Yeni Nesil Bitki Islahı Yöntemleri (Moleküler Bitki Islahı) Bazı Avantaj & Dezavantajları

Year 2018, Volume: 11 Issue: 1, 39 - 49, 24.12.2018

Mehmet Karaca

Abstract

Bu çalışmada geleneksel bitki ıslahı
yöntemlerinden olan introdüksiyon, seleksiyon, mutasyon ve poliploidi ıslahı
ile geleneksel rekombinant DNA teknolojileri (transgenez) dışında kalan
yöntemler yeni nesil bitki ıslahı yöntemleri olarak adlandırılmaktadır. Genlerin aktifleştirilmesi, susturulması veya yerlerinin
değiştirilmesi, sadece genetiği değiştirilmiş organizmaları (GDO) üretmemize
izin vermekle kalmamış aynı zamanda genlerin biyokimyasal, moleküler ve
hücresel mekanizmalarını da daha hızlı bir şekilde anlamamızı sağlamıştır.
Günümüzde genomun yeniden düzenlenmesi mühendislik açısından da
mümkündür. Bitki araştırmacıları tarafından gen ifadesini susturma, artırma ve genlerin
yer değiştirmesi ile genomun yeniden düzenlenmesi ve oluşturulması ile ilgili çalışmalar
önemli bir ivme kazanmıştır. Yeni nesil bitki ıslahı yöntemlerinin bir
bölümünün temel hedefi istenilen özellikleri transgenez ile kazandırılmış ancak
kendisi transgenik olmayan bir hat veya çeşit geliştirmektir. Diğer bazı yeni
nesil bitki ıslahı yöntemlerinin ana hedefi ise geleneksel rekombinant DNA
teknolojileri ile oluşan sorunların düzeltilmesidir. Yeni nesil bitki ıslahı
yöntemleriyle geliştirilen bitkilerin tanısı ise genomik, metabolomik ve
proteomik yöntemlerin kullanılmasını gerekli kılmaktadır. Bu çalışmada genom
düzenleme teknikleri ile birlikte yeni nesil bitki ıslahı yöntemleri,
araştırmacı ve okurlara Türkçe olarak sunulmak üzere hazırlanmıştır. Bu
çalışmada ele alınan konular arasında, Oligonükleotit Yönlendirilmiş Mutagenez
(ODM), cisgenez ve transgenez, transgenik anaçlara aşılama, agro-infilitrasyon,
agro-inokulasyon, floral dip, RNA-bağımlı DNA metilasyonu (RdDM), ters ıslah ve
yeni genom düzenleme yöntemleri olarak Çinko Parmak Nükleaz Teknolojisi (ZFN), transkripsiyon aktifleyici benzeri protein
destekli nükleaz (TALEN) teknolojisi ve düzenli kümelenmiş aralayıcı kısa palindromik
diziler/Cas protein (CRISPR/Cas) sistemleri yer almaktadır.

Keywords

CRISPR/Cas, Oligonükleotit Destekli Mutagenez, TALEN, Ters Islah

New Generation Plant Breeding Methods (Moleculer Plant Breeding) Some Advantages & Disadvantages

Abstract

In the
present study new generation plant breeding methods are defined as those
methods that other than the methods of introduction, selection, mutation and polyploidy breeding, and traditional
recombinant DNA technologies. The main aim of the new generation plant breeding
methods is to develop a non-transgenic line or breed that has the desired
characteristics acquired by the recombinant DNA technologies. Some other new
generation plant breeding methods are aimed at correcting the problems caused
by the traditional recombination DNA technologies. Genomic, metabolomics and proteomic methods have to be used to identify plants
developed with the new generation methods. The ability to activate,
silence or replace genes not just did allow us to produce genetically modified
organisms (GMO) but also let us a rapid understanding of biochemical, molecular
and cellular mechanisms of genes. Today genome rearrangements are also possible
to engineer. Creation and use of such genome rearrangements, gene knockouts and
gene replacements by the plant science community is gaining significant
momentum. In this study relatively new next
generation genetic transformation methods along with some genome editing
techniques were studied to provide knowledgement in Turkish to researcher and
readers. Topics covered include, oligonucleotide directed mutagenesis
(ODM), cisgenesis and transgenesis, grafting to transgenic rootstocks,
agro-infiltration, agro-inoculation, floral dip, RNA-dependent DNA methylation
(RdDM), reverse breeding, and novel methods of
genome editing methods such as zinc finger nuclease technology (ZFN), transcription activator-like effector nucleases (TALEN)
and clustered regulatory interspaced short palindromic repeats/Cas9
(CRISPR/Cas) systems.

Keywords

CRISPR, Oligonucleotide Directed Mutagenesis, Reverse Breeding, TALEN

References

• Akhond, M.A.Y., Machray, G.C. (2009). Biotech crops: technologies, achievements and prospects. Euphytica, 166: 47-59.Aman, R., Ali, Z., Butt, H., Mahas, A., Aljedaani, F., Khan, M.Z., Ding, S., Mahfouz, M. (2018). RNA virus interference via CRISPR/Cas13a system in plants. Genome Biology, 19: 1.Belide, S., Hac, L., Singh, S. P., Green, A. G., Wood, C. C. (2011). Agrobacterium-mediated transformation of safflower and the efficient recovery of transgenic plants via grafting. Plant Methods, 7: 12.Beumer, K., Bhattacharyya, G., Bibikova, M., Trautman, J. K., Carroll, D. (2006). Efficient gene targeting in drosophila with zinc finger nucleases. Genetics, 172: 2391-2403.Breyer, D., Herman, P., Brandenburger, A., Gheysen, G., Remaut, E., Soumillion, P., Van Doorsselaere, J., Custers, R., Pauwels, K., Sneyers, M., Reheul, D. (2009). Genetic modification through oligonucleotide-mediated mutagenesis. a gmo regulatory challenge?. Environmental Biosafety Research, 8: 57-64.Cai, C.Q., Doyon, Y., Ainley, W.M., Miller, J.C., de Kelver, R.C., Moehle, E.A., Rock, J.M., Lee, Y.L., Garrison, R., Schulenberg, L., Blue, R., Worden, A., Baker, L., Faraji, F., Zhang, L., Holmes, M.C., Rebar, E.J., Collingwood, T.N., Rubin-Wilson, B., Gregory, P.D., Urnov, F.D., Petolino, J.F. (2008). Targeted transgene integration in plant cells using designed zinc finger nucleases. Plant Molecular Biology, 69: 699-709.Calarco, J.P., Borges, F., Donoghue, M.T.A., van Ex, F., Jullien, P.E., Lopes, T., Gardner, R., Berger, F., Feijo, F.A., Becker, J.D., Martienssen, R.A. (2012). Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell, 28: 194-205.Calarco, J.P., Martienssen, R.A. (2011). Genome reprogramming and small interfering RNA in the Arabidopsis germline. Current Opinion in Genetics and Development, 21: 134-139.Camenisch, T.D., Brilliant, M.H., Segal, D.J. (2008). Critical parameters for genome editing using zinc finger nucleases. Journal of Medicinal Chemistry, 8: 669-676.Carroll, D., Morton, J.J., Beumer, K.J., Segal, D.J. (2006). Design, construction and in vitro testing of zinc finger nucleases. Nature Protocols, 1: 1329-1341.Curtin, S.J., Zhang, F., Sander, J.D., Haun, W.J., Starker, C., Baltes, N.J. (2011). Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases. Plant Physiol. 156: 466-73.De Jong, H. (2013). Plant genetics in the era of modern genomics. Thai Journal Genetics, 1: 80-82.de Pater, S., Neuteboom, L.W., Pinas, J.E., Hooykaas, P.J., van der Zaal, B.J. (2009). ZFN-induced mutagenesis and gene-targeting in Arabidopsis through Agrobacterium mediated floral dip transformation. Plant Biotechnology Journal, 7: 821-835.de Semir, D., Aran, J.M. (2006). Targeted gene repair: the ups and downs of a promising gene therapy approach. Current Gene Therapy, 6: 481-504.Dirks, R., van Dun, K., de Snoo, C.B., van den Berg, M., Lelivelt, C.L., Voermans, W., Woudenberg, L., de Wit, J.P., Reinink, K., Schut, J.W., van der Zeeuw, E., Vogelaar, A., Freymark, G., Gutteling, E.W., Keppel, M.N., van Drongelen, P., Kieny, M., Ellul, P., Touraev, A., Ma, H., de Jong, H., Wijnker, E. (2009). Reverse breeding: a novel breeding approach based on engineered meiosis. Plant Biotechnology Journal, 7: 837-845.Dong, C., Beetham, P., Vincent, K., Sharp, P. (2006). Oligonucleotide-directed gene repair in wheat using a transient plasmid gene repair assay system. Plant Cell Reports, 25: 457-465.Eck J.V. (2017). Genome editing and plant transformation of Solanaceous food crops. Current Opinion in Biotechnology, 49: 35-41.Espinoza, C., Schlechter, R., Herrera, D., Torres, E., Serrano, A., Medina, C., ArceJohnson, P. (2013). Cisgenesis and intragenesis: new tools for improving crops. Biological Research 46: 4.Fu, Y., Sander, J.D., Reyon, D., Cascio, V.M., Joung, J.K. (2014). Improving CRISPR-Cas nuclease specifi city using truncated guide RNAs. Nat Biotechnol. 32: 279-84.Gaj, T., Gersbach, C.A., Barbas, C.F. (2013). ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends in Biotechnology, 31: 7.Gal-On, A., Wolf, D., Antignus, Y., Patlis, L., Ryu, K.H., Min, B.E., Pearlsman, M., Lachman, O., Gaba, V., Wang, Y., Shiboleth, Y.M., Yang, J., Zelcer, A. (2005). Transgenic Cucumbers harboring the 54-kda putative gene of cucumber fruit mottle mosaic tobamo virus are highly resistant to viral infection and protect non-transgenic scions from soil infection. Transgenic Research, 14: 81-93.Guilinger, J.P., Thompson, D.B., Liu, D.R. (2014). Fusion of catalytically inactive Cas9 to FokI nuclease improves the specifi city of genome modifi cation. Nat Biotechnol. 32: 577-82.Hartung, F., Schiemann, J. (2014). Precise plant breeding using new genome editing techniques: opportunities, safety and regulation in the EU. Plant J. 78: 742-752.Holme, I.B.; Wendt, T.; Holm, P.B. (2013). Intragenesis and cisgenesis as alternatives to transgenic crop development. Plant Biotechnology Journal, 11: 395-407.Huettel, B., Kanno, T., Daxinger, L., Aufsatz, W., Matzke, A.J.M., Matzke, M. (2006). Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. The EMBO Journal, 25: 2828-2836.Igoucheva, O., Alexeev, V., Scharer, O., Yoon, K. (2006). Involvement of ERCC1/XPF and XPG in oligodeoxynucleotide-directed gene modification. Oligonucleotides, 16: 94-104.Jacobsen, E., Schouten, H.J. (2007). Cisgenesis strongly improves introgression breeding and induced translocation breeding of plants. Trends in Biotechnology, 25: 219-223.Jacobsen, E., Schouten, H.J. (2008). Cisgenesis, a new tool for traditional plant breeding, should be exempted from the regulation on genetically modified organisms in a step by step approach. Potato Research, 51: 75-88.Jiang, W.Z., Dumm, S., Knuth, M.E., Sanders, S.L., Weeks, D.P. (2017). Precise oligonucleotide-directed mutagenesis of the Chlamydomonas reinhardtii genome. Plant Cell Reports, 36: 1001-1004.Jin, S., Liang, S., Zhang, X., Nie, Y., Guo, X. (2006). An efficient grafting system for transgenic plant recovery in cotton (Gossypium hirsutum L.). Plant Cell, Tissue and Organ Culture, 85: 181-185.Karaca, M., Ince, A.G. (2017). Molecular Markers in Salvia L.: Past, Present and Future. In: Georgiev V., Pavlov A. (eds) Salvia Biotechnology. pp 291-398 Springer, Cham.Leitao, A.L., Costa, M.C., Enguita, F.J. (2017). Applications of genome editing by programmable nucleases to the metabolic engineering of secondary metabolites. Journal of Biotechnology, 241: 50-60.Lusser, M., Parisi, C., Plan, D., Rodriguez-Cerezo, E. (2012). Deployment of new biotechnologies in plant breeding. Nature Biotechnology, 30: 231-239.Mani, M., Smith, J., Kandavelou, K., Berg, J.M., Chandrasegaran, S. (2005). Binding of two zinc finger nuclease monomers to two specific sites is required for effective double strand DNA cleavage. Biochemical and Biophysical Research Communications, 334: 1191-1197.Matzke, M.A., Kanno, T., Matzke, J.M. (2015). RNA-Directed DNA methylation: The evolution of a complex epigenetic pathway in flowering plants. Ann Rev Plant Biol. 66: 243-267.Matzke, M., Aufsatz, W., Kanno, T., Daxinger, L., Papp, I., Mette, A.F., Matzke, A.J.M. (2004). Genetic analysis of RNA-mediated transcriptional gene silencing. Biochimica et Biophysica Acta - Gene Structure and Expression, 1677: 129-141.Matzke, M., Kanno, T., Huettel, B., Daxinger, L., Matzke, A.J.M. (2007). Targets of RNA-directed DNA Methylation. Current Opinion in Plant Biology, 10: 512-519.Mei, Y., Wang, Y., Chen, H., Sun, Z.S., Ju, X-D. (2016). Recent progress in CRISPR/Cas9 technology. Journal of Genetics and Genomics, 43: 63-75.Ni, Z., Han, Q., He, Y.Q., Huang, S. (2018). Application of genome-editing technology in crop improvement. Cereal Chemistry, 95: 35-48.Ni, Z., Han, Q., He, Y., Huang, S. (2018). Application of genome‐editing technology in crop improvement. Cereal Chemistry, 95: 35-48.Niaz, S. (2018). The AGO proteins: an overview. Biological Chemistry, 399: 525-547.Okuzaki, A., Toriyama, K. (2004). Chimeric RNA/DNA oligonucleotide-directed gene targeting in rice. Plant Cell Reports, 22: 509-512.Osakabe, Y., Osakabe, K. (2015). Genome editing with engineered nucleases in plants. Plant Cell Physiol. 56: 389-400.Osakabe, K., Osakabe, Y., Toki, S. (2010). Site-directed mutagenesis in Arabidopsis using custom designed zinc finger nucleases. Proceedings of the National Academy of Sciences USA, 107: 12034-12039.Petolino, H.F. (2015). Genome editing in plants via designed zinc finger nucleases. In Vitro Cell. Dev. Biol. Plant. 51: 1-8.Porteus, M. H. (2009). Plant biotechnology: Zinc fingers on target. Nature, 459: 337-338.Ricroch, A.E., Henard-Damave, M.C. (2015). Next biotech plants: new traits, crops, developers and technologies for addressing global challenges. Critical Reviews in Biotechnology, 36: 675-690.Rommens, C.M., Haring, M.A., Swords, K., Davies, H.V., Belknap, W.R. (2007). The intragenic approach as a new extension to traditional plant breeding. TRENDS in Plant Science, 12: 389-403.Rousseliere, D., Rousseliere, S. (2017). Is biotechnology (more) acceptable when it enables a reduction in phytosanitary treatments? A European comparison of the acceptability of transgenesis and cisgenesis. PLOS ONE, 12: 9.Ryu, C.M., Anand, A., Kang, L., Mysore, K.S. (2004). Agrodrench: a novel and effective agroinoculation method for virus-induced gene silencing in roots and diverse Solanaceous species. The Plant Journal, 40: 322-331.Sauer, N.J., Mozoruk, J., Miller, R.B., Warburg, Z.J., Walker, K.A., Beetham, P.R., Schöpke, C.R., Gocal, G.F. (2016) Oligonucleotide-directed mutagenesis for precision gene editing. Plant Biotechnol J. 14: 496-502.Savadi, S., Prasad, P., Kashyap, P.L., Bhardwaj, S.C. (2018). Molecular breeding technologies and strategies for rust resistance in wheat (Triticum aestivum) for sustained food security. Plant Pathology, 67: 771-791.Schaart, J.G., Visser, R.G.F. (2009). Novel plant breeding techniques - consequences of new genetic modification-based plant breeding techniques in comparison to conventional plant breeding. COGEM Research Report number 2009-02. The Netherlands Commission on Genetic Modification.Schaart, J.G., Van de Wiel, C.C.M., Lotz, L.A.P., Smulders, M.J.M. (2016). Opportunities for products of new plant breeding techniques. Trends Plant Sci. 21: 438-449.Schoft, V.K., Chumak, N., Mosiolek, M., Slusarz, L., Komnenovic, V., Brownfield, L., Twell, D., Kakutani, T., Tamaru, H. (2009). Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin. EMBO reports, 10: 1015-1021.Schouten, H.J., Jacobsen, E. (2008). cisgenesis and intragenesis, sisters in innovative plant breeding. Trends Plant Science, 13: 261-263.Schouten, H.J., Krens, F.A., Jacobsen, E. (2006). Cisgenic plants are similar to traditionally bred plants. EMBO Reports, 7: 1-3.Shukla, V.K., Doyon, Y., Miller J.C., DeKelver, R.C., Moehle, E.A., Worden, S.E., Mitchell, J.C., Arnold, N.L., Gopalan, S., Meng, X., Choi, V.M., Rock, J.M., Wu, Y., Katibah, G.E., Zhifang, G., McCaskill, D., Simpson, M.A., Blakeslee, B., Greenwalt, S.A., Butler, H.J., Hinkley, S.J., Zhang, L., Rebar, E.J., Gregory, P.D., Urnov, F.D. (2009). Precise genome modification in the crop species Zea mays using zinc-finger nucleases", Nature, 459: 437-441.Singh, V., Braddick, D., Dhar, P.K. (2017). Exploring the potential of genome editing CRISPR-Cas9 technology. Gene, 599: 1-18.Song, G.Q., Walworth, A.E., Loescher, W.H. (2015). Grafting of genetically engineered plants. J Am Soc Horticult Sci. 140: 203-213.Suzuki, T. (2008). Targeted gene modification by oligonucleotides and small DNA fragments in eukaryotes", Frontiers in Bioscience, 13: 737-744.Tovkach, A., Zeevi, V., Tzfira, T. (2009). A toolbox and procedural notes for characterizing novel zinc finger nucleases for genome editing in plant cells. Plant Journal, 57: 747-757.Townsend, J.A., Wright, D.A., Winfrey, R.J., Fu, F., Maeder, M.L., Joung, J.K., Voytas, D.F. (2009). High-frequency modification of plant genes using engineered zinc-finger nucleases. Nature, 459: 442-445.Van Nocker, S., Gardiner, S.E. (2014). Breeding better cultivars, faster: applications of new technologies for the rapid deployment of superior horticultural tree crops. Hortic Res. 1: 14022.Weeks, D.P., Spalding, M.H., Yang, B. (2016). Use of designer nucleases for targeted gene and genome editing in plants. Plant Biotechnology Journal 14: 483-495.Wijnker, E., van Dun, K., Bastiaan de Snoo, C,, Lelivelt, C.L.C., Keurentjes, J.J.B., Naharudin, N.S., Ravi, M., Chan, S.W.L., de Jong, H., Dirks, R. (2012). Reverse breeding in Arabidopsis thaliana generates homozygous parental lines from a heterozygous plant. Nature Genetics, 44: 467-470.Wright, D.A., Townsend, J.A., Winfrey, R.J., Irwin, P.A., Rajagopal, J., Lonosky, P.M., Hall, B.D., Jondle, M.D., Voytas, D.F. (2005). High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant Journal, 44:693-705.Yasmin, A., Jalbani, A.A., Baloch, S. (2013). Agrobacterium-mediated stable transformation of Arabidopsis thaliana plants using β-glucuronidase (gus) gene. Science International (Lahore), 25: 287-290.Zhang, F., Maeder, M.L., Unger-Wallace, E., Hoshaw, J. P., Reyon, D., Christian, M., Li, X., Pierick, C. J., Dobbs, D., Peterson, T. (2010). High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases", Proceedings of the National Academy of Sciences USA, 107: 12028-12033.Zhu, T., Mettenburg, K., Peterson, D.J., Tagliani, L., Baszczynski, C. (2000). Engineering herbicide-resistant maize using chimeric RNA/DNA oligonucleotides. Nature Biotechnology, 18: 555-558.Zottini, M., Barizza, E., Costa, A., Formentin, E., Ruberti, C., Carimi, F., Schiavo, F.L. (2008). Agroinfiltration of grapevine leaves for fast transient assays of gene expression and for long-term production of stable transformed cells. Plant Cell Reports, 27: 845-853.