We examine the relationships between a genetic marker and a locus affecting a quantitative trait
by decomposing the genetic effects of the marker locus into additive and dominance effects under a
classical genetic model. We discuss the structure of the associations between the marker and the
trait locus, paying attention to non-random union of gametes, multiple alleles at the marker and
trait loci, and non-additivity of allelic effects at the trait locus. We consider that this greater-than-usual level of generality leads to additional insights, in a way reminiscent of Cockerham's
decomposition of genetic variance into five terms: three terms in addition to the usual additive and
dominance terms. Using our framework, we examine several common tests of association between
a marker and a trait.