Hello all,

I am building some mixed models using QTLs for several traits. This basically gets at the underlying genetic architecture.  However, I have a Recombinant Inbred Line (RIL) breeding design grown across 5 environments. There are a couple issues I have: 

1. Each RIL is not truly independent from one another (some are more closely related than others)
2. Can measuring traits for a RIL across several environments be considered "repeated" measures?

I originally was using RIL as a random effect in my mixed models, but this kind of removed all the genetic variation from my models. However, perhaps I can fit RIL as a repeated measure with a specified covariance structure? I have also seen a type of "relatedness matrix"  used as a random effect (perhaps some penalized model)?

Any thoughts?

Thanks
Kyle 
Kyle Hernandez, Ph.D.
The University of Texas at Austin
Department of Biological Sciences
Section of Integrative Biology
kmhernan@mail.utexas.edu





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