Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome.

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-...

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Autores principales:	César D Petroli, Carolina P Sansaloni, Jason Carling, Dorothy A Steane, René E Vaillancourt, Alexander A Myburg, Orzenil Bonfim da Silva, Georgios Joannis Pappas, Andrzej Kilian, Dario Grattapaglia
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/96f56b1b907a477fb30a3f2a8eaf8f32
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spelling	oai:doaj.org-article:96f56b1b907a477fb30a3f2a8eaf8f322021-11-18T07:06:01ZGenomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome.1932-620310.1371/journal.pone.0044684https://doaj.org/article/96f56b1b907a477fb30a3f2a8eaf8f322012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22984541/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Diversity 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.César D PetroliCarolina P SansaloniJason CarlingDorothy A SteaneRené E VaillancourtAlexander A MyburgOrzenil Bonfim da SilvaGeorgios Joannis PappasAndrzej KilianDario GrattapagliaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e44684 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q César D Petroli Carolina P Sansaloni Jason Carling Dorothy A Steane René E Vaillancourt Alexander A Myburg Orzenil Bonfim da Silva Georgios Joannis Pappas Andrzej Kilian Dario Grattapaglia Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome.
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.
format	article
author	César D Petroli Carolina P Sansaloni Jason Carling Dorothy A Steane René E Vaillancourt Alexander A Myburg Orzenil Bonfim da Silva Georgios Joannis Pappas Andrzej Kilian Dario Grattapaglia
author_facet	César D Petroli Carolina P Sansaloni Jason Carling Dorothy A Steane René E Vaillancourt Alexander A Myburg Orzenil Bonfim da Silva Georgios Joannis Pappas Andrzej Kilian Dario Grattapaglia
author_sort	César D Petroli
title	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_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_sort	genomic characterization of dart markers based on high-density linkage analysis and physical mapping to the eucalyptus genome.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/96f56b1b907a477fb30a3f2a8eaf8f32
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Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome.

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