Abstract
Aim. Development of an algorithm for creating ILP markers suitable for breeding studies of durum wheat (Triticum durum) and some other types of cereals. Methods. Use of classical bioinformatics tools to locate potential intron sites of target genes in T. durum suitable for use as ILP markers based on homology of T. durum contigs and rice (Oryza sativa) coding sequences. Analysis of exon-intron structure of homologous genes in O. sativa, Hordeum vulgare, Aegilops tauschii and Triricum aestivum followed by selection of appropriate primers for potential ILP markers. Results. A number of potential location sites of target introns in T. durum contig sequences were identified. Degenerate primers were designed for them, taking into account the analysis of the exon-intron structure of the corresponding homologous genes in O. sativa, H. vulgare, A. tauschii and T. aestivum. Conclusions. An algorithm for the creation of ILP markers was developed, which can be used in molecular genetic studies of plants in the case of the absence or incomplete sequenced genome of the studied species and the lack of information about the exon-intron structure of their genes. A number of potential ILP markers that can be used for cereals, in particular T. durum, have been identified.
Publisher
Institute of Molecular Biology and Genetics (NAS Ukraine)
Reference11 articles.
1. 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.
2. Choi H. K., Kim D., Uhm T., Limpens E., Lim H., Mun J. H., Kalo P., Penmetsa R. V., Seres A., Kulikova O., Roe B. A., Bisseling T., Kiss G. B., Cook D. R. A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa. Genetics. 2004. Vol. 166 (3). P. 1463–1502. doi: 10.1534/genetics.166.3.1463.
3. Rabokon A. N., Demkovich A. E., Pirko Ya. V., Blume Ya. B. Studing of ß-tubulin gene intron length polymorphism of Triticum aestivum L. and Hordeum vulgare L. varieties. Factors in Experimental Evolution of Organisms. 2015. Vol. 17. P. 82–86. [in Ukranian]
4. Yang L., Jin G., Zhao X., Zheng Y., Xu Z., Wu W. PIP: a database of potential intron polymorphism markers. Bioinformatics. 2007. Vol. 23 (16). P. 2174–2177. doi: 10.1093/bioinformatics/btm296.
5. Duvick J., Fu A., Muppirala U., Sabharwal M., Wilkerson M. D., Lawrence C. J., Lushbough C., Brendel V. PlantGDB: a resource for comparative plant genomics. Nucl. Acids Res. 2008. Vol. 36. P. 959–965. doi: 10.1093/nar/gkm1041.