Journal of Siberian Federal University. Biology: Virtual In Silico PCR in Two-Dimensional Format as a Tool for Elucidating Phylogenetic Relationship in Allopolyploid Forms with Wheats and Their Wild Relatives Aegilops Used as an Example

Journal of Siberian Federal University. Biology / Virtual In Silico PCR in Two-Dimensional Format as a Tool for Elucidating Phylogenetic Relationship in Allopolyploid Forms with Wheats and Their Wild Relatives Aegilops Used as an Example

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Issue: Journal of Siberian Federal University. Biology. 2024 17 (1)
Authors: Kiryanova, Olga Yu.; Kuluev, Azat R.; Gubaydullin, Irek M.; Kuluev, Bulat R.; Chemeris, Alexey V.
Contact information: Kiryanova, Olga Yu. : Ufa State Petroleum Technological University, Ufa, Russian Federation; ;; Kuluev, Azat R.: Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre RAS, Ufa, Russian Federation; ORCID: 0000-0002-8563-1244; Gubaydullin, Irek M. : Ufa State Petroleum Technological University; Institute of Petrochemistry and Catalysis RAS Ufa, Russian Federation; ORCID: 0000-0002-9848-2882; Kuluev, Bulat R. : Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre RAS, Ufa, Russian Federation; ORCID: 0000-0002-1564-164X; Chemeris, Alexey V. : Institute of Biochemistry and Genetics – Subdivision of the Ufa Federal Research Centre RAS Ufa, Russian Federation; ORCID: 0000-0002-8917-0449
Keywords: Triticum aestivum; Aegilops tauschii; Triticum urartu; Aegilops speltoides; Triticum aestivum; Aegilops tauschii; Triticum urartu; Aegilops spletoides; in silico RAPD analysis; computer simulation of PCR; genomic barcoding
Abstract: Identification of natural donors of three bread wheat (Triticum aestivum L.) BAD subgenomes is of great importance for developing technologies aimed at improving this crop. The question about the species and subspecies of the wheat–Aegilops alliance serving as donors of the B and A subgenomes remains unanswered, while the Aegilops tauschii subspecies of strangulata is considered as a donor of the D subgenome. To identify the donor species of subgenomes of polypoid forms, the comparison of the nucleotide sequences of various genes, as well as fragments of repetitive DNA, is performed to construct phylogenetic trees. In that case, however, only one or a few genetic systems or loci are taken into analysis. The genomic barcoding proposed by the authors, which is not tied to any genetic system, has an advantage, since in silico RAPD analysis «finds» fragments matching in size in the entire genome, making, as it were, a complete «slice» of it. To estimate the phylogenetic relationship of different wheat species, we used the method of virtual multiplex RAPD analysis with 20 undecamer primers, which made it possible to create genomic barcodes of these species and compile two- dimensional maps for individual chromosomes of the analyzed wheat species. The proposed method of computer analysis of genomes showed that T. aestivum subgenome D and Ae. tauschii are very similar to each other, which may indicate their common origin. No such definite conclusions could be drawn about the donors of subgenomes A and B, which is probably due to the more ancient association of these subgenomes in tetraploid wheat and the accumulation of a larger number of mutations over this time
Pages: 45–63
EDN: OIPJJV
Paper at repository of SibFU: https://elib.sfu-kras.ru/handle/2311/152808

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