Stepwise Regression Plugin

[Hrithik Mangla L- A26]

Hii everyone,

I am using Stepwise plugin in TASSEL GUI v5 for QTL mapping of the traits in BC1F2 population, I tried to look for the exact model they are implementing via this plugin like if use nesting option, are the marker effects being nested within the nesting factor by treating nesting factor say family as random effect or fixed one and if we do the stepwise plugin without nesting factor , what's the difference with that analysis? 

One more thing, if we consider this family factor as covariate rather than factor in input file, it still does the stepwise regression without nesting but the results are different from when we consider it as factor, so is this covariate being considered fixed effect here?

In short I want to know are they considering the nesting factor(family) as the fixed or random and what's the difference between covariate and factor?