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.
Highlights
DNA marker technologies for high throughput genome-wide genotyping at affordable costs have become indispensable in the plant geneticist’s toolbox
In this study we investigated the genomic properties of the 7,680 Diversity Arrays Technology (DArT) marker probes that populate the Eucalyptus array by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses using the recently released Eucalyptus grandis reference genome sequence
Based on the genomic characterization of the DArT probe sequences reported in this study, phylogenies or population genetic surveys based on DArT markers can be further explored according to the gene proximity or gene content of particular markers sets
Summary
DNA marker technologies for high throughput genome-wide genotyping at affordable costs have become indispensable in the plant geneticist’s toolbox. Diversity Arrays Technology (DArT) was described over a decade ago [5] and has experienced increasing interest in recent years as a robust, high throughput, cost-effective genome-wide method to assay thousands of presence/absence polymorphisms in a single assay Proprietary, this technique is licensed freely under an open-source model [6], a condition that has stimulated the development of genotyping arrays for more than 60 organisms including many less privileged crops [7,8,9,10,11,12,13,14,15,16,17,18,19,20,21]. Being a DNA-DNA hybridization-based method using relatively long probes (,300–500 bp), DArT provides high and consistent signal to noise ratio even across related taxa [22]
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