γ-tubulin gene intron length polymorphism of Arabidopsis thaliana

  • A. M. Rabokon
  • Yu. O. Bilonozhko
  • A. S. Postovoitovа
  • L. O. Kalafat
  • Ya. V. Pirko
  • Ya. B. Blume

Abstract

Aims. Verification of the possibility of using the γ-tubulin gene intron length polymorphism method in genetic studies of plants on the example of Arabidopsis thaliana. Methods. The γ-tubulin gene intron length polymorphism evaluating method was used. Amplified fragments DNA were fractionated by electrophoresis in non-denaturing polyacrylamide gel. DNA bands were detected using silver nitrate staining. Results. Arabidopsis was first time analyzed using the γ-tubulin gene intron length polymorphism method. During amplification with degenerate primers 2 amplicons (520 bp and 555 bp) were formed in all samples. However, using selected arabidopsis-specific primers for the second intron of the γ-tubulin genes, it was possible to find several samples that differ in their DNA profile. Conclusions. It is established that the proposed method can be used in molecular genetic studies of plants. Moreover, the developed specific primers for γ-tubulin gene introns can probably be used both for the study of Arabidopsis and related species. The use of degenerate primers can be useful in the study of plants for which there is no information about their genome.

Keywords: molecular-genetic markers, intron length polymorphism, γ-tubulin, A. thaliana.

References

Choi H.K., Luckow M.A., Doyle J., Cook D.R. Development of nuclear gene-derived molecular markers linked to legume genetic maps. Mol. Genet. Genomics. 2006. Vol. 276 (1). P. 56–70. doi: 10.1007/s00438-006-0118-8.

Khlestkina E.K. Molecular markers in genetic studies and breeding. Russ. J. Genetics. 2014. Vol. 4 (3). P. 2362–44. doi: 10.1134/S2079059714030022.

Pali V., Kumar S.V., Suchita X., Ravi R.S., Mehta N., Balkrishna S.V. Identification of microsatellite markers for fingerprinting popular Indian flax (Linum usitatissimum L.) cultivars and their utilization in seed genetic purity assessments. Austral. J. Crop. Sci. 2014. Vol. 8 (1). P. 119–126. doi: 10.15258/sst.2011.39.2.02.

Wang X., Zhao X., Zhu J., Wu W. Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.). DNA Res. 2005. Vol. 12 (6). P. 417–427. doi: 10.1093/dnares/dsi019.

Zhao X., Yang L., Zheng Y. et al. Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (Oryza rufipogon L.) in relation to the domestication of cultivated rice (O. sativa L.). J. Genet. Genomics. 2009. Vol. 36 (7). P. 435–442. doi: 10.1016/S1673-8527(08)60133-2.

Shu Y., Li Y., Zhu Y., Zhu Z. et al. Genome-wide identification of intron fragment insertion mutations and their potential use as SCAR molecular markers in the soybean. Theor. Appl. Genet. 2010. Vol. 121 (1). P. 1–8. doi: 10.1007/s00122-010-1285-x.

He C., Liu H., Su S., Lu Y. et al. Genome wide identification of candidate phosphate starvation responsive genes and the development of intron length polymorphism markers in maize. Plant Breed. 2015. Vol. 134 (1). P. 11–16. doi: 10.1111/pbr.12230.

Bardini M., Lee D., Donini P. et al. Tubulin-based polymorphism (TBP): a new tool, based on functionally relevant sequences, to assess genetic diversity in plant species. Genome. 2004. Vol. 47 (2). P. 281–291. doi: 10.1139/g03-132.

Rabokon A.N., Pirko Y.V., Demkovych A.Y., Blume Y.B. Comparative analysis of the efficiency of intron-length polymorphism of β-tubulin genes and microsatellite loci for flax varieties genotyping. Cytol. Genet. 2018. Vol. 5 2(1). P. 3–15. doi: 10.3103/S0095452718010115.

Rabokon A., Demkovich A., Sozinov A., Kozub N., Pirko Ya., Blume Ya. Intron length polymorphism of β-tubulin genes of Aegilops biuncialis Vis. Cell Biol. Int. 2019. Vol. 43. P. 1031–1039. doi: 10.1002/cbin.10886.

Postovoitova A.S., Yotka O.Y., Pirko Y.V., Blume Y.B. Molecular genetic evaluation of Ukrainian flax cultivars homogeneity based on intron length polymorphism of actin genes and microsatellite loci. Cytol. Genet. 2018. Vol. 52 (6). P. 448–460. doi: 10.3103/S0095452718060099.

Breviario D. Plant tubulin genes: regulatory and evolutionary aspects. In: Plant Microtubules. Plant Cell Monogr. (Ed. P. Nick). Berlin Heidelberg: Springer-Verlag, 2008. P. 207–232. doi: 10.1007/7089_2007_160.

Morello L., Breviario D. Plant spliceosomal introns: not only cut and paste. Curr. Genomics. 2008. Vol. 9. P. 227–238. doi: 10.2174/138920208784533629.

Farache D., Emorine L., Haren L., Merdes A. Assembly and regulation of γ-tubulin complexes. Open Biol. 2018. Vol. 8 (3). P. 170266. doi: 10.1098/rsob.170266.

Pirko Ya.V., Buy D.D., Postovoitova A.S., Rabokon A.M., Kalafat L.O., Blume Ya.B. New ILP method based on γ-tubulin genes intron length polymorphism. Reports Natl. Acad. Sci. Ukraine. 2018. No. 12. P. 1025–1030. [in Ukrainian] doi: 10.15407/dopovidi2018.12.087

Doyle J.J., Doyle J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bulletin. 1987. Vol. 19. P. 11–15.

Sambrook J., David W.R. Molecular Сloning: A Laboratory Manual. NY: Cold Spring Harbor, 2001. Vol. 2.

Benbouza H., Jacquemin J-M., Baudoin J-P., Mergeai G. Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gel. Biotechnol. Agron. Soc. Environ. 2006. Vol. 10 (2). P. 77–81.