Would a MYB factor switch be considered a covariate?

[Forest Hunt]

  I am studying color production in a population of grapes (anthocyanins in particular, we have 28 anthocyanin phenotypes with readings from an LCMS). There is a known MYB factor on LG2 at the beginning of the metabolic chain that acts like an on/off switch in grapes. This loci has been showing up in all of my scanone scans with really high LOD scores, from 35 to 168. The problem is that these high LOD scores seem to be masking the detection of any additional loci on other linkage groups, which is mostly what we are looking for. We would like to study the genetic basis of anthocyanin production when they are produced (switch on from LG2), and we were wondering whether this loci could be considered a covariate. If so, how would you do it ? (In your handbook, addition of phenotypic covariates are explained with the x chromosome but it doesn't seem to be similar to what we are encountering in our dataset). If it cannot be considered a covariate like in your tutorial, is there a way within Rqtl to fix the effect of that loci so that we can properly detect additional loci controlling the production of the individual anthocyanins? 

[Karl Broman]

You can include the genotype of that location as an additive covariate. There's an example of this in the R/qtl book in Sect. 7.4 on composite interval mapping, pages 206-208.

karl