qPCR as a Selective Tool for Cytogenetics
qPCR is widely used in quantitative studies of plant genomes and transcriptomes. In this article, this method is considered as an auxiliary step in the preparation and selection of markers for FISH analysis. Several cases from the authors’ research on populations of the same species were reviewed, a...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-12-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/1/80 |
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| author | Mikhail G. Divashuk Ekaterina A. Nikitina Victoria M. Sokolova Anna I. Yurkina Alina A. Kocheshkova Olga V. Razumova Gennady I. Karlov Pavel Yu. Kroupin |
| author_facet | Mikhail G. Divashuk Ekaterina A. Nikitina Victoria M. Sokolova Anna I. Yurkina Alina A. Kocheshkova Olga V. Razumova Gennady I. Karlov Pavel Yu. Kroupin |
| author_sort | Mikhail G. Divashuk |
| collection | DOAJ |
| description | qPCR is widely used in quantitative studies of plant genomes and transcriptomes. In this article, this method is considered as an auxiliary step in the preparation and selection of markers for FISH analysis. Several cases from the authors’ research on populations of the same species were reviewed, and a comparison of the closely related species, as well as the adaptation of the markers, based on satellite tandem repeats (TRs) using quantitative qPCR data was conducted. In the selected cases, TRs with contrast abundance were identified in the cases of the <i>Dasypyrum, Thinopyrum</i> and <i>Aegilops</i> species, and the transfer of TRs between the wheat and related species was demonstrated. TRs with intraspecific copy number variation were revealed in <i>Thinopyrum ponticum</i> and wheat-wheatgrass partial amphidiploids, and the TR showing predominant hybridization to the sea buckthorn Y chromosome was identified. Additionally, problems such as the absence of a reference gene for qPCR, and low-efficiency and self-complementary primers, were illustrated. In the cases considered here, the qPCR results clearly show high correlation with the subsequent results of the FISH analysis, which confirms the value of this method for cytogenetic studies. |
| first_indexed | 2024-03-09T09:42:27Z |
| format | Article |
| id | doaj.art-3c28c2a5c4064da0b20de14a1aa60595 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-09T09:42:27Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-3c28c2a5c4064da0b20de14a1aa605952023-12-02T00:47:30ZengMDPI AGPlants2223-77472022-12-011218010.3390/plants12010080qPCR as a Selective Tool for CytogeneticsMikhail G. Divashuk0Ekaterina A. Nikitina1Victoria M. Sokolova2Anna I. Yurkina3Alina A. Kocheshkova4Olga V. Razumova5Gennady I. Karlov6Pavel Yu. Kroupin7All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, RussiaAll-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, RussiaqPCR is widely used in quantitative studies of plant genomes and transcriptomes. In this article, this method is considered as an auxiliary step in the preparation and selection of markers for FISH analysis. Several cases from the authors’ research on populations of the same species were reviewed, and a comparison of the closely related species, as well as the adaptation of the markers, based on satellite tandem repeats (TRs) using quantitative qPCR data was conducted. In the selected cases, TRs with contrast abundance were identified in the cases of the <i>Dasypyrum, Thinopyrum</i> and <i>Aegilops</i> species, and the transfer of TRs between the wheat and related species was demonstrated. TRs with intraspecific copy number variation were revealed in <i>Thinopyrum ponticum</i> and wheat-wheatgrass partial amphidiploids, and the TR showing predominant hybridization to the sea buckthorn Y chromosome was identified. Additionally, problems such as the absence of a reference gene for qPCR, and low-efficiency and self-complementary primers, were illustrated. In the cases considered here, the qPCR results clearly show high correlation with the subsequent results of the FISH analysis, which confirms the value of this method for cytogenetic studies.https://www.mdpi.com/2223-7747/12/1/80fluorescent in situ hybridizationtandem satellite repeatswheatwheatgrasssea buckthornDNA repeats |
| spellingShingle | Mikhail G. Divashuk Ekaterina A. Nikitina Victoria M. Sokolova Anna I. Yurkina Alina A. Kocheshkova Olga V. Razumova Gennady I. Karlov Pavel Yu. Kroupin qPCR as a Selective Tool for Cytogenetics Plants fluorescent in situ hybridization tandem satellite repeats wheat wheatgrass sea buckthorn DNA repeats |
| title | qPCR as a Selective Tool for Cytogenetics |
| title_full | qPCR as a Selective Tool for Cytogenetics |
| title_fullStr | qPCR as a Selective Tool for Cytogenetics |
| title_full_unstemmed | qPCR as a Selective Tool for Cytogenetics |
| title_short | qPCR as a Selective Tool for Cytogenetics |
| title_sort | qpcr as a selective tool for cytogenetics |
| topic | fluorescent in situ hybridization tandem satellite repeats wheat wheatgrass sea buckthorn DNA repeats |
| url | https://www.mdpi.com/2223-7747/12/1/80 |
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