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Advances in plant gene-targeted and functional markers: a review
Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting mark...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583794/ https://www.ncbi.nlm.nih.gov/pubmed/23406322 http://dx.doi.org/10.1186/1746-4811-9-6 |
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author | Poczai, Péter Varga, Ildikó Laos, Maarja Cseh, András Bell, Neil Valkonen, Jari PT Hyvönen, Jaakko |
author_facet | Poczai, Péter Varga, Ildikó Laos, Maarja Cseh, András Bell, Neil Valkonen, Jari PT Hyvönen, Jaakko |
author_sort | Poczai, Péter |
collection | PubMed |
description | Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated. |
format | Online Article Text |
id | pubmed-3583794 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35837942013-02-28 Advances in plant gene-targeted and functional markers: a review Poczai, Péter Varga, Ildikó Laos, Maarja Cseh, András Bell, Neil Valkonen, Jari PT Hyvönen, Jaakko Plant Methods Review Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the potential to generate phenotypically linked functional markers, especially when fingerprints are generated from the transcribed or expressed region of the genome. It is to be expected that these recently developed techniques will generate larger datasets, but their shortcomings should also be acknowledged and carefully investigated. BioMed Central 2013-02-13 /pmc/articles/PMC3583794/ /pubmed/23406322 http://dx.doi.org/10.1186/1746-4811-9-6 Text en Copyright ©2013 Poczai et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Review Poczai, Péter Varga, Ildikó Laos, Maarja Cseh, András Bell, Neil Valkonen, Jari PT Hyvönen, Jaakko Advances in plant gene-targeted and functional markers: a review |
title | Advances in plant gene-targeted and functional markers: a review |
title_full | Advances in plant gene-targeted and functional markers: a review |
title_fullStr | Advances in plant gene-targeted and functional markers: a review |
title_full_unstemmed | Advances in plant gene-targeted and functional markers: a review |
title_short | Advances in plant gene-targeted and functional markers: a review |
title_sort | advances in plant gene-targeted and functional markers: a review |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583794/ https://www.ncbi.nlm.nih.gov/pubmed/23406322 http://dx.doi.org/10.1186/1746-4811-9-6 |
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