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Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome.
PLoS One. 2012; 7(9):e44684.Plos

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.

Authors+Show Affiliations

Plant Genetics Laboratory, EMBRAPA Genetic Resources and Biotechnology, Brasilia, Brazil.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

22984541

Citation

Petroli, César D., et al. "Genomic Characterization of DArT Markers Based On High-density Linkage Analysis and Physical Mapping to the Eucalyptus Genome." PloS One, vol. 7, no. 9, 2012, pp. e44684.
Petroli CD, Sansaloni CP, Carling J, et al. Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. PLoS ONE. 2012;7(9):e44684.
Petroli, C. D., Sansaloni, C. P., Carling, J., Steane, D. A., Vaillancourt, R. E., Myburg, A. A., da Silva, O. B., Pappas, G. J., Kilian, A., & Grattapaglia, D. (2012). Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. PloS One, 7(9), e44684. https://doi.org/10.1371/journal.pone.0044684
Petroli CD, et al. Genomic Characterization of DArT Markers Based On High-density Linkage Analysis and Physical Mapping to the Eucalyptus Genome. PLoS ONE. 2012;7(9):e44684. PubMed PMID: 22984541.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. AU - Petroli,César D, AU - Sansaloni,Carolina P, AU - Carling,Jason, AU - Steane,Dorothy A, AU - Vaillancourt,René E, AU - Myburg,Alexander A, AU - da Silva,Orzenil Bonfim,Jr AU - Pappas,Georgios Joannis,Jr AU - Kilian,Andrzej, AU - Grattapaglia,Dario, Y1 - 2012/09/11/ PY - 2012/06/01/received PY - 2012/08/06/accepted PY - 2012/9/18/entrez PY - 2012/9/18/pubmed PY - 2013/3/13/medline SP - e44684 EP - e44684 JF - PloS one JO - PLoS ONE VL - 7 IS - 9 N2 - 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. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/22984541/Genomic_characterization_of_DArT_markers_based_on_high_density_linkage_analysis_and_physical_mapping_to_the_Eucalyptus_genome_ L2 - http://dx.plos.org/10.1371/journal.pone.0044684 DB - PRIME DP - Unbound Medicine ER -