Diversity Arrays Technology (DArT) for Pan-Genomic Evolutionary Studies of Non-Model Organisms

Abstract

BackgroundHigh-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms.Methodology/Principal FindingsThis study explores the utility of Diversity Arrays Technology (DArT) in evolutionary studies of non-model organisms. DArT is a hybridization-based genotyping method that uses microarray technology to identify and type DNA polymorphism. Theoretically applicable to any organism (even one for which no prior genetic data are available), DArT has not yet been explored in exclusively wild sample sets, nor extensively examined in a phylogenetic framework. DArT recovered 1349 markers of largely low copy-number loci in two lineages of seed-free land plants: the diploid fern Asplenium viride and the haploid moss Garovaglia elegans. Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants. Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples.Conclusions/SignificanceThese results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns. Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography.

Population genetic analysis and phylogeny reconstruction in Eucalyptus (Myrtaceae) using high-throughput, genome-wide genotyping

“…Only one other study has explored the utility of DArT markers for studies of evolution in wild populations (James et al 2008), but that study focused on relationships between populations within two species of cryptogam (a fern, Asplenium viride and a moss, Garovaglia elegans ssp. dietrichiae) rather than inter-specific relationships within a genus.…”

“…dietrichiae) rather than inter-specific relationships within a genus. James et al (2008) found that DArT markers could be highly informative about relationships among populations of cryptogam species.…”

Tibet is one of the centers of domestication of cultivated barley

“…Genome-wide marker analysis is currently one of the most powerful tools for determining genetic variation of a crop species and its phylogenetic relationships with wild relatives (1,21). Diversity array technology (DArT) markers are widely accepted as powerful whole-genome profiling markers for phylogenetic and population structure analysis (13,(22)(23)(24)(25). Similar results were obtained in 185 barley accessions using both 1,130 DArT and 1,307 single nucleotide polymorphism (SNP) markers, respectively (13,14).…”

Can Parentage Analysis Facilitate Breeding Activities in Root and Tuber Crops?

“…The merits of DArT include a high multiplexing level, simultaneous genotyping of several thousand loci per assay and its simultaneous screening of thousands of polymorphic loci lacking prior genome sequence information; additionally, DArT provides hundreds to tens of thousands of highly reliable markers [120], as well as good genome coverage information [123]. Moreover, sequences of DArT markers are easily accessible compared to AFLPs, making them a preferred technique for non-model species [124]. However, DArT is limited in some applications due to high technicality in preparing genomic representation for the target species, cloning, data management and analysis.…”