Genetic architecture refers to the underlying genetic basis of a phenotypictrait. Phenotypic variation for quantitative traits is, at the most basic level, the result of the segregation of alleles at quantitative trait loci (QTL). Environmental factors and other external influences can also play a role in phenotypic variation. Genetic architecture is a broad term that covers a variety of genetic mechanisms that contribute to phenotype, including epistasis, polygeny, pleiotropy, and robustness.
Epistasis: a phenomenon in which one gene is dependent on the presence of one or more "modifier" genes.
Polygeny: a phenomenon in which multiple genes contribute to a particular phenotypic character.
Pleiotropy: a phenomenon in which a single gene affects one or more phenotypic characteristics.
A genotype-phenotype map is a mathematical attempt to express this relationship between genotype and phenotype. Such maps have been analyzed in terms of these principals as major axes.
Genetic architecture can be at least partially studied through phylogenies, which can be very helpful for identifying the architecture of current-day genotypes by exploring the genetic mechanisms of evolution. For example, one study used phylogeny to compare the genetic architecture of differing human skin color. In this study, researchers were able to suggest a speculative framework for the evolutionary history underlying current-day phenotypic variation in human skin pigmentation based on the similarities and differences they found in the genotype. Evolutionary history is an important consideration in understanding the genetic basis of any trait.