Each gene locus contains two genes, one from the mother, one from the father. These are generally notated by a pair of letters such as AA, Aa, Pp, pp, etc. What letter is used refers to the gene locus. Whether it is capital or lower case refers to whether the gene is dominant or recessive. Usually these letters have some reference to what they stand for and what that gene locus controls.
Capital letters refer to Dominant genes, lower case refer to recessive genes.
You will find what letters refer to what gene locii and how they interact in the genetic information is available for a particular species. Dominant and Recessive Individual genes within a locus are said to be either dominant or recessive, noted by a capital letter for a dominant gene and a lower case letter for a recessive. For example in the A locus, the A gene means the animal will be agouti colored, while the a gene means the animal will be black. Since A is dominant an animal with an Aa combination will be agouti in color. The A is dominant over the a.