Remember that a trait is an aspect of the physical appearance of an organism that can vary. Organisms get their traits from proteins; proteins are produced using the information found in the organism’s DNA. Variation in the DNA between different organisms causes the production of proteins that contain differing orders of amino acids. These proteins can have different shapes and therefore different functions. When proteins function differently, this leads to differences in traits.

Recall that diploid organisms have two copies of each chromosome: a pair of homologous chromosomes. The reason that they have two copies is because they inherited one copy of each chromosome from each parent. Each parent donates one haploid gamete (egg or sperm) to the reproductive process. A haploid gamete contains one copy of each chromosome because during meiosis the number of chromosomes is cut in half: the DNA is copied once and then divided twice. This separation of the homologous chromosomes means that only one of the copies of the gene gets moved into a gamete. The offspring are formed when that gamete unites with one from another parent and the two copies of each gene (and chromosome) are restored.

A diploid organism has two copies of a given gene. The two copies may or may not encode the same version of that characteristic. For example, one individual pea plant (such as those studied by Mendel) would have two copies of the gene that controls flower color. That individual could carry one version of the gene that leads to white flower color and a second different version of that same gene that leads to violet flower color. The interaction between these two different versions of the same gene will lead to the visible flower color in the pea plant. Gene variations that arise by mutation and exist at the same relative locations on homologous chromosomes are called alleles. Mendel examined the inheritance of genes with just two allele forms, but it is common to encounter more than two alleles for many genes in a natural population.

Each individual (assuming it is a diploid organism) will have two alleles for a specific gene: one from each of its two parents. These two alleles are expressed and interact to produce physical characteristics. The observable traits expressed by an organism are referred to as its phenotype. An organism’s underlying genetic makeup, consisting of both the physically visible and the non-expressed alleles, is called its genotype.

Diploid organisms that are homozygous for a gene have two identical alleles, one on each of their homologous chromosomes. If the organism has two different alleles, this is referred to as heterozygous. 

This chapter will address a simple type of inheritance: complete dominance. In this type of inheritance, there are two alleles: dominant and recessive. A dominant allele will completely cover up a recessive allele. This means that if one dominant allele is present, the organism will have the trait conferred by that allele. In order for the recessive phenotype to be seen, the organism must have two recessive alleles. Just because an allele is dominant does not automatically make it better than a recessive trait. It also does not make it more common than the recessive trait. All it means for an allele to be dominant is that it is able to cover up the recessive allele.

We typically abbreviate the genotype of an organism by using single letters. The letter chosen is often the first letter of the dominant trait. A homozygous dominant genotype would be written AA, a heterozygous genotype as Aa, and a homozygous recessive genotype as aa.