As explained in the DNA and DNA Extraction lesson, every cell in an organism contains two copies of every chromosome present in that organism. For example, humans have 46 chromosomes in their body, 23 were inherited from the father and 23 from the mother. Gametes, the reproductive cells of an organism, (egg or sperm), have only one set of chromosomes. When the two gametes unite, they form a living embryo with two sets of genetic information. Therefore, we actually have two copies of the genetic information for each trait, or two copies of each gene.

Often, there are multiple versions of the same gene called alleles. Although each allele codes for the same type of trait, they will each express a different version of the trait. For example, roses have a color trait with genes that specify what color the rose will be (type of trait). However, there are many different colors of roses (versions of the trait) each encoded by different alleles. One allele of a gene for rose color may encode the protein for red rose color, another allele encodes white, while another may encode yellow. The genetic code of each is similar, coding for the color trait, but slightly different in that they each hold the information for a different color. The allelic composition of a cell or organism is called its genotype. The expression of the alleles in a genotype results in observable traits in a plant called a phenotype (red rose color, white rose color, tall stems). The expression and visibility of these traits can be affected by environmental factors. For example, the trait for drought tolerance in corn would not be observable unless the plant was under water stress.


A common notation for labeling genes and alleles is with letters of the alphabet. Each gene is assigned a different letter. The gene for red rose petal color may be denoted with the letter ’A’; the gene for tall stems may be denoted with the letter ’T’. The different alleles of the same gene can be depicted in different ways. If there are only two alleles for the same gene, they are typically distinguished using different cases of a letter in the alphabet. One allele for the red rose petal color would be ’A’, the other ’a’. If there are many different alleles for the same gene, numbers could be used. ’ T1’, ’ T2’, ’ T3’ or ’ T1’, ’ T2’, ’ T3’.


There are 3 types of genotypes. The first is homozygous. Plants that are homozygous for a particular gene have two copies of the same allele for that gene, ’AA’ or ’aa’. Homo = same, zygous = zygote.

The second type is heterozygous. Plants that are heterozygous for a particular gene have one copy each of two different alleles, ’Aa’. Hetero = different, zygous = zygote.

The third type is hemizygous. Plants that are hemizgous for a particular gene have only one copy of one allele of that gene. That copy is on one chromosome in a pair, however, the other chromosome does not have any copies of that gene, ’A_’. Hemi = half, zygous = zygote. All human males are hemizygous for genes on the sex chromosome. They have an X and a Y chromosome that determines their sex.

Hemizygous plants have one copy of a single gene. Homozygous plants have two identical copies of a single gene. Heterozygous plants have two copies of a single gene, but those copies are alleles, or different versions of that gene. Image by P. Hain

Although these chromosomes are paired together, their genes do not match. Therefore, males are hemizgyous for the genes on both their X and Y chromosomes. Another example is a transgenic plant. Using transformation, a single gene has been inserted into one chromosome in a pair. However, the other chromosome does not have a copy of that gene.

What happens when two different alleles come together?

Another factor in our rose example is that alleles interact with each other. The phenotype of the organism is affected by the combination of alleles. In some cases, one allele is dominant over another. That allele is called the ’dominant allele’. When the dominant allele masks the expression of the second allele, the allele for which expression is masked is called the ’recessive allele’.


’A’ = red rose petal color

’a’ = white rose petal color

and the ’A’ allele is dominant.

Example of alleles controlling a trait for susceptibility to a lesion-causing disease. Image by P. Hain


’AA’ = red rose petal color

’Aa’ = red rose petal color

’aa’ = white rose petal color

Since expression of the ’a’ allele is masked by the ’A’ allele, the only way a rose could have white petal color is if it had two copies of the recessive ’a’ allele, homozygous recessive.