The allele frequency of an allele x is simply the number of x’s present in the population divided by the total number of alleles. Consider, for example, pea color in Mendel’s pea plants. In Chapter 16, we discussed how pea color (yellow or green) results from variation at a single gene. Two alleles of this gene are the dominant A (yellow) allele and the recessive a (green) allele. AA homozygotes and Aa heterozygotes produce yellow peas, and aa homozygotes produce green peas. Imagine that in a population every pea plant produces green peas, meaning that only one allele, a, is present: The allele frequency of a is 100%, and the allele frequency of A is 0%. When a population exhibits only one allele at a particular gene, we say that the population is fixed for that allele.

Now consider another population of 100 pea plants with genotype frequencies of 50% aa, 25% Aa, and 25% AA. A genotype frequency is the proportion in a population of each genotype at a particular gene or set of genes. These genotype frequencies give us 50 green-pea pea plants (aa), 25 yellow-pea heterozygotes (Aa), and 25 yellow-pea homozygotes (AA). What is the allele frequency of a in this population? Each of the 50 aa homozygotes has two a alleles and each of the 25 heterozygotes has one a allele. Of course, there are no a alleles in AA homozygotes. The total number of a alleles is thus (2 × 50) + 25 = 125. To determine the allele frequency of a, we divide the number of a alleles by the total number of alleles in the population, 200 (because each pea plant is diploid, meaning that it has two alleles): 125/200 = 62.5%. Because we are dealing with only two alleles in this example, the allele frequency of A is 100% – 62.5% = 37.5%

Thus, the allele frequencies of A and a provide a measure of genetic variation at one gene in a given population. In this example, we were given the genotype frequencies, and from this information we determined the allele frequencies. But how are genotype and allele frequencies measured? We consider three ways to measure genotype and allele frequencies in populations: observable traits, gel electrophoresis, and DNA sequencing.

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Quick Check 1 Using the example of pea color in Mendel’s pea plants, can you devise equations to determine the allele frequencies of A and a from the genotype frequencies of aa, Aa, and AA?