Human population geneticists have enormous numbers of polymorphic markers at their disposal. The HapMap project, for example, makes data from 3.2 million mapped single nucleotide polymorpisms freely available on its website. That's one SNP every kb on average. Those working on model organisms, like Drosophila or Arabidopsis don't have quite that much information available, but they have complete genome sequences and access to a wide variety of genomic tools.
Those of us working on non-model groups, like the plant genus Protea have a much more limited set of tools available to us. There are a few widely used chloroplast and nucelar sequences in plants – matK, rbcL, the trnL-trnF intron, ITS, ETS, waxy, and a few more. But identifying new possibilities has been very tedious and has had a low probability of success.
Now nunatak at The Beagle Project Blog points out a paper in PLoS One that I missed. The technology described there – Diversity Arrays Technology (DArT) – seems quite promising.
An outline of the approach is provided here. In brief, the approach uses microarrays for high-throughput identification of variable genomic regions within a samle. As I understand it, the basic idea is to construct an anonymous fragment library by digesting genomic DNA from a pool of individuals chosen to represent the expected diversity in the entire sample. Clones from this library are then printed on a microarray and hybridized with fluourescently-labeled DNA samples isolated from single individuals. If a particular individual has a sequence that matches one of those on the microarray, there will be a fluorescent dot at that place on the plate. DArT simply tries to identify positions in the microarray where individuals differ in presence or absence of the spot. Once identified, the clone can be sequenced, allowing investigators to determine whether the polymorphism is due to SNPs or to indels.
DArT has been used primarily to investigate patterns of diversity in cultivated plants, rice, barley, grand eucalyptus, cassava, and wheat. In the PLoSOne paper, Karen James and her associates apply the approach to a fern (Asplenium viride) and a moss (Garovaglia elegans). They identified 444 polymorphic markers in Asplenium and 905 polymorphic markers in Garovaglia.and selected 74 polymorphic fragments from each sample for sequencing and analysis. A BLAST search identifies potential homologs for 42 of these fragments, 18 from Asplenium and 24 from Garovaglia.
Any way you slice it, that's a lot of candidates for further analysis. It suggests that developing a few hundred SNP markers for non-model plants or animals is possible even now. Not trivial in expense or in the expertise and time required, but not out of reach. It looks like a very promising approach and one that many of us may want to consider.
James, K.E., Schneider, H., Ansell, S.W., Evers, M., Robba, L., Uszynski, G., Pedersen, N., Newton, A.E., Russell, S.J., Vogel, J.C., Kilian, A., Michalak, P. (2008). Diversity Arrays Technology (DArT) for Pan-Genomic Evolutionary Studies of Non-Model Organisms. PLoS ONE, 3(2), e1682. DOI: 10.1371/journal.pone.0001682
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