Digenic genotypes: The interface of inbreeding, linkage, and linkage disequilibrium

Many traits in populations are well understood as being Mendelian effects at single loci or additive polygenic effects across numerous loci. However, there are important phenomena and traits that are intermediate between these two extremes and are known as oligogenic traits. Here we investigate digenic, or two-locus, traits and how their frequencies in populations are affected by non-random mating, specifically inbreeding, linkage disequilibrium, and selection. These effects are examined both separately and in combination to demonstrate how many digenic traits, especially double homozygous ones, can show significant, sometimes unexpected, changes in population frequency with inbreeding, linkage, and linkage disequilibrium. The effects of selection on deleterious digenic traits are also detailed. These results are applied to both digenic traits of medical significance as well as measuring inbreeding in natural populations.