A single gene that occurred in two contrasting varieties controlled each of the traits that Mendel studied. When biologists describe the traits of an organism, they are referencing the organism’s phenotype.

The different forms of a gene are called alleles. Mendel noticed that when he crossed a true breeding plant with one characteristic, such as purple flowers, with a true breeding plant with the opposite characteristic, such as white flowers, one trait hid, or masked, the other characteristic.

When one trait is "stronger" than the other trait, the "stronger" trait is called dominant trait, and the one that is hidden is called the recessive trait. A capital letter is used to represent the dominant form of an allele or gene, and a lower case letter is used to represent the recessive form of the allele. In general, the first letter of the dominant trait is used to determine the symbol. For example, in pea plants, tall is the dominant trait for plant height, so T would be used for tall and t for short.

The traits that Mendel studied would use the letter system as shown in the chart below.

Source: Pea Plant Characteristics, Mariana Ruiz, Wikimedia Commons

The genotype is the actual gene makeup of an organism. When an organism has two dominant genes (two capital letters) for a trait, that genotype is called homozygous dominant. If an organism has two recessive genes (two lowercase letters) for a trait, that genotype is called homozygous recessive. When there is one dominant and one recessive trait (one capital and one lower case), that genotype is called heterozygous or hybrid.

The plants that Mendel called true breeding were homozygous dominant and homozygous recessive. In the diagram below, the phenotype is shown in purple, and the genotype is shown in green.