DOI: https://doi.org/10.21498/2518-1017.16.2.2020.209257

Bioinformatic analysis of nucleotide sequences of the acetolactate synthase (als) gene of different members of the Poaceae family

А. В. Кирієнко, Н. Л. Щербак, Ю. В. Симоненко

Abstract


Purpose. Provide bioinformatic analysis and comparison of target regions of the acetolactate synthase (als) gene in several members of the Poaceae family and, on the basis of the obtained data, explore the possibility of creating a unified genetic construct for als gene editing using the CRISPR-Cas9 system.

Methods. The als gene sequences of various members of the Poaceae family were obtained from the NCBI: Nucleotide database. For comparison, a fragment of the imi-2 gene of wheat of the soft line ‘TealIMI11A’ was used in two regions of the 367–390 and 1729–1749 nucleotide sequences. The Sequence Viewer 3.37.0 tool was used to assess the presence of nucleotide substitutions in the working sequence of the imi-2 gene. The dendrogram was built using the “Blast Tree” tool from the NCBI: Blast: Nucleotide resource. Results. A comparative analysis of the nucleotide sequences of seven different species was carried out: soft wheat (Triticum aestivum L.), common wild oat (Avena fatua L.), barley (Hordeum vulgare L.), Asian rice (Oryza sativa L.), maize (Zea mays L.), aleppo grass (Sorghum halepense Pers.) and Tausch’s goatgrass (Aegilops tauschii Coss.). The dendrogram is based on the gene sequence als, showed that all studied genotypes can be divided into two blocks: the first block included maize and aleppo grass, and the second block, a separate branch includes Asian rice and common wild oat, barley, soft wheat and Tausch’s goatgrass. 367–390 nucleotide sequences of soft wheat showed the highest 100% homology to Asian rice, Tausch’s goatgrass and common wild oat. The lowest homo­logy was for maize and aleppo grass at 83.3%. Evaluation of the nucleotide sequence 1729–1749 showed no complete homology at the 100% level. It was the highest for barley and Tausch’s goatgrass – 95.2%, and the lowest for rice, maize and aleppo grass – 80.9% each.

Conclusions. The analysis confirms a significant degree of homology of the als gene sequence for various species of the Poaceae family, which allows us to create a universal genetic vector. However, taking into account the high degree of sequence homology for species such as soft wheat, Tausch’s goatgrass, barley, Asian rice and common wild oat, it can be assumed that the corresponding genetic vector can be used with the greatest efficiency to alter the als gene of these genotypes.


Keywords


common wheat; herbicide resistance; gene als; genome editing

References


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Mallory-Smith, C. A., & Retzinger, E. J. Jr. (2003). Revised classification of herbicides by site of action for weed resistance management strategies weed technology. Weed Technol., 17(3), 605–619. doi: 10.1614/0890-037x(2003)017[0605:rcohbs]2.0.co;2

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McCourt, J. A., & Duggleby, R. G. (2006). Acetohydroxyacid synthase and its role in the biosynthetic pathway for branched-chain amino acids. Amino Acids., 31(2), 173–210. doi: 10.1007/s00726-005-0297-3

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Yu, Q., & Powles, S. B. (2014). Resistance to AHAS inhibitor herbicides: current understanding. Pest Manag. Sci., 70(9), 1–11. doi: 10.1002/ps.3710

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Anderson, J. A., Matthiesen, L., & Hegstad, J. (2004). Resistance to an imidazolinone herbicide is conferred by a gene on chromosome 6DL in the wheat line cv. 9804. Weed Sci., 52(1), 83–90. doi: 10.1614/WS-03-055R

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Dubey, S., Bist, R., & Misra, S. (2017). Sodium azide induced mutagenesis in wheat plant. World J. Pharm. Res. Sci., 6(10), 294–304. doi: 10.20959/wjpps201710-10199

Jafri, I. F., Khan, A. H., & Gulfishan, M. (2011). Genotoxic effects of 5-bromouracil on cytomorphological characters of Cichorium intybus L. Afr. J. Biotechnol., 10(52), 10595–10599. doi: 10.5897/AJB11.412

Jiang, F., & Doudna, J. (2017). CRISPR-Cas9 structures and mechanisms. Annu. Rev. Biophys., 22(46), 505–529. doi: 10.1146/annurev-biophys-062215-010822

Zhang, R., Liu, J., Chai, Z., Chen, S., Bai, Y., Zong, Y., … Gao, C. (2019). Generation of herbicide tolerance traits and a new selectable marker in wheat using base editing. Nat. Plants, 5(5), 480–485. doi: 10.1038/s41477-019-0405-0

Leach, L. J., Belfield, E. J., Jiang, C., Brown, C., Mithani, A., & Harberd, N. P. (2014). Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat. BMC Genomics, 15(276), 1–19. doi: 10.1186/1471-2164-15-276

Dvorak, J., Luo, M.-C., Yang, Z.-L., & Zhang, H.-B. (1998). The structure of the Aegilops tauschii genepool and the evolution of hexaploid wheat. Theor Appl Genet., 97(4), 657–670. doi: 10.1007/s001220050942

Beckie, H. J., Warwick, S. I., & Sauder, C. A. (2012). Basis for herbicide resistance in canadian populations of wild oat (Avena fatua). Weed Sci., 60(1), 10–18. doi: 10.1614/WS-D-11-00110.1

Piao, Z., Wang, W., Wei, Y., Zonta, F., Wan, C., Bai, J., … Fang, J. (2018). Characterization of an acetohydroxy acid synthase mutant conferring tolerance to imidazolinone herbicides in rice (Oryza sativa). Planta, 247(3), 693–703. doi: 10.1007/s00425-017-2817-2

Wenefrida, I., Utomo, H. S., Meche, M. M., & Nash, J. L. (2007). Inheritance of herbicide resistance in two germplasm lines of Clearfield rice (Oryza sativa L.). Can. J. Plant Sci., 87(3), 659–669. doi: 10.4141/P05-086


GOST Style Citations


1. Bo Bo A., Won O. J., Sin H. T. et al. Mechanisms of herbicide resistance in weeds. Korean J. Environ. Agric. Sci. 2017. Vol. 44. P. 1–15. doi: 10.7744/kjoas.2017000

2. Mallory-Smith C. A., Retzinger E. J. Jr. Revised classification of herbicides by site of action for weed resistance management stra­tegies weed technology. Weed Technol. 2003. Vol. 17, Iss. 3. P. 605–619. doi: 10.1614/0890-037X(2003)017[0605:RCOHBS]2.0.CO;2

3. Pang S. S., Duggleby R. G., Guddat L. W. Crystal structure of yeast acetohydroxyacid synthase: a target for herbicidal inhibitors. J. Mol. Biol. 2002. Vol. 317, Iss. 2. P. 249–262.                          doi: 10.1006/jmbi.2001.5419

4. Tan S., Evans R. R., Dahmer M. L. et al. Imidazolinone-tolerant crops: history, current status and future. Pest Manag. Sci. 2005. Vol. 61, Iss. 3. P. 246–257. doi: 10.1002/ps.993

5. Duggleby R. G., Pang S. S., Yu H., Guddat L. W. Systematic characterization of mutations in yeast acetohydroxyacid synthase. Eur. J. Biochem. 2003. Vol. 270, Iss. 13. P. 2895–2904. doi: 10.1046/j.1432-1033.2003.03671.x

6. McCourt J. A., Duggleby R. G. Acetohydroxyacid synthase and its role in the biosynthetic pathway for branched-chain amino acids. Amino Acids. 2006. Vol. 31, Iss. 2. P. 173–210. doi: 10.1007/s00726-005-0297-3

7. Lee H., Rustgia S., Kumara N. et al. Single nucleotide mutation in the barley acetohydroxy acid synthase (AHAS) gene confers resistance to imidazolinone herbicides. PNAS.  2011. Vol. 108, Iss. 21. P. 8909–8913. doi: 10.1073/pnas.1105612108.

8. Yu Q., Powles S. B. Resistance to AHAS inhibitor herbicides: current understanding. Pest Manag. Sci. 2014. Vol. 70, Iss. 9. P. 1–11. doi: 10.1002/ps.3710

9. Domínguez-Mendez R., Alcántara-de la Cruz R.,Rojano-Delgado A. M. et al. Multiple mechanisms are involved in new imazamox-resistant varieties of durum and soft wheat. Sci. Rep. 2017. Vol. 7, Iss. 1. 14839. doi: 10.1038/s41598-017-13874-3

10. Pozniak C. J., Hucl P. J. Genetic analysis of imidazolinone resistance in mutation-derived lines of common wheat. Crop Sci. 2004. Vol. 44, Iss. 1. P. 23–30. doi: 10.2135/cropsci2004.0023

11. Anderson J. A., Matthiesen L., Hegstad J. Resistance to an imi­dazolinone herbicide is conferred by a gene on chromosome 6DL in the wheat line cv. 9804. Weed Sci. 2004. Vol. 52, Iss. 1. P. 83–90. doi: 10.1614/ws-03-055r

12. Patent US2004/0237134A1 Wheat plants having increased resistance to imidazoline herbicides /  Pozniak C. J., Hucl P. J. ; Sutherland Asbill & Brennan Llp, 999 Achtree Street, N.E. Atlanta, GA 30309 (US).Nov. 25, 2004.

13. Newhouse K. E., Smith W. A., Starrett M. A. et al. Tolerance to imidazolinone herbicides in wheat. Plant Physiol. 1992. Vol. 100, Iss. 2. P. 882–886. doi: 10.1104/pp.100.2.882

14. Dubey S., Bist R., Misra S. Sodium azide induced mutagenesis in wheat plant. World J. Pharm. Pharm. Sci. 2017. Vol. 6, Iss. 10. P. 294–304. doi: 10.20959/wjpps201710-10199

15. Jafri I. F., Khan A. H., Gulfishan M. Genotoxic effects of 5-bromouracil on cytomorphological characters of Cichorium intybus L. Afr. J. Biotechnol. 2011. Vol. 10, Iss. 52. P. 10595–10599. doi: 10.5897/AJB11.412

16. Jiang F., Doudna J. CRISPR-Cas9 structures and mechanisms. Annu. Rev. Biophys. 2017. Vol. 22, Iss. 46. P. 505–529. doi: 10.1146/annurev-biophys-062215-010822

17. Zhang R., Liu J., Chai Z., et al. Generation of herbicide tolerance traits and a new selectable marker in wheat using base editing. Nat. Plants. 2019. Vol. 5, Iss. 5. P. 480–485. doi: 10.1038/s41477-019-0405-0

18. Leach L. J., Belfield E. J., Jiang C. et al. Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat. BMC Genomics. 2014. Vol. 15, Iss. 276. P. 1–19.  doi: 10.1186/1471-2164-15-276

19. Dvorak J., Luo M.-C., Yang Z.-L. et al. The structure of the Aegi­lops tauschii genepool and the evolution of hexaploid wheat. Theor. Appl. Genet. 1998. Vol. 97, Iss. 4. P. 657–670. doi: 10.1007/s001220050942

20. Beckie H. J., Warwick S. I., Sauder C. A. Basis for herbicide resistance in canadian populations of wild oat (Avena fatua). Weed Sci. 2012. Vol. 60, Iss. 1. P. 10–18. doi: 10.1614/WS-D-11-00110.1

21. Piao Z., Wang W., Wei Y. et al. Characterization of an acetohydroxy acid synthase mutant conferring tolerance to imidazolinone herbicides in rice (Oryza sativa). Planta, 2018. Vol. 247, Iss. 3. P. 693–703. doi: 10.1007/s00425-017-2817-2

22. Wenefrida I., Utomo H. S., Meche M. M., Nash J. L. Inheritance of herbicide resistance in two germplasm lines of Clearfield rice (Oryza sativa L.). Can. J. Plant Sci. 2007. Vol. 87, Iss. 3. P. 659–669. doi: 10.4141/P05-086







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DOI: 10.21498/2518-1017

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