(‘Journal club of one’ will be quick notes on papers, probably mostly about my favourite topics — genetics and the noble chicken.)
Abe, Nagao & Inoue-Murayama (2013), recently published this paper in PLOS ONE about copy number variants and tonic immobility in two kinds of domestic chicken. This obviously interests me for several reasons: I’m working on the genetic basis of some traits in the chicken; tonic immobility is a fun and strange behaviour — how it works and if it has any adaptive importance is pretty much unknown, but it is a classic from the chicken literature — and the authors use QTL regions derived directly from the F2 generation of cross that I’m working on — we’ve published one paper so far on the F8 generation.
Results: They use arrays and qPCR to search for copy number variants in three regions on chromosome one in two breeds (White Leghorn and Nagoya, a Japanese breed). After quite a bit of filtering they end up with a few variants that differ between the breeds. The breeds also differ in their tonic immobility behaviour with Leghorns going into tonic immobility after three attempts on average and lying still for 75 s and Nagoya taking 4.5 attempts and lying for 100 s on average. But the copy number variants were not associated with tonic immobility attempts or duration within breeds, so there is not really any evidence that they affect tonic immobility behaviour.
Apart from the issue that the regions (more than 60 Mb) will contain lots of other variants, we do not know whether these regions affect tonic immobility behaviour in these breeds in the first place. The intercross that the QTL come from is a wild by domestic Red Junglefowl x White Leghorn cross, and while Nagoya seem a very interesting breed that is distant from White Leghorn they are not junglefowl. When it comes to the Leghorn side of the experiments, I wouldn’t be surprised White Leghorn bred on a Swedish research institute and a Japanese research institute differed quite a bit. The breed differences in tonic immobility is not necessarily due to the genetic variants identified in this particular cross, especially since behaviour is probably very polygenic, and an F2 QTL study by necessity only scratches the surface.
In the discussion the authors bring up power: There were 71 Nagoya and 39 White Leghorn individuals and the experiment might be unable to reliably detect associations within the breeds. That does seem likely, but making a good informed guess about the expected effect is not so easy. A hint could come from looking at the effect sizes in the QTL study, but there is no guarantee that genetic background will not affect them. I don’t know really what this calculation comes from: ”Sample sizes would need to be increased more than 20-fold over the current study design” — maybe 11 tested copy number variants times two breeds? To me, that seems both overly optimistic, because it assumes that the entire breed difference would be due to these three QTL on chromosome 1, and overly pessimistic, since it assumes that the three QTL would fractionate into 11 variants.
Finally, with all diversity in the chicken, there’s certainly a place both for within and between population studies of various chickens with all kinds of genomic! Comparing breeds with different selection histories should be very interesting for distinguishing early ‘domestication QTL’ from ‘productivity QTL’ selected under modern chicken breeding. And I wish somebody would figure out a little more about how tonic immobility works.
Abe H, Nagao K, Inoue-Murayama M (2013) Short Copy Number Variations Potentially Associated with Tonic Immobility Responses in Newly Hatched Chicks. PLoS ONE 8(11): e80205. doi:10.1371/journal.pone.0080205