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Geçmişten Günümüze Genetik ve Kromozom Mühendisliği Çalışmalarının Sürdürülebilir Tarım ve Bitki Islahına Katkısı

Year 2021, , 246 - 258, 30.03.2021
https://doi.org/10.29133/yyutbd.787094

Abstract

2050 yılında nüfusun 9.2 milyara ulaşacağı ve dünya genelinde eşit ve insani temel ihtiyaçlara olan taleplerin karşılanması gerektiği öngörülmektedir. Günümüze kadar, tarımsal üretimin arttırılmasına yönelik çeşitli çalışmalar gerçekleştirilmiştir. Bununla birlikte birim alandan daha yüksek verim alınmasını sağlayan yeni teknoloji ve yöntemlerin geliştirilip bitki ıslah programlarına entegre edilmesi gerekmektedir. Bu entegrasyon sayesinde hem sürdürülebilir tarım anlayışına uyumsuz aşırı girdi ve mekanizasyon kullanımı azaltılabilecek hem de bitki biyolojisi, evrimi, genom yapısı anlaşılarak tarımda verimlilik arttırılabilecektir. Ayrıca genetik çeşitlilikten yararlanılması, model bitkilerden sağlanan verilerin bitki ıslah programlarına adapte edilmesi, yetim bitkilerin genetik kaynak potansiyelinin kullanılmasına yönelik çalışmalar yeni genotiplerin eldesine katkı sağlayacaktır. Bugüne kadar gen transformasyonu, DNA dizilemesi, genom haritalaması ve genom düzenleme gibi modern teknolojiler bitkilerde genom yapısının anlaşılmasında etkin rol oynamıştır. FISH, GISH, telomer aracılığıyla kromozom kesimi, minikromozomlar, organizmalar arası sintenik kromozomal lokuslarının saptanması, tekrarlayan DNA elementlerinin keşfi ve yapısal CENH3 proteininin kullanımı gibi çok sayıda kromozom mühendisliği yöntemleri de tarımsal gelişmede itici güç oluşturacaktır. Temel bilimlerdeki ilerlemelerden faydalanan tarımsal araştırmalar uzun vadede istenilen amaca ulaşmayı destekleyecek ve gelecekte kromozom mühendisliği yöntemleri özelinde tarımsal üretimin artırılmasına katkı sağlayacaktır. Tüm bunlara ek olarak, bu derleme makalesinde bir araya getirilen güncel ve hızlı gelişen disiplinler arası tematik çalışmalar ve aynı zamanda tarım, ıslah ve genetik disiplinlerinden sentezlenen perspektiflerin, bu alanlarda çalışan araştırmacılara yönlendirici bir tartışma platformu sunması hedeflenmiştir.

Supporting Institution

TÜBİTAK (118O670; 118Z589), COST-INDEPTH CA16212 projeleri, YÖK 100/2000 programı, Ayhan Şahenk Vakfı

Project Number

118O670; 118Z589; COST-INDEPTH CA16212; YÖK 100/2000

Thanks

ALT, SDKÖ, BŞY ve HY TÜBİTAK (118O670; 118Z589), COST CA16212 - Impact of Nuclear Domains On Gene Expression and Plant Traits projesi tarafından desteklenmektedir. SDKÖ, BŞY ve HY YÖK 100/2000 programı tarafından desteklenmektedir. Bitki Kromozom Laboratuvarındaki çalışmalarımız Ayhan Şahenk Vakfı tarafından desteklenmektedir.

References

  • Acquaah, G. (2009). Principles of Plant Genetics and Breeding. John Wiley & Sons. 1-22.
  • Agarwal, M., Shrivastava, N., & Padh, H. (2008). Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports, 27(4), 617-631. https://doi.org/10.1007/s00299-008-0507-z
  • Aguilar-Rivera, N., Michel-Cuello, C., & Cárdenas-González, J. F. (2019). Green Revolution and Sustainable Development. In W. Leal Filho (Ed.), Encyclopedia of Sustainability in Higher Education (pp. 833-850). Springer International Publishing.
  • Armstead, I., Huang, L., Ravagnani, A., Robson, P., & Ougham, H. (2009). Bioinformatics in the orphan crops. Briefings in Bioinformatics, 10(6), 645-653. https://doi.org/10.1093/bib/bbp036
  • Barampuram, S., & Zhang, Z. J. (2011). Recent advances in plant transformation. Methods in Molecular Biology (Clifton, N.J.), 701, 1-35. https://doi.org/10.1007/978-1-61737-957-4_1
  • Bennetzen, J. L., & Chen, M. (2008). Grass Genomic Synteny Illuminates Plant Genome Function and Evolution. Rice, 1(2), 109-118. https://doi.org/10.1007/s12284-008-9015-6
  • Birchler, J. A., Yu, W., & Han, F. (2008). Plant engineered minichromosomes and artificial chromosome platforms. Cytogenetic and Genome Research, 120(3-4), 228-232. https://doi.org/10.1159/000121071
  • Biscotti, M. A., Olmo, E., & Heslop-Harrison, J. S. P. (2015). Repetitive DNA in eukaryotic genomes. Chromosome Research: An International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology, 23(3), 415-420. https://doi.org/10.1007/s10577-015-9499-z
  • Bonierbale, M. W., Plaisted, R. L., & Tanksley, S. D. (1988). RFLP Maps Based on a Common Set of Clones Reveal Modes of Chromosomal Evolution in Potato and Tomato. Genetics, 120(4), 1095-1103.
  • Brodt, S., Six, J., Feenstra, G., Ingels, C. & Campbell, D. (2011) Sustainable Agriculture. Nature Education Knowledge 3(10):1. https://www.nature.com/scitable/knowledge/library/sustainable-agriculture-23562787/. Erişim tarihi: 12.05.2020.
  • Cerit, İ., Cömertpay, G., Oyucu, R., Çakir, B., Hatipoğlu, R., & Özkan, H. (2016). Melez Mısır Islahında In-Vivo Katlanmış Haploid Tekniğinde Kullanılan Farklı Inducer Genotiplerin Haploid İndirgeme Oranların Belirlenmesi. Tarla Bitkileri Merkez Araştırma Enstitüsü Dergisi, 25(1), 52-57. https://doi.org/10.21566/tarbitderg.280162
  • Chang, C., Bowman, J. L., & Meyerowitz, E. M. (2016). Field Guide to Plant Model Systems. Cell, 167(2), 325-339. https://doi.org/10.1016/j.cell.2016.08.031
  • Charlesworth, B., Sniegowski, P., & Stephan, W. (1994). The evolutionary dynamics of repetitive DNA in eukaryotes. Nature, 371(6494), 215-220. https://doi.org/10.1038/371215a0
  • Che, P., Anand, A., Wu, E., Sander, J. D., Simon, M. K., Zhu, W., Sigmund, A. L., Zastrow-Hayes, G., Miller, M., Liu, D., Lawit, S. J., Zhao, Z.-Y., Albertsen, M. C., & Jones, T. J. (2018). Developing a flexible, high-efficiency Agrobacterium-mediated sorghum transformation system with broad application. Plant Biotechnology Journal, 16(7), 1388-1395. https://doi.org/10.1111/pbi.12879
  • Clark, W. C. (2007). Sustainability Science: A room of its own. Proceedings of the National Academy of Sciences, 104(6), 1737-1738. https://doi.org/10.1073/pnas.0611291104
  • Cody, J. P., Swyers, N. C., McCaw, M. E., Graham, N. D., Zhao, C., & Birchler, J. A. (2015). Minichromosomes: Vectors for Crop Improvement. Agronomy, 5(3), 309-321. https://doi.org/10.3390/agronomy5030309
  • Cook, D. R., & Varshney, R. K. (2010). From genome studies to agricultural biotechnology: Closing the gap between basic plant science and applied agriculture. Current Opinion in Plant Biology, 13(2), 115-118. https://doi.org/10.1016/j.pbi.2010.03.003
  • Dhar, M. K., Kaul, S., & Kour, J. (2011). Towards the development of better crops by genetic transformation using engineered plant chromosomes. Plant Cell Reports, 30(5), 799-806. https://doi.org/10.1007/s00299-011-1001-6
  • Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., Bibillo, A., Bjornson, K., Chaudhuri, B., Christians, F., Cicero, R., Clark, S., Dalal, R., deWinter, A., Dixon, J., … Turner, S. (2009). Real-Time DNA Sequencing from Single Polymerase Molecules. Science, 323(5910), 133-138. https://doi.org/10.1126/science.1162986
  • Falistocco, E. (2020). Insight into the Chromosome Structure of the Cultivated Tetraploid Alfalfa (Medicago sativa subsp. Sativa L.) by a Combined Use of GISH and FISH Techniques. Plants, 9(4), 542. https://doi.org/10.3390/plants9040542
  • Faris, J., Sirikhachornkit, A., Haselkorn, R., Gill, B., & Gornicki, P. (2001). Chromosome Mapping and Phylogenetic Analysis of the Cytosolic Acetyl-CoA Carboxylase Loci in Wheat. Molecular Biology and Evolution, 18(9), 1720-1733. https://doi.org/10.1093/oxfordjournals.molbev.a003960
  • FAO (2020). Food and Agriculture organization. http://www.fao.org/sustainability/en/. Erişim 15.04.2020.
  • Fears, R. (2007). Genomıcs and genetıc resources for food and agrıculture. Commıssıon on genetıc resources for food and agrıculture. http://www.fao.org/3/a-k0174e.pdf. Erişim 12.06.2020.
  • Fleury, D., Baumann, U., & Langridge, P. (2012). Plant genome sequencing: Models for developing synteny maps and association mapping. In A. Altman & P. M. Hasegawa (Ed.), Plant Biotechnology and Agriculture (pp. 83-97). Academic Press.
  • Galasso, I., Harrison, G. E., Pignone, D., Brandes, A., & Heslop-harrison, J. S. (1997). The Distribution and Organization of Ty1-copia-like Retrotransposable Elements in the Genome of Vigna unguiculata (L.) Walp. (Cowpea) and its Relatives. Annals of Botany, 80(3), 327-333. https://doi.org/10.1006/anbo.1997.0443.
  • Gill, B. S., Friebe, B., & Endo, T. R. (1991). Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat (Triticum aestivum). Genome, 34(5), 830-839. https://doi.org/10.1139/g91-128
  • Govindaraj, M., Vetriventhan, M., & Srinivasan, M. (2015). Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genetics Research International, 2015, 431487. https://doi.org/10.1155/2015/431487
  • Gross, B. L., Kellogg, E. A., & Miller, A. J. (2014). Speaking of food: Connecting basic and applied plant science. American Journal of Botany, 101(10), 1597-1600. https://doi.org/10.3732/ajb.1400409
  • Harris, T. D., Buzby, P. R., Babcock, H., Beer, E., Bowers, J., Braslavsky, I., Causey, M., Colonell, J., Dimeo, J., Efcavitch, J. W., Giladi, E., Gill, J., Healy, J., Jarosz, M., Lapen, D., Moulton, K., Quake, S. R., Steinmann, K., Thayer, E., … Xie, Z. (2008). Single-molecule DNA sequencing of a viral genome. Science (New York, N.Y.), 320(5872), 106-109. https://doi.org/10.1126/science.1150427
  • Henikoff, S., Ahmad, K., Platero, J. S., & van Steensel, B. (2000). Heterochromatic deposition of centromeric histone H3-like proteins. Proceedings of the National Academy of Sciences of the United States of America, 97(2), 716-721. https://doi.org/10.1073/pnas.97.2.716
  • Heslop‐Harrison, J. (Pat), & Schmidt, T. (2012). Plant nuclear genome composition. In ELS. American Cancer Society. https://doi.org/10.1002/9780470015902.a0002014.pub2
  • Hidalgo, O., Pellicer, J., Christenhusz, M., Schneider, H., Leitch, A. R., & Leitch, I. J. (2017). Is there an upper limit to genome size? Trends in Plant Science, 22(7), 567-573. https://doi.org/10.1016/j.tplants.2017.04.005
  • Houben, A., & Schubert, I. (2003). DNA and proteins of plant centromeres. Current Opinion in Plant Biology, 6(6), 554-560. https://doi.org/10.1016/j.pbi.2003.09.007
  • Houben, A., Nasuda, S., & Endo, T. R. (2011). Plant B chromosomes. Methods in Molecular Biology (Clifton, N.J.), 701, 97-111. https://doi.org/10.1007/978-1-61737-957-4_5
  • Hribová, E., Neumann, P., Matsumoto, T., Roux, N., Macas, J., & Dolezel, J. (2010). Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing. BMC Plant Biology, 10, 204. https://doi.org/10.1186/1471-2229-10-204
  • Kato, A., Vega, J. M., Han, F., Lamb, J. C., & Birchler, J. A. (2005). Advances in plant chromosome identification and cytogenetic techniques. Current Opinion in Plant Biology, 8(2), 148-154. https://doi.org/10.1016/j.pbi.2005.01.014
  • Ku, H.-M., Vision, T., Liu, J., & Tanksley, S. D. (2000). Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny. Proceedings of the National Academy of Sciences, 97(16), 9121-9126. https://doi.org/10.1073/pnas.160271297
  • Kuppu, S., Ron, M., Marimuthu, M. P. A., Li, G., Huddleson, A., Siddeek, M. H., Terry, J., Buchner, R., Shabek, N., Comai, L., & Britt, A. B. (2020). A variety of changes, including CRISPR/Cas9-mediated deletions, in CENH3 lead to haploid induction on outcrossing. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13365
  • Lermontova, I., & Schubert, I. (2013). CENH3 for Establishing and Maintaining Centromeres. In J. Jiang & J. A. Birchler (Eds). Plant Centromere Biology (pp. 67-82). John Wiley & Sons, Ltd.
  • Lusser, M., Parisi, C., Plan, D., & Rodríguez-Cerezo, E. (2012). Deployment of new biotechnologies in plant breeding. Nature Biotechnology, 30(3), 231-239. https://doi.org/10.1038/nbt.2142
  • Mabhaudhi, T., Chimonyo, V. G. P., Hlahla, S., Massawe, F., Mayes, S., Nhamo, L., & Modi, A. T. (2019). Prospects of orphan crops in climate change. Planta, 250(3), 695-708. https://doi.org/10.1007/s00425-019-03129-y
  • Mandáková, T., & Lysak, M. A. (2008). Chromosomal Phylogeny and Karyotype Evolution in x=7 Crucifer Species (Brassicaceae). The Plant Cell, 20(10), 2559-2570. https://doi.org/10.1105/tpc.108.062166
  • McCouch, S. R. (2001). Genomics and Synteny. Plant Physiology, 125(1), 152-155. https://doi.org/10.1104/pp.125.1.152
  • Mehrotra, S., & Goyal, V. (2014). Repetitive sequences in plant nuclear DNA: Types, distribution, evolution and function. Genomics, Proteomics & Bioinformatics, 12(4), 164-171. https://doi.org/10.1016/j.gpb.2014.07.003
  • Michael, T. P., & VanBuren, R. (2020). Building near-complete plant genomes. Current Opinion in Plant Biology, 54, 26-33. https://doi.org/10.1016/j.pbi.2019.12.009
  • Mondini, L., Noorani, A., & Pagnotta, M. A. (2009). Assessing Plant Genetic Diversity by Molecular Tools. Diversity, 1(1), 19-35. https://doi.org/10.3390/d1010019
  • Moose, S. P., & Mumm, R. H. (2008). Molecular Plant Breeding as the Foundation for 21st Century Crop Improvement. Plant Physiology, 147(3), 969-977. https://doi.org/10.1104/pp.108.118232
  • Muiruri, K. S., Britt, A., Amugune, N. O., Nguu, E. K., Chan, S., & Tripathi, L. (2017). Expressed centromere specific histone 3 (CENH3) variants in cultivated triploid and wild diploid bananas (Musa spp.). Frontiers in Plant Science, 8, 1034. https://doi.org/10.3389/fpls.2017.01034
  • Murata, M. (2014). Minichromosomes and artificial chromosomes in Arabidopsis. Chromosome Research, 22(2), 167-178. https://doi.org/10.1007/s10577-014-9421-0
  • Nagaki, K., Cheng, Z., Ouyang, S., Talbert, P. B., Kim, M., Jones, K. M., Henikoff, S., Buell, C. R., & Jiang, J. (2004). Sequencing of a rice centromere uncovers active genes. Nature Genetics, 36(2), 138-145. https://doi.org/10.1038/ng1289
  • Naylor, R. L., Falcon, W. P., Goodman, R. M., Jahn, M. M., Sengooba, T., Tefera, H., & Nelson, R. J. (2004). Biotechnology in the developing world: A case for increased investments in orphan crops. Food Policy, 29(1), 15-44. https://doi.org/10.1016/j.foodpol.2004.01.002
  • O’Neill, C. M., & Bancroft, I. (2000). Comparative physical mapping of segments of the genome of Brassica oleracea var. Alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. The Plant Journal: For Cell and Molecular Biology, 23(2), 233-243. https://doi.org/10.1046/j.1365-313x.2000.00781.x
  • Paoletti, M. G., Gomiero, T., & Pimentel, D. (2011). Introduction to the Special Issue: Towards A More Sustainable Agriculture. Critical Reviews in Plant Sciences, 30(1-2), 2-5. https://doi.org/10.1080/07352689.2011.553148
  • Palmer, D. K., O’Day, K., Trong, H. L., Charbonneau, H., & Margolis, R. L. (1991). Purification of the centromere-specific protein CENP-A and demonstration that it is a distinctive histone. Proceedings of the National Academy of Sciences of the United States of America, 88(9), 3734-3738. https://doi.org/10.1073/pnas.88.9.3734
  • Pretty, J. (2008). Agricultural sustainability: Concepts, principles and evidence. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1491), 447-465. https://doi.org/10.1098/rstb.2007.2163
  • Ramanatha Rao, V., & Hodgkin, T. (2002). Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell, Tissue and Organ Culture, 68(1), 1-19. https://doi.org/10.1023/A:1013359015812
  • Ravi, M., & Chan, S. W. L. (2010). Haploid plants produced by centromere-mediated genome elimination. Nature, 464(7288), 615-618. https://doi.org/10.1038/nature08842
  • Ribaut, J.-M., & Ragot, M. (2019). Modernising breeding for orphan crops: Tools, methodologies, and beyond. Planta, 250(3), 971-977. https://doi.org/10.1007/s00425-019-03200-8
  • Ronald, P. (2011). Plant Genetics, Sustainable Agriculture and Global Food Security. Genetics, 188(1), 11-20. https://doi.org/10.1534/genetics.111.128553
  • Ronald, P. C. (2014). Lab to Farm: Applying Research on Plant Genetics and Genomics to Crop Improvement. PLoS Biology, 12(6), e1001878. https://doi.org/10.1371/journal.pbio.1001878
  • Sanei, M., Pickering, R., Kumke, K., Nasuda, S., & Houben, A. (2011). Loss of centromeric histone H3 (CENH3) from centromeres precedes uniparental chromosome elimination in interspecific barley hybrids. Proceedings of the National Academy of Sciences, 108(33), E498-E505. https://doi.org/10.1073/pnas.1103190108
  • Saraswathy, N., & Ramalingam, P. (2011). Genome mapping. In N. Saraswathy & P. Ramalingam (Eds.), Concepts and Techniques in Genomics and Proteomics (pp. 77-93). Woodhead Publishing. https://doi.org/10.1533/9781908818058.77
  • Schmidt, T., & Heslop-Harrison, J. S. (1998). Genomes, genes and junk: The large-scale organization of plant chromosomes. Trends in Plant Science, 3(5), 195-199. https://doi.org/10.1016/S1360-1385(98)01223-0
  • Shamim, Z., & Armstrong, S. J. (2020). Using Genome In Situ Hybridization (GISH) to Distinguish the Constituent Genomes of Brassica nigra and B. rapa in the Hybrid B. juncea. In M. Pradillo & S. Heckmann (Eds.), Plant Meiosis: Methods and Protocols (pp. 69-78). Springer. https://doi.org/10.1007/978-1-4939-9818-0_7
  • Stajič, E., Kiełkowska, A., Murovec, J., & Bohanec, B. (2019). Deep sequencing analysis of CRISPR/Cas9 induced mutations by two delivery methods in target model genes and the CENH3 region of red cabbage (Brassica oleracea var. Capitata f. Rubra). Plant Cell, Tissue and Organ Culture (PCTOC), 139(2), 227-235. https://doi.org/10.1007/s11240-019-01665-9
  • Stoler, S., Keith, K. C., Curnick, K. E., & Fitzgerald-Hayes, M. (1995). A mutation in CSE4, an essential gene encoding a novel chromatin-associated protein in yeast, causes chromosome nondisjunction and cell cycle arrest at mitosis. Genes & Development, 9(5), 573-586. https://doi.org/10.1101/gad.9.5.573
  • Talbert, P. B., Masuelli, R., Tyagi, A. P., Comai, L., & Henikoff, S. (2002). Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. The Plant Cell, 14(5), 1053-1066. https://doi.org/10.1105/tpc.010425
  • Tek, A. L., Stevenson, W. R., Helgeson, J. P., & Jiang, J. (2004). Transfer of tuber soft rot and early blight resistances from Solanum brevidens into cultivated potato. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 109(2), 249-254. https://doi.org/10.1007/s00122-004-1638-4
  • Tek, A. L., Song, J., Macas, J., & Jiang, J. (2005). Sobo, a Recently Amplified Satellite Repeat of Potato, and Its Implications for the Origin of Tandemly Repeated Sequences. Genetics, 170(3), 1231-1238. https://doi.org/10.1534/genetics.105.041087
  • Tek, A. L., Kashihara, K., Murata, M., & Nagaki, K. (2010). Functional centromeres in soybean include two distinct tandem repeats and a retrotransposon. Chromosome Research, 18(3), 337-347. https://doi.org/10.1007/s10577-010-9119-x
  • Tek, A.L. (2013, Eylül). Moleküler sitogenetik yöntemlerle bitki genom analizi. Konya Tarla Bitkileri Kongresi. Konya.
  • Tek, A. L., Stupar, R. M., & Nagaki, K. (2015). Modification of centromere structure: A promising approach for haploid line production in plant breeding. Turkish Journal of Agriculture and Forestry, 39(4), 557-562. https://doi.org/10.3906/tar-1405-137
  • Varshney, R. K., & May, G. D. (2012). Next-generation sequencing technologies: Opportunities and obligations in plant genomics. Briefings in Functional Genomics, 11(1), 1-2. https://doi.org/10.1093/bfgp/els001
  • Vats, S., Kumawat, S., Kumar, V., Patil, G. B., Joshi, T., Sonah, H., Sharma, T. R., & Deshmukh, R. (2019). Genome Editing in Plants: Exploration of Technological Advancements and Challenges. Cells, 8(11), 1386. https://doi.org/10.3390/cells8111386
  • Wang, G., Zhang, X., & Jin, W. (2009). An overview of plant centromeres. Journal of Genetics and Genomics, 36(9), 529-537. https://doi.org/10.1016/S1673-8527(08)60144-7
  • Yu, W., Han, F., Gao, Z., Vega, J. M., & Birchler, J. A. (2007). Construction and behavior of engineered minichromosomes in maize. Proceedings of the National Academy of Sciences, 104(21), 8924-8929. https://doi.org/10.1073/pnas.0700932104
  • Yu, W., Yau, Y.-Y., & Birchler, J. A. (2016). Plant artificial chromosome technology and its potential application in genetic engineering. Plant Biotechnology Journal, 14(5), 1175-1182. https://doi.org/10.1111/pbi.12466
  • Zhong, C. X., Marshall, J. B., Topp, C., Mroczek, R., Kato, A., Nagaki, K., Birchler, J. A., Jiang, J., & Dawe, R. K. (2002). Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. The Plant Cell, 14(11), 2825-2836. https://doi.org/10.1105/tpc.006106

Contribution of Genetic and Chromosome Engineering Studies from Past to Present to Sustainable Agriculture and Plant Breeding

Year 2021, , 246 - 258, 30.03.2021
https://doi.org/10.29133/yyutbd.787094

Abstract

It is predicted that by 2050 the population will reach 9.2 billion and the demands for equal and basic needs must be met worldwide. Until today, various studies have been carried out to increase agricultural production. However, new technologies and methods that ensure higher yields per unit area should be developed and integrated into plant breeding programs. While contradictory practices to sustainable agriculture should still be reduced, productivity in agriculture can be increased by understanding plant biology, evolution, and genome structure. In addition, efficient use of genetic diversity, adaptation of knowledge from model plants to breeding programs, and the genetic resource potential of orphan plants will contribute to the development of new genotypes. So far, modern technologies such as gene transformation, DNA sequencing, genome mapping and genome editing have played an active role in understanding the genome structure in plants. Numerous chromosome engineering methods such as FISH, GISH, chromosome truncation via telomeres, mini chromosomes, detection of syntenic chromosomal loci between organisms, discovery of repetitive DNA elements and the use of structural CENH3 protein will also be a driving force in agricultural development. Agricultural research, benefiting from the advances in basic sciences, will support achieving the desired goal in the long term. Potentially, chromosome engineering methods contribute to the increase of agricultural production in the future. In this review article, we aim to create a discussion platform for researchers by providing unique perspectives synthesized from agriculture, breeding and genetics and bringing together the current and rapidly developing interdisciplinary thematic studies.

Project Number

118O670; 118Z589; COST-INDEPTH CA16212; YÖK 100/2000

References

  • Acquaah, G. (2009). Principles of Plant Genetics and Breeding. John Wiley & Sons. 1-22.
  • Agarwal, M., Shrivastava, N., & Padh, H. (2008). Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports, 27(4), 617-631. https://doi.org/10.1007/s00299-008-0507-z
  • Aguilar-Rivera, N., Michel-Cuello, C., & Cárdenas-González, J. F. (2019). Green Revolution and Sustainable Development. In W. Leal Filho (Ed.), Encyclopedia of Sustainability in Higher Education (pp. 833-850). Springer International Publishing.
  • Armstead, I., Huang, L., Ravagnani, A., Robson, P., & Ougham, H. (2009). Bioinformatics in the orphan crops. Briefings in Bioinformatics, 10(6), 645-653. https://doi.org/10.1093/bib/bbp036
  • Barampuram, S., & Zhang, Z. J. (2011). Recent advances in plant transformation. Methods in Molecular Biology (Clifton, N.J.), 701, 1-35. https://doi.org/10.1007/978-1-61737-957-4_1
  • Bennetzen, J. L., & Chen, M. (2008). Grass Genomic Synteny Illuminates Plant Genome Function and Evolution. Rice, 1(2), 109-118. https://doi.org/10.1007/s12284-008-9015-6
  • Birchler, J. A., Yu, W., & Han, F. (2008). Plant engineered minichromosomes and artificial chromosome platforms. Cytogenetic and Genome Research, 120(3-4), 228-232. https://doi.org/10.1159/000121071
  • Biscotti, M. A., Olmo, E., & Heslop-Harrison, J. S. P. (2015). Repetitive DNA in eukaryotic genomes. Chromosome Research: An International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology, 23(3), 415-420. https://doi.org/10.1007/s10577-015-9499-z
  • Bonierbale, M. W., Plaisted, R. L., & Tanksley, S. D. (1988). RFLP Maps Based on a Common Set of Clones Reveal Modes of Chromosomal Evolution in Potato and Tomato. Genetics, 120(4), 1095-1103.
  • Brodt, S., Six, J., Feenstra, G., Ingels, C. & Campbell, D. (2011) Sustainable Agriculture. Nature Education Knowledge 3(10):1. https://www.nature.com/scitable/knowledge/library/sustainable-agriculture-23562787/. Erişim tarihi: 12.05.2020.
  • Cerit, İ., Cömertpay, G., Oyucu, R., Çakir, B., Hatipoğlu, R., & Özkan, H. (2016). Melez Mısır Islahında In-Vivo Katlanmış Haploid Tekniğinde Kullanılan Farklı Inducer Genotiplerin Haploid İndirgeme Oranların Belirlenmesi. Tarla Bitkileri Merkez Araştırma Enstitüsü Dergisi, 25(1), 52-57. https://doi.org/10.21566/tarbitderg.280162
  • Chang, C., Bowman, J. L., & Meyerowitz, E. M. (2016). Field Guide to Plant Model Systems. Cell, 167(2), 325-339. https://doi.org/10.1016/j.cell.2016.08.031
  • Charlesworth, B., Sniegowski, P., & Stephan, W. (1994). The evolutionary dynamics of repetitive DNA in eukaryotes. Nature, 371(6494), 215-220. https://doi.org/10.1038/371215a0
  • Che, P., Anand, A., Wu, E., Sander, J. D., Simon, M. K., Zhu, W., Sigmund, A. L., Zastrow-Hayes, G., Miller, M., Liu, D., Lawit, S. J., Zhao, Z.-Y., Albertsen, M. C., & Jones, T. J. (2018). Developing a flexible, high-efficiency Agrobacterium-mediated sorghum transformation system with broad application. Plant Biotechnology Journal, 16(7), 1388-1395. https://doi.org/10.1111/pbi.12879
  • Clark, W. C. (2007). Sustainability Science: A room of its own. Proceedings of the National Academy of Sciences, 104(6), 1737-1738. https://doi.org/10.1073/pnas.0611291104
  • Cody, J. P., Swyers, N. C., McCaw, M. E., Graham, N. D., Zhao, C., & Birchler, J. A. (2015). Minichromosomes: Vectors for Crop Improvement. Agronomy, 5(3), 309-321. https://doi.org/10.3390/agronomy5030309
  • Cook, D. R., & Varshney, R. K. (2010). From genome studies to agricultural biotechnology: Closing the gap between basic plant science and applied agriculture. Current Opinion in Plant Biology, 13(2), 115-118. https://doi.org/10.1016/j.pbi.2010.03.003
  • Dhar, M. K., Kaul, S., & Kour, J. (2011). Towards the development of better crops by genetic transformation using engineered plant chromosomes. Plant Cell Reports, 30(5), 799-806. https://doi.org/10.1007/s00299-011-1001-6
  • Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., Peluso, P., Rank, D., Baybayan, P., Bettman, B., Bibillo, A., Bjornson, K., Chaudhuri, B., Christians, F., Cicero, R., Clark, S., Dalal, R., deWinter, A., Dixon, J., … Turner, S. (2009). Real-Time DNA Sequencing from Single Polymerase Molecules. Science, 323(5910), 133-138. https://doi.org/10.1126/science.1162986
  • Falistocco, E. (2020). Insight into the Chromosome Structure of the Cultivated Tetraploid Alfalfa (Medicago sativa subsp. Sativa L.) by a Combined Use of GISH and FISH Techniques. Plants, 9(4), 542. https://doi.org/10.3390/plants9040542
  • Faris, J., Sirikhachornkit, A., Haselkorn, R., Gill, B., & Gornicki, P. (2001). Chromosome Mapping and Phylogenetic Analysis of the Cytosolic Acetyl-CoA Carboxylase Loci in Wheat. Molecular Biology and Evolution, 18(9), 1720-1733. https://doi.org/10.1093/oxfordjournals.molbev.a003960
  • FAO (2020). Food and Agriculture organization. http://www.fao.org/sustainability/en/. Erişim 15.04.2020.
  • Fears, R. (2007). Genomıcs and genetıc resources for food and agrıculture. Commıssıon on genetıc resources for food and agrıculture. http://www.fao.org/3/a-k0174e.pdf. Erişim 12.06.2020.
  • Fleury, D., Baumann, U., & Langridge, P. (2012). Plant genome sequencing: Models for developing synteny maps and association mapping. In A. Altman & P. M. Hasegawa (Ed.), Plant Biotechnology and Agriculture (pp. 83-97). Academic Press.
  • Galasso, I., Harrison, G. E., Pignone, D., Brandes, A., & Heslop-harrison, J. S. (1997). The Distribution and Organization of Ty1-copia-like Retrotransposable Elements in the Genome of Vigna unguiculata (L.) Walp. (Cowpea) and its Relatives. Annals of Botany, 80(3), 327-333. https://doi.org/10.1006/anbo.1997.0443.
  • Gill, B. S., Friebe, B., & Endo, T. R. (1991). Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat (Triticum aestivum). Genome, 34(5), 830-839. https://doi.org/10.1139/g91-128
  • Govindaraj, M., Vetriventhan, M., & Srinivasan, M. (2015). Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genetics Research International, 2015, 431487. https://doi.org/10.1155/2015/431487
  • Gross, B. L., Kellogg, E. A., & Miller, A. J. (2014). Speaking of food: Connecting basic and applied plant science. American Journal of Botany, 101(10), 1597-1600. https://doi.org/10.3732/ajb.1400409
  • Harris, T. D., Buzby, P. R., Babcock, H., Beer, E., Bowers, J., Braslavsky, I., Causey, M., Colonell, J., Dimeo, J., Efcavitch, J. W., Giladi, E., Gill, J., Healy, J., Jarosz, M., Lapen, D., Moulton, K., Quake, S. R., Steinmann, K., Thayer, E., … Xie, Z. (2008). Single-molecule DNA sequencing of a viral genome. Science (New York, N.Y.), 320(5872), 106-109. https://doi.org/10.1126/science.1150427
  • Henikoff, S., Ahmad, K., Platero, J. S., & van Steensel, B. (2000). Heterochromatic deposition of centromeric histone H3-like proteins. Proceedings of the National Academy of Sciences of the United States of America, 97(2), 716-721. https://doi.org/10.1073/pnas.97.2.716
  • Heslop‐Harrison, J. (Pat), & Schmidt, T. (2012). Plant nuclear genome composition. In ELS. American Cancer Society. https://doi.org/10.1002/9780470015902.a0002014.pub2
  • Hidalgo, O., Pellicer, J., Christenhusz, M., Schneider, H., Leitch, A. R., & Leitch, I. J. (2017). Is there an upper limit to genome size? Trends in Plant Science, 22(7), 567-573. https://doi.org/10.1016/j.tplants.2017.04.005
  • Houben, A., & Schubert, I. (2003). DNA and proteins of plant centromeres. Current Opinion in Plant Biology, 6(6), 554-560. https://doi.org/10.1016/j.pbi.2003.09.007
  • Houben, A., Nasuda, S., & Endo, T. R. (2011). Plant B chromosomes. Methods in Molecular Biology (Clifton, N.J.), 701, 97-111. https://doi.org/10.1007/978-1-61737-957-4_5
  • Hribová, E., Neumann, P., Matsumoto, T., Roux, N., Macas, J., & Dolezel, J. (2010). Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing. BMC Plant Biology, 10, 204. https://doi.org/10.1186/1471-2229-10-204
  • Kato, A., Vega, J. M., Han, F., Lamb, J. C., & Birchler, J. A. (2005). Advances in plant chromosome identification and cytogenetic techniques. Current Opinion in Plant Biology, 8(2), 148-154. https://doi.org/10.1016/j.pbi.2005.01.014
  • Ku, H.-M., Vision, T., Liu, J., & Tanksley, S. D. (2000). Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny. Proceedings of the National Academy of Sciences, 97(16), 9121-9126. https://doi.org/10.1073/pnas.160271297
  • Kuppu, S., Ron, M., Marimuthu, M. P. A., Li, G., Huddleson, A., Siddeek, M. H., Terry, J., Buchner, R., Shabek, N., Comai, L., & Britt, A. B. (2020). A variety of changes, including CRISPR/Cas9-mediated deletions, in CENH3 lead to haploid induction on outcrossing. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13365
  • Lermontova, I., & Schubert, I. (2013). CENH3 for Establishing and Maintaining Centromeres. In J. Jiang & J. A. Birchler (Eds). Plant Centromere Biology (pp. 67-82). John Wiley & Sons, Ltd.
  • Lusser, M., Parisi, C., Plan, D., & Rodríguez-Cerezo, E. (2012). Deployment of new biotechnologies in plant breeding. Nature Biotechnology, 30(3), 231-239. https://doi.org/10.1038/nbt.2142
  • Mabhaudhi, T., Chimonyo, V. G. P., Hlahla, S., Massawe, F., Mayes, S., Nhamo, L., & Modi, A. T. (2019). Prospects of orphan crops in climate change. Planta, 250(3), 695-708. https://doi.org/10.1007/s00425-019-03129-y
  • Mandáková, T., & Lysak, M. A. (2008). Chromosomal Phylogeny and Karyotype Evolution in x=7 Crucifer Species (Brassicaceae). The Plant Cell, 20(10), 2559-2570. https://doi.org/10.1105/tpc.108.062166
  • McCouch, S. R. (2001). Genomics and Synteny. Plant Physiology, 125(1), 152-155. https://doi.org/10.1104/pp.125.1.152
  • Mehrotra, S., & Goyal, V. (2014). Repetitive sequences in plant nuclear DNA: Types, distribution, evolution and function. Genomics, Proteomics & Bioinformatics, 12(4), 164-171. https://doi.org/10.1016/j.gpb.2014.07.003
  • Michael, T. P., & VanBuren, R. (2020). Building near-complete plant genomes. Current Opinion in Plant Biology, 54, 26-33. https://doi.org/10.1016/j.pbi.2019.12.009
  • Mondini, L., Noorani, A., & Pagnotta, M. A. (2009). Assessing Plant Genetic Diversity by Molecular Tools. Diversity, 1(1), 19-35. https://doi.org/10.3390/d1010019
  • Moose, S. P., & Mumm, R. H. (2008). Molecular Plant Breeding as the Foundation for 21st Century Crop Improvement. Plant Physiology, 147(3), 969-977. https://doi.org/10.1104/pp.108.118232
  • Muiruri, K. S., Britt, A., Amugune, N. O., Nguu, E. K., Chan, S., & Tripathi, L. (2017). Expressed centromere specific histone 3 (CENH3) variants in cultivated triploid and wild diploid bananas (Musa spp.). Frontiers in Plant Science, 8, 1034. https://doi.org/10.3389/fpls.2017.01034
  • Murata, M. (2014). Minichromosomes and artificial chromosomes in Arabidopsis. Chromosome Research, 22(2), 167-178. https://doi.org/10.1007/s10577-014-9421-0
  • Nagaki, K., Cheng, Z., Ouyang, S., Talbert, P. B., Kim, M., Jones, K. M., Henikoff, S., Buell, C. R., & Jiang, J. (2004). Sequencing of a rice centromere uncovers active genes. Nature Genetics, 36(2), 138-145. https://doi.org/10.1038/ng1289
  • Naylor, R. L., Falcon, W. P., Goodman, R. M., Jahn, M. M., Sengooba, T., Tefera, H., & Nelson, R. J. (2004). Biotechnology in the developing world: A case for increased investments in orphan crops. Food Policy, 29(1), 15-44. https://doi.org/10.1016/j.foodpol.2004.01.002
  • O’Neill, C. M., & Bancroft, I. (2000). Comparative physical mapping of segments of the genome of Brassica oleracea var. Alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. The Plant Journal: For Cell and Molecular Biology, 23(2), 233-243. https://doi.org/10.1046/j.1365-313x.2000.00781.x
  • Paoletti, M. G., Gomiero, T., & Pimentel, D. (2011). Introduction to the Special Issue: Towards A More Sustainable Agriculture. Critical Reviews in Plant Sciences, 30(1-2), 2-5. https://doi.org/10.1080/07352689.2011.553148
  • Palmer, D. K., O’Day, K., Trong, H. L., Charbonneau, H., & Margolis, R. L. (1991). Purification of the centromere-specific protein CENP-A and demonstration that it is a distinctive histone. Proceedings of the National Academy of Sciences of the United States of America, 88(9), 3734-3738. https://doi.org/10.1073/pnas.88.9.3734
  • Pretty, J. (2008). Agricultural sustainability: Concepts, principles and evidence. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1491), 447-465. https://doi.org/10.1098/rstb.2007.2163
  • Ramanatha Rao, V., & Hodgkin, T. (2002). Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell, Tissue and Organ Culture, 68(1), 1-19. https://doi.org/10.1023/A:1013359015812
  • Ravi, M., & Chan, S. W. L. (2010). Haploid plants produced by centromere-mediated genome elimination. Nature, 464(7288), 615-618. https://doi.org/10.1038/nature08842
  • Ribaut, J.-M., & Ragot, M. (2019). Modernising breeding for orphan crops: Tools, methodologies, and beyond. Planta, 250(3), 971-977. https://doi.org/10.1007/s00425-019-03200-8
  • Ronald, P. (2011). Plant Genetics, Sustainable Agriculture and Global Food Security. Genetics, 188(1), 11-20. https://doi.org/10.1534/genetics.111.128553
  • Ronald, P. C. (2014). Lab to Farm: Applying Research on Plant Genetics and Genomics to Crop Improvement. PLoS Biology, 12(6), e1001878. https://doi.org/10.1371/journal.pbio.1001878
  • Sanei, M., Pickering, R., Kumke, K., Nasuda, S., & Houben, A. (2011). Loss of centromeric histone H3 (CENH3) from centromeres precedes uniparental chromosome elimination in interspecific barley hybrids. Proceedings of the National Academy of Sciences, 108(33), E498-E505. https://doi.org/10.1073/pnas.1103190108
  • Saraswathy, N., & Ramalingam, P. (2011). Genome mapping. In N. Saraswathy & P. Ramalingam (Eds.), Concepts and Techniques in Genomics and Proteomics (pp. 77-93). Woodhead Publishing. https://doi.org/10.1533/9781908818058.77
  • Schmidt, T., & Heslop-Harrison, J. S. (1998). Genomes, genes and junk: The large-scale organization of plant chromosomes. Trends in Plant Science, 3(5), 195-199. https://doi.org/10.1016/S1360-1385(98)01223-0
  • Shamim, Z., & Armstrong, S. J. (2020). Using Genome In Situ Hybridization (GISH) to Distinguish the Constituent Genomes of Brassica nigra and B. rapa in the Hybrid B. juncea. In M. Pradillo & S. Heckmann (Eds.), Plant Meiosis: Methods and Protocols (pp. 69-78). Springer. https://doi.org/10.1007/978-1-4939-9818-0_7
  • Stajič, E., Kiełkowska, A., Murovec, J., & Bohanec, B. (2019). Deep sequencing analysis of CRISPR/Cas9 induced mutations by two delivery methods in target model genes and the CENH3 region of red cabbage (Brassica oleracea var. Capitata f. Rubra). Plant Cell, Tissue and Organ Culture (PCTOC), 139(2), 227-235. https://doi.org/10.1007/s11240-019-01665-9
  • Stoler, S., Keith, K. C., Curnick, K. E., & Fitzgerald-Hayes, M. (1995). A mutation in CSE4, an essential gene encoding a novel chromatin-associated protein in yeast, causes chromosome nondisjunction and cell cycle arrest at mitosis. Genes & Development, 9(5), 573-586. https://doi.org/10.1101/gad.9.5.573
  • Talbert, P. B., Masuelli, R., Tyagi, A. P., Comai, L., & Henikoff, S. (2002). Centromeric localization and adaptive evolution of an Arabidopsis histone H3 variant. The Plant Cell, 14(5), 1053-1066. https://doi.org/10.1105/tpc.010425
  • Tek, A. L., Stevenson, W. R., Helgeson, J. P., & Jiang, J. (2004). Transfer of tuber soft rot and early blight resistances from Solanum brevidens into cultivated potato. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 109(2), 249-254. https://doi.org/10.1007/s00122-004-1638-4
  • Tek, A. L., Song, J., Macas, J., & Jiang, J. (2005). Sobo, a Recently Amplified Satellite Repeat of Potato, and Its Implications for the Origin of Tandemly Repeated Sequences. Genetics, 170(3), 1231-1238. https://doi.org/10.1534/genetics.105.041087
  • Tek, A. L., Kashihara, K., Murata, M., & Nagaki, K. (2010). Functional centromeres in soybean include two distinct tandem repeats and a retrotransposon. Chromosome Research, 18(3), 337-347. https://doi.org/10.1007/s10577-010-9119-x
  • Tek, A.L. (2013, Eylül). Moleküler sitogenetik yöntemlerle bitki genom analizi. Konya Tarla Bitkileri Kongresi. Konya.
  • Tek, A. L., Stupar, R. M., & Nagaki, K. (2015). Modification of centromere structure: A promising approach for haploid line production in plant breeding. Turkish Journal of Agriculture and Forestry, 39(4), 557-562. https://doi.org/10.3906/tar-1405-137
  • Varshney, R. K., & May, G. D. (2012). Next-generation sequencing technologies: Opportunities and obligations in plant genomics. Briefings in Functional Genomics, 11(1), 1-2. https://doi.org/10.1093/bfgp/els001
  • Vats, S., Kumawat, S., Kumar, V., Patil, G. B., Joshi, T., Sonah, H., Sharma, T. R., & Deshmukh, R. (2019). Genome Editing in Plants: Exploration of Technological Advancements and Challenges. Cells, 8(11), 1386. https://doi.org/10.3390/cells8111386
  • Wang, G., Zhang, X., & Jin, W. (2009). An overview of plant centromeres. Journal of Genetics and Genomics, 36(9), 529-537. https://doi.org/10.1016/S1673-8527(08)60144-7
  • Yu, W., Han, F., Gao, Z., Vega, J. M., & Birchler, J. A. (2007). Construction and behavior of engineered minichromosomes in maize. Proceedings of the National Academy of Sciences, 104(21), 8924-8929. https://doi.org/10.1073/pnas.0700932104
  • Yu, W., Yau, Y.-Y., & Birchler, J. A. (2016). Plant artificial chromosome technology and its potential application in genetic engineering. Plant Biotechnology Journal, 14(5), 1175-1182. https://doi.org/10.1111/pbi.12466
  • Zhong, C. X., Marshall, J. B., Topp, C., Mroczek, R., Kato, A., Nagaki, K., Birchler, J. A., Jiang, J., & Dawe, R. K. (2002). Centromeric retroelements and satellites interact with maize kinetochore protein CENH3. The Plant Cell, 14(11), 2825-2836. https://doi.org/10.1105/tpc.006106
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Details

Primary Language Turkish
Subjects Agricultural Engineering (Other), Agricultural, Veterinary and Food Sciences
Journal Section Articles
Authors

Sevim Kara Öztürk 0000-0001-7522-0575

Bilge Yıldırım 0000-0001-6593-4312

Hümeyra Yıldız 0000-0002-7791-6100

Ahmet L. Tek 0000-0002-3292-5142

Project Number 118O670; 118Z589; COST-INDEPTH CA16212; YÖK 100/2000
Publication Date March 30, 2021
Acceptance Date February 3, 2021
Published in Issue Year 2021

Cite

APA Kara Öztürk, S., Yıldırım, B., Yıldız, H., Tek, A. L. (2021). Geçmişten Günümüze Genetik ve Kromozom Mühendisliği Çalışmalarının Sürdürülebilir Tarım ve Bitki Islahına Katkısı. Yuzuncu Yıl University Journal of Agricultural Sciences, 31(1), 246-258. https://doi.org/10.29133/yyutbd.787094

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