Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome
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| Publication Date: | 2012 |
| Other Authors: | , , , , , , , , |
| Format: | Article |
| Language: | eng |
| Source: | Repositório Institucional da UnB |
| Download full: | http://repositorio.unb.br/handle/10482/23772 https://dx.doi.org/10.1371/journal.pone.0044684 |
Summary: | Diversity Arrays Technology (DArT) provides a robust, high throughput, cost effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization. |
| _version_ | 1871442282167664640 |
|---|---|
| author | Petroli, César Daniel |
| author2 | Sansaloni, Carolina Paola Carling, Jason Steane, Dorothy A. Vaillancourt, René E. Myburg, Alexander A. Silva Júnior, Orzenil Bonfim da Pappas Júnior, Georgios Joannis Kilian, Andrzej Grattapaglia, Dario |
| author2_role | author author author author author author author author author |
| author_browse | Carling, Jason Grattapaglia, Dario Kilian, Andrzej Myburg, Alexander A. Pappas Júnior, Georgios Joannis Petroli, César Daniel Sansaloni, Carolina Paola Silva Júnior, Orzenil Bonfim da Steane, Dorothy A. Vaillancourt, René E. |
| author_facet | Petroli, César Daniel Sansaloni, Carolina Paola Carling, Jason Steane, Dorothy A. Vaillancourt, René E. Myburg, Alexander A. Silva Júnior, Orzenil Bonfim da Pappas Júnior, Georgios Joannis Kilian, Andrzej Grattapaglia, Dario |
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| bitstream.url.fl_str_mv | http://repositorio2.unb.br/jspui/bitstream/10482/23772/1/ARTIGO_GenomicCharacterizationDArT.PDF http://repositorio2.unb.br/jspui/bitstream/10482/23772/2/license.txt |
| collection | Repositório Institucional da UnB |
| dc.contributor.author.fl_str_mv | Petroli, César Daniel Sansaloni, Carolina Paola Carling, Jason Steane, Dorothy A. Vaillancourt, René E. Myburg, Alexander A. Silva Júnior, Orzenil Bonfim da Pappas Júnior, Georgios Joannis Kilian, Andrzej Grattapaglia, Dario |
| dc.date.accessioned.fl_str_mv | 2017-06-28T14:56:35Z |
| dc.date.available.fl_str_mv | 2017-06-28T14:56:35Z |
| dc.date.issued.fl_str_mv | 2012-09-11 |
| dc.identifier.citation.fl_str_mv | PETROLI, César Daniel. et al. Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome. Plos One, v. 7, n. 9, Article e44684, 11 set. 2012. Disponível em: <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044684>. Acesso em: 13 jun. 2017. doi: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044684. |
| dc.identifier.doi.pt_BR.fl_str_mv | https://dx.doi.org/10.1371/journal.pone.0044684 |
| dc.identifier.uri.fl_str_mv | http://repositorio.unb.br/handle/10482/23772 |
| dc.language.iso.fl_str_mv | eng |
| dc.publisher.none.fl_str_mv | Plos One |
| dc.rights.driver.fl_str_mv | info:eu-repo/semantics/openAccess |
| dc.source.none.fl_str_mv | reponame:Repositório Institucional da UnB instname:Universidade de Brasília (UnB) instacron:UNB |
| dc.subject.keyword.pt_BR.fl_str_mv | Genotipagem Marcadores genéticos Eucalipto |
| dc.title.pt_BR.fl_str_mv | Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome |
| dc.type.driver.fl_str_mv | info:eu-repo/semantics/article |
| dc.type.status.fl_str_mv | info:eu-repo/semantics/publishedVersion |
| description | Diversity Arrays Technology (DArT) provides a robust, high throughput, cost effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | UNB_3a363d9f962ffdf4e36eed76c77d91ff |
| identifier_str_mv | PETROLI, César Daniel. et al. Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome. Plos One, v. 7, n. 9, Article e44684, 11 set. 2012. Disponível em: <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044684>. Acesso em: 13 jun. 2017. doi: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044684. |
| instacron_str | UNB |
| institution | UNB |
| instname_str | Universidade de Brasília (UnB) |
| language | eng |
| network_acronym_str | UNB |
| network_name_str | Repositório Institucional da UnB |
| oai_identifier_str | oai:repositorio.unb.br:10482/23772 |
| publishDate | 2012 |
| publishDateSort | 2012 |
| publisher.none.fl_str_mv | Plos One |
| reponame_str | Repositório Institucional da UnB |
| repository.mail.fl_str_mv | repositorio@unb.br |
| repository.name.fl_str_mv | Repositório Institucional da UnB - Universidade de Brasília (UnB) |
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| spelling | Petroli, César DanielSansaloni, Carolina PaolaCarling, JasonSteane, Dorothy A.Vaillancourt, René E.Myburg, Alexander A.Silva Júnior, Orzenil Bonfim daPappas Júnior, Georgios JoannisKilian, AndrzejGrattapaglia, Dario2017-06-28T14:56:35Z2017-06-28T14:56:35Z2012-09-11PETROLI, César Daniel. et al. Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome. Plos One, v. 7, n. 9, Article e44684, 11 set. 2012. Disponível em: <http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044684>. Acesso em: 13 jun. 2017. doi: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044684.http://repositorio.unb.br/handle/10482/23772https://dx.doi.org/10.1371/journal.pone.0044684Plos OneCopyright: 2012 Petroli et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Fonte: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044684. Acesso em: 13 jun. 2017.info:eu-repo/semantics/openAccessGenomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genomeinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleGenotipagemMarcadores genéticosEucaliptoDiversity Arrays Technology (DArT) provides a robust, high throughput, cost effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization.engreponame:Repositório Institucional da UnBinstname:Universidade de Brasília (UnB)instacron:UNBORIGINALARTIGO_GenomicCharacterizationDArT.PDFARTIGO_GenomicCharacterizationDArT.PDFapplication/pdf993058http://repositorio2.unb.br/jspui/bitstream/10482/23772/1/ARTIGO_GenomicCharacterizationDArT.PDFbf781b9c4af7c6fae980bdfef85b1efaMD51open accessLICENSElicense.txtlicense.txttext/plain160http://repositorio2.unb.br/jspui/bitstream/10482/23772/2/license.txtcd7f2de909e07c008880b5201378c22eMD52open access10482/237722023-05-24 20:34:36.155open accessoai:repositorio.unb.br:10482/23772U3VibWlzcz9vIGVmZXRpdmFkYSBwb3IgaW50ZWdyYW50ZSBkYSBlcXVpcGUgZG8gUmVwb3NpdD9yaW8gSW5zdGl0dWNpb25hbCBkYSBVbkIgZGUgYWNvcmRvIGNvbSBsaWNlbj9hIGNvbmNlZGlkYSBwZWxvIGF1dG9yIGUvb3UgZGV0ZW50b3IgZG9zIGRpcmVpdG9zIGF1dG9yYWlzLg==Repositório InstitucionalPUBhttps://repositorio.unb.br/oai/requestrepositorio@unb.bropendoar:2023-05-24T23:34:36Repositório Institucional da UnB - Universidade de Brasília (UnB) |
| spellingShingle | Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome Petroli, César Daniel Genotipagem Marcadores genéticos Eucalipto |
| status_str | publishedVersion |
| title | Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome |
| title_full | Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome |
| title_fullStr | Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome |
| title_full_unstemmed | Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome |
| title_short | Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome |
| title_sort | Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus Genome |
| topic | Genotipagem Marcadores genéticos Eucalipto |
| url | http://repositorio.unb.br/handle/10482/23772 https://dx.doi.org/10.1371/journal.pone.0044684 |