Perspectives for study of Brachypodium distachyon as a model object for genetic and biochemical study in Kazakhstan
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Keywords:
model plant object, genomics, metabolomics, sequencing, genome, phylogenetics, morphology, biofuel, biochemistry, lifecycle, transformation, wheat, rice, barley, switchgrassAbstract
The species so far the most used as model plant, Arabidopsis thaliana, has provided a wealth of useful information and valuable tools for understanding plant biology. However, Arabidopsis is too phylogenetically distant from the temperate cereals to be used as a model system for cereal-specific metabolisms and responses to the environment. For this reason, Brachypodium distachyon has been recently proposed as a new model for grasses and temperate cereals. It has many qualities that make it an excellent model organism for functional genomics research in temperate grasses, cereals like barley and wheat, and dedicated biofuel crops such as switchgrass. These attributes include small genome, which is fully sequenced, a small physical stature, self-fertility, a short lifecycle, simple growth requirements, and an efficient transformation system.References
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23. Thole V., Peraldi A., Worland B., Nicholson P., Doonan J.H., Vain Ph. T-DNA mutagenesis in
Brachypodium distachyon. Journal of Experimental Botany, 2012, Vol. 63, Issue 2, Pp. 567-576.
24. Bennett M.D., Leitch I.J. Nuclear DNA amounts in angiosperms: progress, problems and prospects. Annals of Botany, 2005, Vol. 95, Pp. 45–90.
25. Vogel J.P., Gu Y.Q., Twigg P. et al. EST sequencing and phylogenetic analysis of the model
grass Brachypodium distachyon. Theoretical and Applied Genetics, 2006, Vol. 113, No. 2, Pp. 186-195.
26. Vain P., Worland B., Thole V. et al. Agrobacterium- mediated transformation of the temperate grass Brachypodium distachyon (genotype Bd21) for T-DNA insertional mutagenesis. Plant Biotechnology Journal, 2008, Vol. 6, No. 3, Pp. 236–245.
27. Vogel J., Hill T. High-efficiency Agrobacterium- mediated transformation of Brachypodium
distachyon inbred line Bd21–3. Plant Cell Reports, 2008, Vol. 27, Pp. 471–478
28. Vogel J.P., Garvin D.F., Leong O.M., Hayden D.M. Agrobacterium-mediated transformation and inbred line development in the model grass Brachypodium distachyon. Plant Cell, Tissue and Organ Culture. 2006, Vol. 84, Pp. 100179–100191
29. Filiz E., Ozdemir B.S., Budak F., Vogel J.P., Tuna M., Budak H. Molecular, morphological and
cytological analysis of diverse Brachypodium distachyon inbred lines. Genome, 2009, Vol. 52, Pp. 876–890
30. Vogel J.P., Tuna M., Budak H., Huo N., Gu Y.Q., Steinwand M.A. Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biology, 2009, Vol. 9, P.88
31. Garvin D.F., McKenzie N., Vogel J.P., Mockler T.C., Blankenheim Z.J., Wright J., Cheema J.J.,
Dicks J., Huo N., Hayden D.M., Gu Y., Tobias C., Chang J.H., Chu A., Trick M., Michael T.P., Bevan
M.W., Snape J.W. An SSR-based genetic linkage map of the model grass Brachypodium distachyon. Genome, 2009, Vol. 53, Pp. 1–13
32. Huo N., Gu Y.Q., Lazo G.R., Vogel J.P., Coleman-Derr D., Luo M.C., Thilmony R., Garvin D.F., Anderson O.D. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome, 2006, Vol. 49, No. 9, Pp. 1099–1108
33. Huo N., Lazo G.R., Vogel J.P et al. The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Functional and Integrative Genomics, 2008, Vol. 8, Pp. 135–147
34. Gu Y.Q., Ma Y., Huo N., Vogel J.P., You F.M., Lazo G.R., Nelson W.M., Soderlund C., Dvorak J., Anderson O.D., Luo M.C. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics, 2009, Vol. 10, P. 496
35. Omirbekova N., Zhussupova A., Malik A., Almaganbetov Zh., Zhakaeva L. Preliminary study
on activity of nitrogen enzymes and energy metabolism in Brachypodium distachyon. 1st International
Brachypodium Conference. Abstract book, P. 78, Abstract No. S6.P01
36. Zhussupova A., Omirbekova N. Initial study on activity of enzymes, participating in nitrogen and energy metabolism in Brachypodium distachyon. SEB, 2013. Plant abstracts 175, P3.32
2. Kellogg E.A. Evolutionary history of the grasses. Plant Physiology, 2001, Vol. 125, Pp. 1198- 1205.
3. Gaut B.S. Evolutionary dynamics of grass genomes. New Phytologist, 2002, Vol. 154, Pp. 15-28.
4. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature, 2005, 436, 793–800.
5. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G,
Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK,
Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS. The Sorghum bicolor genome and the diversification of grasses. Nature, 2009, Vol. 457, Pp. 551–556.
6. Wei F, Coe E, Nelson W, Bharti AK, EnglerF, Butler E, Kim H, Goicoechea JL, Chen M, Lee S, Fuks G, Sanchez-Villeda H, Schroeder S, Fang Z, McMullen M, Davis G, Bowers JE, Paterson AH, Schaeffer M, Gardiner J, Cone K, Messing J, Soderlund C, Wing RA. Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genetics, 2007, Vol.3, No.7, e123.
7. G. Moore, K.M. Devos, Z. Wang, M.D. Gale. Cereal genome evolution. Grasses, line up and form a circle. Current Biology, 1995, Vol.5, Pp. 737-739.
8. Salamini F., Ozkan H., Brandolini A., Schafer- Pregl R., Martin W. Genetics and geography of
wild cereal domestication in the near east. Nature Reviews. Genetics, 2002, Vol. 3, Pp. 429–441.
9. Draper J., Mur L.A., Jenkins G., Ghosh- Biswas G.C., Bablak P., Hasterok R., Routledge A.P. Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiology, 2001, Vol. 127, Pp. 1539–1555.
10. Watson L. and Dallwitz M.J. 1992 onwards. The grass genera of the world: descriptions, illustrations,
identification, and information retrieval; including synonyms, morphology, anatomy, physiology, phytochemistry, cytology, classification, pathogens, world and local distribution, and references. Version: 28th November 2005.
11. Callaway E. Stone Age flour found across Europe. Published online 18 October 2010 | Nature
| doi:10.1038/news.2010.549 12. Aragon-Alcaide L., Miller T, Schwarzacher T, Reader S, Moore G. A cereal centromeric sequence. Chromosoma, 1996, Vol. 105, No. 5, Pp. 261–268.
13. Foote T.N., Griffiths S., Allouis S., Moore G. Construction and analysis of a BAC library in the grass Brachypodium sylvaticum: its use as a tool to bridge the gap between rice and wheat in elucidating gene content. Functional and integrative genomics, 2004, Vol. 4, Pp. 26–33.
14. Moore G., Gale M.D., Kurata N., Flavell R. Molecular analysis of small grain cereals. Nature Biotechnology, 1993, Vol. 11, Pp. 584–589.
15. Griffiths S., Sharp R., Foote T.N., Bertin I., Wanous M., Reader S., Colas I., Moore G. Molecular
characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature, 2006, Vol. 439, Pp. 749–752.
16. Turner A., Beales J., Faure S., Dunford R.P., Laurie D.A. The pseudo-response regulator Ppd-H1
provides adaptation to photoperiod in barley. Science, 2005, Vol. 310, Pp.1031–1034.
17. Cucciolla V., Borriello A., Oliva A., Galletti P., Zappia V., Della Ragione F. Resveratrol: from basic science to the clinic. Cell Cycle, 2007, Vol. 6, Pp. 2495-510.
18. Maor R., Shirasu K. The arms race continues: battle strategies between plants and fungal pathogens. Current opinion in microbiology, 2005, Vol. 8, Pp. 399-404.
19. Allwood J.W., Ellis D.I., Heald J.K., Goodacre R., Mur L.A. Metabolomic approaches reveal that phospatidic and phospatidyl glycerol phospholipids are major discriminatory non-polar metabolites in
responses by Brachypodium distachyon to challenge by Magnaporthe grisea. The Plant journal: for cell and molecular biology, 2006, Vol. 46, Pp. 351-68.
20. The International Brachypodium Initiative. Genome sequencing and analysis of the model grass
Brachypodium distachyon Pp. 763-768.
21. Thole V., Worland B., Wright J., Bevan M.W., Vain Ph. Distribution and characterization
of more than 1000 T-DNA tags in the genome of Brachypodium distachyon community standard line
Bd21. Plant Biotechnology Journal, 2010, Vol. 8. Issue 6, Pp. 734–747.
22. Vain Ph., Thole V., Worland B., Opanowicz M., Bush M.S., Doonan J.H. A T-DNA mutation in the RNA helicase eIF4A confers a dose-dependent dwarfing phenotype in Brachypodium distachyon. The Plant Journal, 2011, Vol. 66, Issue 6, Pp. 929–940.
23. Thole V., Peraldi A., Worland B., Nicholson P., Doonan J.H., Vain Ph. T-DNA mutagenesis in
Brachypodium distachyon. Journal of Experimental Botany, 2012, Vol. 63, Issue 2, Pp. 567-576.
24. Bennett M.D., Leitch I.J. Nuclear DNA amounts in angiosperms: progress, problems and prospects. Annals of Botany, 2005, Vol. 95, Pp. 45–90.
25. Vogel J.P., Gu Y.Q., Twigg P. et al. EST sequencing and phylogenetic analysis of the model
grass Brachypodium distachyon. Theoretical and Applied Genetics, 2006, Vol. 113, No. 2, Pp. 186-195.
26. Vain P., Worland B., Thole V. et al. Agrobacterium- mediated transformation of the temperate grass Brachypodium distachyon (genotype Bd21) for T-DNA insertional mutagenesis. Plant Biotechnology Journal, 2008, Vol. 6, No. 3, Pp. 236–245.
27. Vogel J., Hill T. High-efficiency Agrobacterium- mediated transformation of Brachypodium
distachyon inbred line Bd21–3. Plant Cell Reports, 2008, Vol. 27, Pp. 471–478
28. Vogel J.P., Garvin D.F., Leong O.M., Hayden D.M. Agrobacterium-mediated transformation and inbred line development in the model grass Brachypodium distachyon. Plant Cell, Tissue and Organ Culture. 2006, Vol. 84, Pp. 100179–100191
29. Filiz E., Ozdemir B.S., Budak F., Vogel J.P., Tuna M., Budak H. Molecular, morphological and
cytological analysis of diverse Brachypodium distachyon inbred lines. Genome, 2009, Vol. 52, Pp. 876–890
30. Vogel J.P., Tuna M., Budak H., Huo N., Gu Y.Q., Steinwand M.A. Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biology, 2009, Vol. 9, P.88
31. Garvin D.F., McKenzie N., Vogel J.P., Mockler T.C., Blankenheim Z.J., Wright J., Cheema J.J.,
Dicks J., Huo N., Hayden D.M., Gu Y., Tobias C., Chang J.H., Chu A., Trick M., Michael T.P., Bevan
M.W., Snape J.W. An SSR-based genetic linkage map of the model grass Brachypodium distachyon. Genome, 2009, Vol. 53, Pp. 1–13
32. Huo N., Gu Y.Q., Lazo G.R., Vogel J.P., Coleman-Derr D., Luo M.C., Thilmony R., Garvin D.F., Anderson O.D. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome, 2006, Vol. 49, No. 9, Pp. 1099–1108
33. Huo N., Lazo G.R., Vogel J.P et al. The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Functional and Integrative Genomics, 2008, Vol. 8, Pp. 135–147
34. Gu Y.Q., Ma Y., Huo N., Vogel J.P., You F.M., Lazo G.R., Nelson W.M., Soderlund C., Dvorak J., Anderson O.D., Luo M.C. A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat. BMC Genomics, 2009, Vol. 10, P. 496
35. Omirbekova N., Zhussupova A., Malik A., Almaganbetov Zh., Zhakaeva L. Preliminary study
on activity of nitrogen enzymes and energy metabolism in Brachypodium distachyon. 1st International
Brachypodium Conference. Abstract book, P. 78, Abstract No. S6.P01
36. Zhussupova A., Omirbekova N. Initial study on activity of enzymes, participating in nitrogen and energy metabolism in Brachypodium distachyon. SEB, 2013. Plant abstracts 175, P3.32
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Zhussupova, A. I., N. Zh. Omirbekova, A. Malik, and Zh. Almaganbetov. 2013. “Perspectives for Study of Brachypodium Distachyon As a Model Object for Genetic and Biochemical Study in Kazakhstan”. International Journal of Biology and Chemistry 6 (2):13-19. https://ijbch.kaznu.kz/index.php/kaznu/article/view/93.
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