Hello All,
I would like to know possible explanations on why DArTseq (http://www.diversityarrays.com/dart-application-dartseq) have been used so little in Population genetics/Phylogeography studies. The technology was proposed in 2001, but since then we have a very reduced number of studies using it (except for studies with crop plants).
I appreciate any thoughts on this issue.
Thanks,
Hello Manolo,
Basic answer is that DArTseq is mainly used to enrich for active regions of the genome. This is great for doing breeding designs and genome wide selection studies common in agriculture and thus why it is most often used there.
For population genetics and phylogeography you ideally want to use neutral (or nearly-neutral) regions of the genome, so enriching for active regions is not wanted. More often methods for more random reduced representation of the genome are thus used in these fields (i.e RADseq, GBS, ddRADseq, UCE, AHE, etc.).
There is some application for examining functional genes in these fields (although not as common), but these studies are on wild populations that do not have a set breeding design, so application of RNAseq is often preferred over a method like DArTseq.
Best Regards,
dear Manolo Perez
this paper can be helpdul
http://edepot.wur.nl/32223
My answer to this (based on my modest experience) would be that standard phylogentics and PopGen using traditional gene fragments is far more straightforward. There isn't a great deal of initial investment especially when you applying things such as Folmer Primers and others of similar capability.
Measuring genetic diversity and undertaking phylogentic tasks can be far more readily answered through the use of standard gene fragments. Also, there is a great deal of comparative data.
While DArtSeq may have some very specific applications I think that the standard approach can't (and hasn't) been superseded by this methodology.
Might be a case of 'If it ain't broke, don't fix it'
Would be interested to hear other's answers to this.
Hello Manolo,
Basic answer is that DArTseq is mainly used to enrich for active regions of the genome. This is great for doing breeding designs and genome wide selection studies common in agriculture and thus why it is most often used there.
For population genetics and phylogeography you ideally want to use neutral (or nearly-neutral) regions of the genome, so enriching for active regions is not wanted. More often methods for more random reduced representation of the genome are thus used in these fields (i.e RADseq, GBS, ddRADseq, UCE, AHE, etc.).
There is some application for examining functional genes in these fields (although not as common), but these studies are on wild populations that do not have a set breeding design, so application of RNAseq is often preferred over a method like DArTseq.
Best Regards,
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