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

Citation

Petroli, CD and Sansaloni, CP and Carling, J and Steane, DA and Vaillancourt, RE and Myburg, AA and da Silva, OB and Pappas, GJ and Kilian, A and Grattapaglia, D, Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome, PLoS One, 7, (9) Article e44684. ISSN 1932-6203 (2012) [Refereed Article]


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Licenced under Creative Commons Attribution 2.5 Generic (CC BY 2.5) http://creativecommons.org/licenses/by/2.5/

DOI: doi:10.1371/journal.pone.0044684

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.

Item Details

Item Type:Refereed Article
Keywords:molecular markers
Research Division:Biological Sciences
Research Group:Genetics
Research Field:Population, Ecological and Evolutionary Genetics
Objective Division:Plant Production and Plant Primary Products
Objective Group:Forestry
Objective Field:Hardwood Plantations
Author:Steane, DA (Dr Dorothy Steane)
Author:Vaillancourt, RE (Professor Rene Vaillancourt)
ID Code:80166
Year Published:2012
Funding Support:Australian Research Council (DP110101621)
Web of Science® Times Cited:43
Deposited By:Plant Science
Deposited On:2012-10-24
Last Modified:2013-05-13
Downloads:256 View Download Statistics

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