For many traits, such as the color of a mouses fur, differences in the appearance (or phenotype) between individuals is often due to underlying differences in those individuals genetic structure (their genotype). Within cells, the genetic instructions used to build the pigments that give mice their distinctive colors, is encoded in their DNA (an abbreviation for Deoxyribonucleic acid). DNA is written using four types of molecules (bases) that make up the language in which the instructions are written. A sequence of bases that encodes a specific set of instructions is called a gene, and there are thousands of genes scattered at different locations (or loci plural, locus singular) across the chromosomes in cells. Each individual possesses twocopies of each gene, one inherited from the mother, the other from the father. These two copies may not match- that is the specific sequence of DNA encoded in the maternally-inherited and paternally inherited copies may differ in their base composition. Different spellings in gene sequence at specific locus are called different alleles. How the two alleles at a given locus influence the phenotype of an individuals trait (such as fur color) will depend on several factors.

The first factor is whether the differences in spelling produce meaningful changes to the set of genetic instructions. Some differences in DNA sequence make no difference to the end product of the instructions, but sometimes the differences in bases results in dramatically different end products. The second factor is how the two different alleles at a given locus interact. Some alleles are dominant that is they are always produced, and expressed in the cell. Other types of alleles are recessive that is their expression can be masked if there is a dominant allele at the other gene locus. The expression of recessive allele in the phenotype will only occur if the other allele at the same locus is also recessive. Of course, in reality, many genes do not perfectly fit the recessive and dominant categories, and there is some intermediary level of expression of the allele in the phenotype. An element that factors into how differences in genotype affect phenotype is that in some cases, there are epistatic interactions between genes at different loci that affect expression patterns. The cumulative effect of these three factors can be seen in a recent study of two sub-species (isolated populations) Old fieldmice (Peromyscus polionotus), that differ in fur coloration (paper source listed below). This study identified that differences in phenotype between the lighter-furred beach-living sub-species and the darker-furred inland subspecies was due to the presence of different alleles in each population, and that most of the variation in fur was due to allele variation at two gene loci. They also found that there was a strong interaction between the loci that affected the mouse coloration patterns, with the phenotypic effects the alleles at one locus depending on the alleles at the second locus.

So to summarize, when individuals possessing differently encoded genetic information (alleles) mate, the appearance (phenotype) of their off springwill depend on which type of alleles they inherit, the specific properties of the two alleles at that gene locus (recessive, dominant, or some intermediary form), the number of genes that contribute to the traits phenotype, and any interactions between these genes.

Steiner, C.C., J.N. Weber and H.E. Hoekstra. 2007. Adaptive variation in beach mice caused by two interacting pigmentation genes. PLoS Biology. 5(9):1880-1889