DDIG

It's been a while since my last post. I've been working on a couple things recently that I should start writing about, but first, I should announce that I was awarded the NSF DDIG. The award money will go towards mapping the maternally inherited factors that result in POE overgrowth in dwarf hamsters.
The crossing scheme is this: make a small F1 (cam x sun) and then back cross those females to a campbelli male. See the figure.

I am focusing only maternally inherited factors because F1 hybrid males are sterile so I cannot do an F2 cross or a sun x F1 male backcross. As should be clear in the figure, the variation occurs due to recombination in the F1 female between P. campbelli and P. sungorus chromosomes, but that variation is only inherited through the mother, I cannot send variation through the father.

While it's kind of a bummer that I will be blind to anything that causes POE overgrowth when inherited from the paternal line, it's not the end of the world. We expect that maternally inherited things that are silenced are growth factors and their failure to be silenced is what causes overgrowth. In other words, we don't have an a priori expectation that paternally inherited factors are involved.

The grant money will support a RAD digest (Peterson et al. 2012) and Illumina sequencing in order to build the genetic map and map the causative factors. The shortcoming of using RADs is that they are anonymous markers - I don't know what genes are near them in the genome. In order to actually localize genes, I will do two things: (1) use a custom-designed array capture to sequence exons from the mapping panel and associate them with the anonymous markers  on the genetic map and (2) use RNAseq on the placentas of small and large backcross offspring to associate genes that are mis-expressed in those individuals with the genetic map.

I'm pretty excited about this whole approach as I think that it will give me the ability to get almost down to the gene level without fine-mapping. We'll see if I'm right or not, but it's pretty exciting that NSF is impressed enough to give me monies for it.

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Peterson, B. K., J. N. Weber, E. H. Kay, H. S. Fisher, and H. E. Hoekstra. 2012. Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species. PLOS ONE 7:e37135.