Bioinformatic analysis of chickpea acetohydroxyacid synthase gene

  • H. I. Slishchuk
  • N. E. Volkova
  • O. O. Zakharova
  • A. V. Korchmaryоvа
DOI: https://doi.org/10.7124/FEEO.v24.1127

Abstract

Aim. Analysis of homologues of chickpea gene encoding acetohydroxyacid synthase, by bioinformatics methods. Methods. Alignment of nucleotide sequences, UPGMA method, Maximum Composite Likelihood method, homologous modeling of three-dimensional structure of enzyme. Results. Homologues of the acetohydroxyacid syntase gene (AHAS) of  chickpea were found among representatives of different families. A certain level of conservativeness of mRNA homologues sequences of AHAS gene within the families was noted, including legumes. The distribution of clusters corresponds to the taxonomic position of the investigated plant species. The single nucleotide polymorphism
C / T at position 581, potentially associated with herbicide resistance, was detected. Based on the homologous modeling results, two models of the enzyme AHAS were constructed. The replacement of C / T, which leads to the replacement of the amino acids of alanine with valine, leads to a change in the conformation in the A chain of protein. Conclusions. Marker screening of the source breeding material by «real-time» polymerase chain reaction with the developed primers and the TaqMan probe to the polymorphic region of the AHAS gene will allow differentiating the herbicide «resistant» and «tolerant» alleles of the gene for the selection of target genotypes.

Keywords: chickpea, acetohydroxyacid syntase gene, single nucleotide polymorphism, resistance to herbicides.

References

Sichkar V.I., Burikina S.I., Velver M.O. Nut: fakti i perspektivi naukovih doslidzhen v sviti ta Ukrayini (oglyadova). Tavriysk. nauk. visnik. 2018. Vip. 99. S. 133–141. [in Ukrainian]

Bushulyan O.V., SIchkar V.I., Babayants O.V. Suchasna integrovana sistema zahistu posiviv nutu: metod. rekomend. Odesa: SGI NT. 2017. 26 s. [in Ukrainian]

Garcia M., Nouwens A., Lonhienne T., Guddata L. Comprehensive understanding of acetohydroxyacid synthase inhibition by different herbicide families. Proc. Natl. Acad. Sci. USA. 2017. Vol. 114 (7). P. E1091–E1100. doi: 10.1073/pnas.1616142114.

National Center for Biotechnology Information Database. URL: http://www.ncbi.nlm.nih.gov/ (Last accessed: 1.03.2019).

Kumar S., Stecher G., Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 2016. Vol. 33. P. 1870–1874. doi: 10.1093/molbev/msw054.

Sneath P., Sokal R. Numerical taxonomy: The principles and practice of numerical classification. San Francisco : W.H. Freeman & Co, 1973. 573 р.

Tamura K., Nei M., Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. USA. 2004. Vol. 101. P. 11030–11035. doi: 10.1073/pnas.0404206101.

Waterhouse A., Bertoni M., Bienert S. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018. Vol. 46 (W1). P. W296–W303. doi: 10.1093/nar/gky427.

Bienert S., Waterhouse A., de Beer T. et al. The SWISS-MODEL Repository – new features and functionality. Nucleic Acids Res. 2017. Vol. 45. P. D313–D319. doi: 10.1093/nar/gkw1132.

Guex N., Peitsch M., Schwede T. Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis. 2009. Vol. 30. P. S162–S173. doi: 10.1002/elps.200900140.

Benkert P., Biasini M., Schwede T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics. 2011. Vol. 27. P. 343–350. doi: 10.1093/bioinformatics/btq662.

Bertoni M., Kiefer F., Biasini M., Bordoli L., Schwede T. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Sci. Rep. 2017. Vol. 7 (1). P. 10480. doi: 10.1038/s41598-017-09654-8.

Untergasser A., Cutcutache I., Koressaar T. et al. Primer3 - new capabilities and interfaces. Nucl. Acids Res. 2012. Vol. 40 (15). P. e115. doi: 10.1093/nar/gks596.

Koressaar T., Remm M. Enhancements and modifications of primer design program Primer3. Bioinformatics. Vol. 23 (10). P. 1289–1291. doi: 10.1093/bioinformatics/btm091.