anaç olma özelliği olan yirmi üç genotipin genetik yapıları SSR (Simple Sequence Repeat) markırları ile belirlenmiştir. Genotiplerin genetik ilişkilerinin belirlenmesi amacıyla toplam on SSR primer çifti kullanılmıştır. Kullanılan primerlerden Ci03C08 primeri istenilen amplifikasyonu vermediği için değerlendirmeye alınmamıştır. Değerlendirmeye alınan 9 mikrosatellit primer çifti her genotip için 1 ile 3 arasında değişen bantlar vermiştir. CI03D12a primer çifti, proje kapsamında çalışılan genotiplerle toplam 10 bant vererek en yüksek polimorfizm oranını sergilemiştir. Bu primer için elde edilen bantlar 238bp-258bp aralığında dağılmışlardır. Elde edilen genetik veriler ile genetik benzerlikler hesaplanmış ve genetik benzerliklere dayalı dendrogram elde edilmiştir. Araştırma kapsamında kullanılan genotipler arasındaki genetik benzerlikler tartışılmıştır.

Anahtar Kelimeler:

PAGE, mikrosatellitler, anaçlar, moleküler genetik, nükleotit dizileri, DNA, DNA parmakizi, turunçgiller

Genetic characterization of some Citrus rootstocks by using SSR markers

In this study genetic characterization of twenty-three Citrus rootstocks has been conducted by using SSR markers. The ten SSR primer pairs were used to fingerprint the rootstock collection. Primer pair Ci03C08 did not give clear amplification and reproducible fragments with all genotypes. The number of fragments amplified from individual citrus genotypes with each primer pair ranged from one to three. Primer pair CI03D12a was the most informative and polymorphic that produced ten fragment with the genotypes studied ranged from 238 bp to 258 bp. The data were analyzed to calculate genetic similarity values and UPGMA Cluster Analysis was performed to generate a dendrogram. The genetic relationships between genotypes are discussed.

Keywords:

PAGE, microsatellites, rootstocks, molecular genetics, nucleotide sequences, DNA, DNA fingerprinting, Citrus,

PDF

___

Abkenar, A.A., Isshiki, S., Tashiro, Y., 2004. Phylogenetic relationships in the “true citrus fruit trees” revealed by PCR-RFLP analysis of cpDNA. Sci. Hortic. 102(2): 233–242.
Abkenar, A.A., Isshiki, S., Matsumoto, R., 2008. Comparative analysis of organelle DNAs acid citrus grown in Japan using PCR-RFLP method. Genet. Res. Crop. Evol. 55(4): 487–492.
Aka-Kacar, Y., Demirel, A., Tuzcu, O., Yesiloglu, T., Ulas, M., Yildirim, B., 2005. Preliminary results on Fingerprinting Lemon genotypes tolerant to Mal Secco (Phoma tracheipfhila) Disease by RAPD Markers. Biologia, Bratislava 60(3): 295–300.
Aka-Kacar, Y., Cetiner, S., Cantini, C. Iezzoni, A.F., 2006. Simple sequence repeat (SSR) markers differentiate Turkish sour cherry germplasm. Journal of American Pomological Society, 60(3): 136-143.
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). Theor. Appl. Genet. 112(8):1519–1531.
Broun, P., Tanksley, S.D., 1996. Characterization and genetic mapping of simple repeat sequences in the tomato genome. Mol. Gen Genet. 250(1): 39–49.
Brown, S.K., Iezzoni, A.F., Fogle, H.W., 1996. Cherries. In: Fruit Breeding, Vol 1: Tree and Tropical Fruits, ed: J. Janick and J.N. Moore p.212.
Chase, M., Kesseli, R., Bawa, K., 1996. Microsatellite markers for population and conservation genetics of tropical trees. Amer. Jour. Bot. 83(1):51-57.
Coletta-Filho, H.D., Machado, M.A., Targon, M.L.P.N., Moreira, M.C.P.Q.D.G., Pompeu, J., 1998. Analysis of the Genetic Diversity among Mandarins (Citrus spp.) Using RAPD Markers. Euphytica, 102(1):133–139.
Corazza-Nunes, M.J., Machado, M.A., Nunes, W.M.C., Cristofani, M., Targon, M.L.P.N., 2002. Assessment of genetic variability in grapefruits (Citrus paradisi Macf.) and pummelos (C. maxima Burm. Merr.) using RAPD and SSR markers, Euphytica 126(2): 169–176.
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. Sci. Hort. 109(1):54-59.
Devos, K.M., Bryan, G.J., Collins, A.J., Stephenson, P., Gale, M.D., 1995. Application of two microsatellite sequences in wheat storage proteins as molecular markers. Theor. Appl. Genet. 90 (2): 247-252.
Dow, B.D., Asley, M.V., Howe, H.F., 1995. Charecterization of highly variable (GA/CT)n microsatellites in the bur oak, (Quercus macrocarpa). Theor Appl Genet 91(1): 137–141.
Echt, C.S., May-Marquardt, P., Hseih, M., Zahorochak, R., 1996. Characterization of microsatellite markers in eastern white pine. Genome 39(6): 1102–1108.
Fang, D.Q., Roose, M.L. 1997. Identification of closely related Citrus cultivars with intersimple sequence repeat markers. Theor. Appl. Genet. 95(3): 408–41.
Fang, D.Q., Krueger, R.R., Roose, M.L., 1998. Phylogenetic relationships among selected Citrus germplasm accessions revealed by inter-simple sequence repeat (ISSR) markers. J. Amer. Soc. Hort. 123(4): 612–617.
Federici C.T., Fang, D.Q., Scora, R.W., Roose, M.L., 1998. Phyllogenetic Relationship within the Genus Citrus by RFLP Analysis. Theoretical and Applied Genetics, 96 (6–7):812–822.
Gulsen, O., Roose, M.L., 2000. The origin of Interdonato lemon inferred from cpRFLP, SSR, isozyme and ISSR markers, Proc. Int. Soc. Citricult. IX Congr. 158–159.
Gulsen, O., Roose, M.L., 2001. Lemons: diversity and relationships with selected citrus genotypes as measured with nuclear genome markers. J. Am. Soc. Hort. Sci. 126(3):309–317.
Hokanson, S.C., Szewc-MCFadden, A.K., Lamboy, W.F., McFerson, J.R., 1998. Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus x domestica Borkh. core subset collection. Theor. Appl. Genet. 97(5-6):671–683.
Hodgson, R.W., 1967. Horticultural varieties of citrus. In: Reuther W., Webber H.J., Batchelor, L.D. (eds). The citrus industry. University of California Press, Berkeley. 431-591.
Jarret, R.L., Merrick, L.C., Holms, T., Evans, J., Aradhya, M.K., 1997. Simple sequence repeats in watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai). Genome 40(4):433–441.
Katzir, N., Danin-Poleg, Y., Tzuri, G., Karchi, Z., Lavi, U., Cregan, P.B., 1996. Length poymophism and homologies of microsatellites in several Cucurbitaceae species. Theor. Appl. Genet. 93(8): 1282–1290.
Kijas, J.M.H., Fowler, J.C.S., Thomas, M.R., 1995. An evaluation of sequence-tagged microsatellite site markers for genetic analysis within Citrus and related species. Genome 38(2): 349–355.
Komatsu, A., Akihama, T., Hidaka, T., Omura, M., 1993. IdentiÞcation of Poncirus strains by DNA fingerprinting. In: Hayashi T, Omura M, Scott NS (eds) Techniques on gene diagnosis and breeding in fruit trees. Fruit Trees Research Station, Okitsu, Japan, 88-95.
Lamboy, W.F., Alpha, C.G., 1998. Using simple sequence repeats (SSRs) for DNA fingerprinting germplasm accessions of grape (Vitis L.) species. J. Amer. Soc. Hort. Sci. 123(2):182–188.
Lavi, U., Akkaya, M., Bhagwat, A., Lahav, E., Cregan, P.B., 1994. Methodology of generation and characteristics of simple sequence repeat DNA markers in avocado (Persea americana Mill.). Euphytica 80(3):171-177.
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, Theor. Appl. Genet. 100 (8): 1155–1166.
Özgen, M., Adak, M.S., Söylemezoğlu, G., Ulukan, H., 2000. Bitkisel Gen Kaynaklarının Korunma Ve Kullanımında Yeni Yaklaşımlar: Türkiye Ziraat Mühendisliği V. Teknik Kongresi.
Pang, X.M., Hu, C.G., Deng, X.X., 2007. Phylogenetic relationship within Citrus and related genera as inferred from AFLP markers. Genetic Resources and Crop Evolution 54(2):429-436.
Pfeiffer, A., Oliveri, A.M., Morgante, M., 1997. Identification and characterization of microsatellites in Norway spruce (Picea abies K.). Genome 40(4): 411-419.
Plaschke, J., Ganal, M.W., Roder, M.S., 1995. Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor. Appl. Genet. 91(6-7): 1001–1007.
Powell W., Macharay G.C., Provan. J. 1996. Polymorphism revealed by simple sequence repeats. Trends Plant Genet. 1(7):215-222.
Prasad, M., Varshney, R.K., Roy, J.K., Balyan, H.S., Gupta, P.K., 2000. The use of microsatellites for detecting DNA polymophism, genotype identification and genetic diversity in wheat. Theor. Appl. Genet. 100(3-4):584-592.
Röder, M.S., Plaschke, J., Konig, S.U., Borner, A., Sorrels, M.E., Tanksley, S.D., Ganal, M.W., 1995. Abundance, variabilty and chromosomal location of microsatellites in wheat. Mol Gen Genet 246(3): 327-333.
Rohlf, F.J., 1993. NTSYS-PC, Numerical Taxonomy and Multivariate Analysis System. Version 1.80. Exeter Software, Setauket, New York.
Saunt, J., 2000. Citrus Varieties of the World. Sinclair Int. Limited, Norwich, England, 156 p.
Schafer, G., Bastianel, M., Dornelles, A.L.C., 2004. Genetic diversity of citrus rootstocks based on RAPD marker analysis. Ciência Rural, Santa Maria. 34: 1437-1442.
Smith, D.N., Devey, M.E., 1994. Occurance and inharitance of microsatellites in Pinus radiata. Genome 37(6): 977–983.
Smulders, M.J.M., Bredmeijer, G., Rus-Kortekaas, W., Arens, P., Vosman, B., 1997. Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theor. Appl. Genet. 94(2): 264–272.
Thomas, M.R., Scott, N.S. 1993. Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence-tagged sites (STSs). Theor. Appl. Genet. 86(8):985-990.
Uzun, A., Yesiloglu, T., Aka-Kacar, Y., Gulsen, O., 2009. Genetic diversity and relationships within Citrus and related genera based on sequence related amplified polymorphism markers (SRAPs) Sci. Hort, 121(3): 306-312.
Ven, WTG van de, McNicol, R.J., 1996. Microsatellites as DNA markers in Sitka spruce. Theor. Appl. Genet. 93(4): 613–617.