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

Show simple item record Petroli, Cesar D. Sansaloni, Carolina P. Carling, Jason Steane, Dorothy A. Vaillancourt, Rene E. Myburg, Alexander Andrew Da Silva Jr., Orzenil Bonfim Pappas Jr., Georgios Joannis Kilian, Andrzej Grattapaglia, Dario 2012-10-16T07:09:31Z 2012-10-16T07:09:31Z 2012-09-11
dc.description.abstract 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. en_US
dc.description.sponsorship The Brazilian Ministry of Science and Technology (CNPq Project Grants 559245/2008-4 and 560831/2008-0) and PRONEX FAP-DF Project Grant "NEXTREE" 193.000.570/2009 to DG. en_US
dc.description.uri en_US
dc.identifier.citation Petroli CD, Sansaloni CP, Carling J, Steane DA, Vaillancourt RE, et al. (2012) Genomic Characterization of DArT Markers Based on High-Density Linkage Analysis and Physical Mapping to the Eucalyptus Genome. PLoS ONE 7(9): e44684. DOI: 10.1371/journal.pone.0044684 en_US
dc.identifier.issn 1932-6203
dc.identifier.other 10.1371/journal.pone.0044684
dc.language.iso en en_US
dc.publisher Public Library of Science en_US
dc.rights © 2012 Petroli et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use en_US
dc.subject Diversity Arrays Technology (DArT) en_US
dc.subject DArT markers en_US
dc.subject Eucalyptus en_US
dc.title Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome en_US
dc.type Article en_US

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