New ilp method based on γ-tubulin genes intron length polymorphism

Authors

  • Ya.V. Pirko Institute of Food Biotechnology and Genomics of the NAS of Ukraine, Kiev
  • D.D. Buy Institute of Food Biotechnology and Genomics of the NAS of Ukraine, Kiev
  • A.S. Postovoitova Institute of Food Biotechnology and Genomics of the NAS of Ukraine, Kiev
  • A.M. Rabokon Institute of Food Biotechnology and Genomics of the NAS of Ukraine, Kiev
  • L.O. Kalafat Institute of Food Biotechnology and Genomics of the NAS of Ukraine, Kiev
  • Ya.B. Blume Institute of Food Biotechnology and Genomics of the NAS of Ukraine, Kiev

DOI:

https://doi.org/10.15407/dopovidi2018.12.087

Keywords:

gene, intron, length of introns, molecular genetic markers, polymorphism, γ-tubulin

Abstract

A new marker system for the estimation of a genetic diversity based on the γ-tubulin genes intron length polymorphism is proposed. A pair of degenerate primers to γ-tubulin genes was developed based on the characteristics of their exon-intron structures. The simplicity and versatility of the marker system in the moleculargenetic analysis of plants are demonstrated on species and varieties of Arabidopsis thaliana, Linum usitatissimum, Solanum tuberosum, Oryza sativa, Triticum aestivum.

Downloads

Download data is not yet available.

References

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

Rabokon, A. N., Demkovych, A. Ye., Pirko, Ya. V., & Blume, Ya. B. (2015). Intron length polymorphism of β-tubulin gene as an effective tool for genotyping of plants. Molecular and Applied Genetics (Minsk), 19, 35–44.

Morello, L., & Breviario, D. (2008). Plant spliceosomal introns: Not only cut and paste. Current Genomics, 9, 227–238. https://doi.org/10.2174/138920208784533629

Braglia, L., Manca, A., Mastromauro, F., & Breviario, D. (2010). cTBP: A successful intron length polymorphism (ILP)-based genotyping method targeted to well-defined experimental needs. Diversity, 2, 572–585. https://doi.org/10.3390/d2040572

Thomas, B. C., Rapaka, L., Lyons, E., Pedersen, B., & Freeling, M. (2007). Arabidopsis intragenomic conserved noncoding sequence. Proceedings of the National Academy of Sciences of the United States of America, 104, 3348–3353. https://doi.org/10.1073/pnas.0611574104

Li, X., Tan, L., Wang, L., Hu, S., & Sun, C. (2009). Isolation and characterization of conserved non-coding sequences among rice (Oryza sativa L.) paralogous regions. Molecular Genetics and Genomics, 281, 11–18. https://doi.org/10.1007/s00438-008-0388-4

Ferreira, A. O., Cardoso, H. G., Macedo, E. S., Breviario, D., & Arnholdt-Schmitt, B. (2009). Intron polymorphism pattern in AOX1b of wild St John’s wort (Hypericum perforatum) allows discrimination between individual plants. Physiologia Plantarum, 137, 520–531. https://doi.org/10.1111/j.1399-3054.2009.01291.x

Perumal, B. S., Sakharkar, K. R., Chow, V. T. K., Kangueane, P., & Sakharkar, M. K. (2005). Intron position conservation across eukaryotic lineages in tubulin genes. Frontiers in Bioscience, 10, 2412–2419.

Bardini, M., Lee, D., Donini, P., Mariani, A., Giani, S., Toschi, M., Lowe, C., & Breviario, D. (2004). Tubulin-based polymorphism (TBP): A new tool, based on functionally relevant sequences, to assess genetic diversity in plant species. Genome, 47(2), 281–291. https://doi.org/10.1139/g03-132

Pydiura, N., Pirko, Ya., Galinousky, D., Postovoitova, A., Yemets, A., Kilchevsky, A., & Blume, Ya. (2018). Genome-wide identification, phylogenetic classification, and exon-intron structure characterisation of the tubulin and actin genes in flax (Linum usitatissimum). Cell Biology International. https://doi.org/10.1002/cbin.11001

Ovechkina, Y., & Oakley, B. R. (2001). Gamma tubulin in plant cells. Methods in Cell Biology, 67, 195–212. https://doi.org/10.1016/S0091-679X(01)67014-6

Okonechnikov, K., Golosova, O., & Fursov, M. (2012). Unipro UGENE: A unified bioinformatics toolkit. Bioinformatics, 28, 1166–1167. https://doi.org/10.1093/bioinformatics/bts091

Sambrook, J. F., & Russell, D. W. (2001). Molecular cloning: A laboratory manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Benbouza, H., Jacquemin, J.-M., Baudoin, J.-P., & Mergeai, G. (2006). Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels. Biotechnology, Agronomy, Society and Environment, 10(2), 77–81.

Rabokon, A. N., Pirko, Ya. V., Demkovych, A. Ye., & Blume, Ya. B. (2018). Comparative analysis of the efficiency of intron-length polymorphism of β-tubulin genes and microsatellite loci for flax varieties genotyping. Cytology and Genetics, 52(1), 3–15.

Published

28.12.2018

How to Cite

Pirko, Y., Buy, D., Postovoitova, A., Rabokon, A., Kalafat, L., & Blume, Y. (2018). New ilp method based on γ-tubulin genes intron length polymorphism . Reports of the National Academy of Sciences of Ukraine, (12), 87–92. https://doi.org/10.15407/dopovidi2018.12.087