Genomic Characterization of DArT Markers Based on High-Density Linkage Analysis and Physical Mapping to the Eucalyptus Genome

C D Petroli; C P Sansaloni; J Carling; Dorothy A Steane; R E Vaillancourt; A A Myburg; O Bonfim da Silva; G J Pappas; A Kilian; D Grattapaglia

doi:10.1371/journal.pone.0044684

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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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Genomic Characterization of DArT Markers Based on High-Density Linkage Analysis and Physical Mapping to the Eucalyptus Genome

C D Petroli, C P Sansaloni, J Carling, Dorothy A Steane, R E Vaillancourt, A A Myburg, O Bonfim da Silva, G J Pappas, A Kilian and D Grattapaglia

PLoS One, Vol.7(9), e44684

2012

DOI: https://doi.org/10.1371/journal.pone.0044684

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Abstract

Eucalyptus

genome

DArT markers

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.

Details

Title: Genomic Characterization of DArT Markers Based on High-Density Linkage Analysis and Physical Mapping to the Eucalyptus Genome
Authors: C D Petroli (Author) - Universidade de Brasília, Brazil
C P Sansaloni (Author) - Universidade de Brasília, Brazil
J Carling (Author) - Diversity Arrays Technology Pty. Ltd.
Dorothy A Steane (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
R E Vaillancourt (Author) - University of Tasmania
A A Myburg (Author) - University of Pretoria, South Africa
O Bonfim da Silva (Author) - Universidade de Brasília, Brazil
G J Pappas (Author) - Universidade de Brasília, Brazil
A Kilian (Author) - Diversity Arrays Technology Pty. Ltd.
D Grattapaglia (Author) - Universidade de Brasília, Brazil
Publication details: PLoS One, Vol.7(9), e44684
Publisher: Public Library of Science
Date published: 2012
DOI: 10.1371/journal.pone.0044684
ISSN: 1932-6203
Copyright note: Copyright © 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. This published version is reproduced in accordance with this policy.
Organisation Unit: University of the Sunshine Coast, Queensland
Language: English
Record Identifier: 99450024202621
Output Type: Journal article

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Web Of Science research areas: Genetics & Heredity

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