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.
