İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.)

TOK, Dilek; UNCUOĞLU, Altınkut Ahu; AYDIN, yıldız; ŞENTÜRK AKFIRAT, Funda; SEVİNÇ, Duygu

İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.)

Dilek TOK, (Marmara Üniversitesi, Fen Edebiyat Fakültesi, Biyoloji Bölümü, İstanbul, Türkiye)

Funda ŞENTÜRK AKFIRAT, (Gebze Yüksek Teknoloji Enstitüsü, Moleküler Biyoloji ve Genetik Bölümü, Kocaeli, Türkiye)

Duygu SEVİNÇ, (İstanbul Üniversitesi, Fen Fakültesi, Biyoloji Bölümü, İstanbul, Türkiye)

Yıldız AYDIN, (Marmara Üniversitesi, Fen Edebiyat Fakültesi, Biyoloji Bölümü, İstanbul, Türkiye)

ALTINKUT Ahu UNCUOĞLU (Marmara Üniversitesi, Mühendislik Fakültesi, Biyomühendislik Bölümü, İstanbul, Türkiye)

Turkish Journal of Field Crops

0 2

Yıl: 2011 Cilt: 16 Sayı: 2 Sayfa Aralığı: 157 - 165 Metin Dili: İngilizce İndeks Tarihi: 29-07-2022

İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.)

Öz:

SSR, RAPD, ISSR and SRAP markers have been used to examine the genetic and epigenetic diversity of wheat (Triticum aestivum L.) germplasm. PCR amplification of the DNA isolated from six wheat genotypes yielded a total of 2118 amplified products, of which 1105 were polymorphic and 1013 were monomorphic. The average PIC value for all molecular marker data was 0.8704 and average percentage of polymorphism was 40.86%. All primers used for RAPD analysis, were also tested by CRED-RA analysis, a method to detect DNA methylation. There were differences between genetic and methylation polymorphism in the studied cultivars. Dendrogram created based on genetic polymorphism showed that PI178383 and Sonmez2001 (0.30) were genetically very different from each other, but in the dendrogram constructed by methylation polymorphism Sonmez2001 and ES14 (0.44) were grouped in one subcluster. Similar to this, in the dendrogram created based on epimarker data Izgi2001 and Harmankaya99 (0.59) were grouped in one subcluster as well as Sonmez2001 and ES14 (0.57) as in the second sub-cluster. The present study has provided the genetic data that diagnose the level of polymorphisms and epigenetic data which present natural variations of DNA methylation.

Anahtar Kelime: genetic polymorphism genetic diversity SSR wheat DNA methylation Triticum aestivum identification

Konular: Ziraat Mühendisliği

Belge Türü: Makale Makale Türü: Araştırma Makalesi Erişim Türü: Erişime Açık

Akfirat, F.S., Y. Aydin, F. Ertugrul, S. Hasancebi, K. Kazan, H. Budak, K. Akan, Z. Mert, N. Bolat, O. Yorgancılar, A.A. Uncuoglu, 2010. A Microsatelite Marker for Yellow Rust Resistance in Wheat. Cereal Res. Commun. 38, 204-211.
Anderson, J.A., G.A. Churchill, J.E. Autrique, S.C. Tanksley, M.E. Sorrells, 1993. Optimizing parental selection for genetic linkage maps. Genome 36, 181-186.
Ashikawa, I. 2001. Surveying CpG methylation at 50-CCGG in the genomes of rice cultivars. Plant Mol. Biol. 45, 31-39.
Barrett, B.A., K.K. Kidwell, 1998. AFLP-based genetic diversity assessment among wheat cultivars from the Pacific Northwest. Crop Sci. 38, 1261-1271
Bednarek, P.T., R. Orlowska, R.M. Koebner, J. Zimny, 2007. Quantification of the tissue-culture induced variation in barley (Hordeum vulgare L.). BMC Plant Biol. 7, 10-19.
Börner, A., E. Schumann, A. Furste, H. Coster, B. Leithold, S. Roder, E. Weber, 2002. Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L.). Theor. Appl. Genet. 105, 921-936.
Cantu, D., L.S. Vanzetti, A. Sumner, M. Dubcovsky, M. Matvienko, A. Distelfeld, R.W. Michelmore, J. Dubcovsky, 2010. Small RNAs DNA methylation transposable elements in wheat. BMC Genomics 11, 408-423.
Cai, Q., C.L. Guy, G.A. Moore, 1996. Detection of cytosine methylation mapping of a gene influencing cytosine methylation in the genome of Citrus. Genome 39, 235-242.
Carvalho, A., M. Matos, J. Lima-Brito, H. Guedes-Pinto, C. Benito, 2005. DNA fingerprint to F1 interspecific hybrids from the Triticeae tribe using ISSRs. Euphytica 143, 93-99.
Carvalho, A., J. Lima-Brito, B. Macas, H.Guedes-Pinto, 2009. Genetic diversity variation among botanical varieties of old portuguese wheat cultivars revealed by ISSR assays. Biochem. Genet. 47, 276-294.
Chen, H.B., J.M. Martin, M. Lavin, L.E. Talbert, 1994. Genetic diversity in hard red spring wheat based on sequence-tagged-site PCR markers. Crop Sci. 34, 1628-1632.
Cooke, R.J. 1995. Variety identification of crop plants. In: Skerrit, J.H., Appels, R. (eds) New diagnostics in crop sciences. CAB International, Wallingford, UK, pp 33-63.
Cubas, P., C. Vincent, E. Coen, 1999. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401, 157-161.
Dong, Z.Y., Y.M. Wang, Z.J. Zhang, Y. Shen, X.Y. Lin, X.F. Ou, F.P. Han, B. Liu, 2006. Extent pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice Zizania latifolia Griseb. Theor. Appl. Genet. 113, 196-205.
Ercan, S., F. Ertugrul, Y. Aydın, F. Senturk-Akfırat, S. Hasancebi, L. Cetin, K. Akan, Z. Mert, N. Bolat, M. Cakmak, A. Altınkut-Uncuoglu, 2010. An EST-SSR marker linked with yellow rust resistance in wheat (Triticum aestivum L.). Biol. Plantarum 54, 691-696.
Emon, R.M., J.P. Gustafson, H. Nguyen, T. Musket, M. Jahiruddin, M.A. Islam, M.S. Haque, M. Islam, S.N. Begum, M.M. Hassan, 2010. Molecular marker-based characterization genetic diversity of wheat genotypes in relation to Boron use efficiency. Indian J. Genet. 70, 339-348.
Galovic, V., S. Dengic, D. Jelovac, 2005. Determination of polymorphism of microsatellite primers in hexaploid wheat. Genetika, 37, 217-223.
Grewal, S., P. Kharb, R. Malik, S. Jain, R.K. Jain, 2007. Assessment of genetic diversity among some Indian wheat cultivars using random amplified polymorphic DNA (RAPD) markers. Indian J. of Biotech. 6, 18-23.
Guadagnuolo, R., D.S. Bianchi, F. Felber, 2001. Specific genetic markers for wheat, spelt, four wild relatives: comparison of isozymes, RAPDs, wheat microsatellites. Genome 44, 610-621.
Han, F.P., G. Fedak, T. Ouellet, B. Liu, 2003. Rapid genomic changes in interspecific intergeneric hybrids allopolyploids of Triticeae. Genome 46, 716-723.
Huang, X.Q., A. Börner, M.S. Röder, M.W. Ganal, 2002. Assessing genetic diversity of wheat (Triticum aestivum L.) germplasm using microsatellite markers. Theor Appl Genet 105, 699-707.
Joshi, C.P., H.T. Nguyen, 1993. RAPD (random amplied polymorphic DNA) analysis based intervarietal genetic relationships among hexaploid wheats. Plant Sci. 93, 95-103.
Kaeppler, S., R. Phillips, 1993. Tissue culture-induced DNA methylation variation in maize. Proc. National Acad. Sci. USA. 90, 8773-8776.
Kalisz, S., M.D. Purugganan, 2004. Epialleles via DNA methylation: consequences for plant evolution. Trends Ecol. Evol. 19, 309-314.
Kim, H. S., R.W. Ward, 2000. Patterns of RFLP-based genetic diversity in germplasm pools of common wheat with different geographical or breeding program origins. Euphytica 115, 197-208.
Kovach, W.L. 1999. MVSP-A Multivariate Statistical Package for Windows, v. 3.1. Kovach Computing Services, Pentraeth, 133.
Lee, H.S., Z.J. Chen, 2001. Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc. Natl. Acad. Sci. USA 98, 6753-6758.
Leljak-Levanic, D., N. Bauer, S. Mihaljevic, S. Jelaska, 2004. Changes in DNA methylation during somatic embryogenesis in Cucurbita pepo L. Plant Cell Rep. 23, 120-127.
Li, G., C.F. Quiros, 2001. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping gene tagging in Brassica. Theor. App. Genet. 103, 455-461.
Li, S., J. Jia, X. Wei, X. Zhang, L. Li, H. Chen, Y.Fan, H. Sun, X. Zhao, T. Lei, Y. Xu, F. Jiang, H. Wang, L. Li, 2007a. A intervarietal genetic map QTL analysis for yield traits in wheat. Mol. Breed. 20, 167-178.
Li, X., X. Yu, N. Wang, Q. Feng, Z. Dong, L. Liu, J. Shen, B. Liu, 2007b. Genetic epigenetic instabilities induced by tissue culture in wild barley (Hordeum brevisubulatum). Plant Cell Tissue Organ Cult. 90, 153-168.
Liu, Y., D. Liu, H. Zhang, J. Wang, J. Sun, X. Guo, A. Zhang, 2005. Allelic variation, sequence determination microsatellite screening at the XGWM261 locus in Chinese hexaploid wheat (Triticum aestivum) varieties. Euphytica 145, 103-112.
Lukens, L.N., S. Zhan, 2007. The plant genome‟s methylation status response to stress: implications for plant improvement. Curr. Opinion Plant Biol. 10, 317-322.
Ma, Z.Q., M.S. Roder, M.E. Sorrells, 1996. Frequencies sequence characteristics of di-, tri-, tetra-nucleotide microsatellites in wheat. Genome 39, 123-130.
Marfil, C.F., E.L. Camadro, R.W. Masuelli, 2009. Phenotypic instability epigenetic variability in a diploid potato of hybrid origin, Solanum ruiz-leali., BMC Plant Biol. 9, 21.
Martienssen, R.A., V. Colot, 2001. DNA methylation epigenetic inheritance in plants lamentous fungi. Science 293, 1070-1074.
Matzke, M.A., M.F. Mette, W. Aufsatz, J. Jakowitsch, A.J.M. Matzke, 1999. Host defenses to parasitic sequences the evolution of epigenetic control mechanisms. Genetica 107, 271-287.
Mukhtar, M.S., M.U. Rehman, Y. Zafar, 2002. Assessment of genetic diversity among wheat (T. aestivum L.) cultivars from a range of localities across Pakistan using random amplified polymorphic DNA (RAPD) analysis. Euphytica 28, 417-425.
Nagaoka, T., Y. Ogihara, 1997. Applicability of inter-simple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP RAPD markers. Theor. Appl. Genet. 94, 597-602.
Nei, M. 1978. Estimation of average heterozygosity genetic distance from a small number of individuals. Genetics 583-590.
Nei, M., W.H. Li, 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76, 5269-5273.
Peng, J.H., N.L.V. Lapitan, 2005. Characterization of EST-derived microsatellites in the wheat genome development of eSSR markers. Funct. Inter. Genom. 5, 80-96.
Pestsova, E., M.W. Ganal, M.S. Roder, 2000. Isolation mapping of microsatellite markers specific for the D genome of bread wheat. Genome 43, 689-697.
Portis, E., A. Acquadro, C. Comino, A. Lanteri, 2004. Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP). Plant Sci. 166, 169-178.
Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S., Rafalski, A. (1996) The comparison of RFLP, RAPD, AFLP SSR (microsatellite) marker for germplasm analysis. Mol. Breed. 2, 225-238.
Rangwala, S.H., E.J. Richards, 2004. The value-added genome: building maintaining genomic cytosine methylation landscapes. Cur. Opinion Genet. Dev. 14, 686-691.
Rapp, R.A., J.F. Wendel, 2005. Epigenetics plant evolution. New Phytol. 168, 81-91.
Repkova, J., A. Dreiseitl, 2009. Candidate markers for powdery mildew resistance genes from wild barley PI284752. Euphytica DOI 10.1007/s10681-009-0096-0.
Roder, M.S., J. Plaschke, S.U. Konig, A. Borner, M.E. Sorrells, 1995. Abundance, variability chromosomal location of microsatellites in wheat. Mol. Gen. Genet. 246, 327-333.
Roldan-Ruiz, I., J. Dendauw, E. Van Bockstaele, A. Depicker, M. De Loose, 2000. AFLP markers reveal high polymorphic rates in rye grasses (Lolium spp.). Mol. Breed. 6, 125-134.
Selker, E.U. 1997. Epigenetic phenomena in filamentous fungi: useful paradigms or repeat-induced confusion? Trends Genet. 13, 296-301.
Shaked, H.K., K. Kashkush, H. Ozkan, M. Feldman, A.A. Levy, 2001. Sequence elimination cytosine methylation are rapid reproduciple responces of the genome to wide hybridization allopolploidy in wheat. Plant Cell 13, 1749-1759.
Takata, M., Y. Kishima, Y. Sano, 2005. DNA methylation polymorphisms in rice wild rice strains: detection of epigenetic markers. Breed. Sci. 55, 57-63.
Temel, A., G. Kartal, N. Gozukirmizi, 2008. Genetic and epigenetic variations in barley calli cultures. Biotechnol. & Biotechnol. Eq. 22(4), 911-914.
Teshale, E.T., S. Bansal, A. Mishra, Vijaipal, V.K. Khanna, 2003. DNA fingerprinting of wheat genotypes by RAM markers. Wheat Infor. Serv. 96, 23-27. Tsaftaris, A.S., A.N. Polidoros, 2000. DNA methylation plant breeding. Plant Breed. Rev. 18, 87-176.
Xiao, W., K.D. Custard, R.C. Brown, B.E. Lemmon, J.J. Harada, R.B. Goldberg, R.L. Fischer, 2006. DNA methylation is critical for Arabidopsis embryogenesis seed viability. Plant Cell 18, 805-814.
Xiong, L.Z., C.G. Xu, M.A. Saghai Maroof, Q.F. Zhang, 1999. Patterns of cytosine methylation in an elite rice hybrid its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol. Genet. Genom. 261, 439-446.
Wang, G., J.S. Pan, X.Z. Li, H.L. He, A.Z. Wu, R. Cai, 2005. Construction of a cucumber genetic linkage map with SRAP markers location of the genes for lateral branch traits. Sci. China Ser. C: Life Sciences 48, 213-220.
Wang, Y., X. Lin, B. Dong, Y. Wang, B. Liu, 2004. DNA methylation polymorphism in a set of elite rice cultivars and its possible contribution to intercultivar differential gene expression. Cellular and Molecular Biology Letters 9, 543-556.
Weining, S., P. Langridge, 1991 Identification mapping of polymorphisms in cereals based on the polymerase chain reaction. Theor. Appl. Genet. 82, 209-216.
Wenguang, C., P. Hucl, G. Scoles, R.N. Chibbar, P.N. Fox, B. Skovm, 2002. Cultivar identification pedigree assessment of common wheat based on RAPD analysis. Wheat Infor. Serv. 95, 29-35.
Zietkiewicz, E., A. Rafalski, D. Labuda, 1994. Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20, 176-183.

APA	TOK D, ŞENTÜRK AKFIRAT F, SEVİNÇ D, AYDIN y, UNCUOĞLU A (2011). İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.). , 157 - 165.
Chicago	TOK Dilek,ŞENTÜRK AKFIRAT Funda,SEVİNÇ Duygu,AYDIN yıldız,UNCUOĞLU Altınkut Ahu İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.). (2011): 157 - 165.
MLA	TOK Dilek,ŞENTÜRK AKFIRAT Funda,SEVİNÇ Duygu,AYDIN yıldız,UNCUOĞLU Altınkut Ahu İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.). , 2011, ss.157 - 165.
AMA	TOK D,ŞENTÜRK AKFIRAT F,SEVİNÇ D,AYDIN y,UNCUOĞLU A İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.). . 2011; 157 - 165.
Vancouver	TOK D,ŞENTÜRK AKFIRAT F,SEVİNÇ D,AYDIN y,UNCUOĞLU A İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.). . 2011; 157 - 165.
IEEE	TOK D,ŞENTÜRK AKFIRAT F,SEVİNÇ D,AYDIN y,UNCUOĞLU A "İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.)." , ss.157 - 165, 2011.
ISNAD	TOK, Dilek vd. "İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.)". (2011), 157-165.

APA	TOK D, ŞENTÜRK AKFIRAT F, SEVİNÇ D, AYDIN y, UNCUOĞLU A (2011). İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.). Turkish Journal of Field Crops, 16(2), 157 - 165.
Chicago	TOK Dilek,ŞENTÜRK AKFIRAT Funda,SEVİNÇ Duygu,AYDIN yıldız,UNCUOĞLU Altınkut Ahu İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.). Turkish Journal of Field Crops 16, no.2 (2011): 157 - 165.
MLA	TOK Dilek,ŞENTÜRK AKFIRAT Funda,SEVİNÇ Duygu,AYDIN yıldız,UNCUOĞLU Altınkut Ahu İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.). Turkish Journal of Field Crops, vol.16, no.2, 2011, ss.157 - 165.
AMA	TOK D,ŞENTÜRK AKFIRAT F,SEVİNÇ D,AYDIN y,UNCUOĞLU A İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.). Turkish Journal of Field Crops. 2011; 16(2): 157 - 165.
Vancouver	TOK D,ŞENTÜRK AKFIRAT F,SEVİNÇ D,AYDIN y,UNCUOĞLU A İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.). Turkish Journal of Field Crops. 2011; 16(2): 157 - 165.
IEEE	TOK D,ŞENTÜRK AKFIRAT F,SEVİNÇ D,AYDIN y,UNCUOĞLU A "İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.)." Turkish Journal of Field Crops, 16, ss.157 - 165, 2011.
ISNAD	TOK, Dilek vd. "İdentification of genetic polymorphism and dna methylation pattern in wheat (triticum aestivum l.)". Turkish Journal of Field Crops 16/2 (2011), 157-165.