Solving a Genetic Mystery

show/hide words to know

Allele: a different version of a gene.

Dominant: a trait that is visible and can cover up other traits when there is more than one present.

Genotype: the genetic makeup of an organism, or the versions of a gene that an organism has.

Heterozygous: having two different versions of a gene.

Homozygous: having two identical versions of a gene.

Phenotype: the appearance of an individual that results from the interaction between their genetic makeup and the environment. Phenotypic trait... more

Probability: a number, usually in percentages, that tells you the likelihood that an event will happen.

Recessive: a trait that is hidden when other traits are present.

Punnett Squares

Punnett squares are a useful tool for predicting what the offspring will look like when mating plants or animals. Reginald Crundall Punnett, a mathematician, came up with these in 1905, long after Mendel's experiments. Let's take a look at how Punnet squares work using the yellow and green peas example from Mendel’s garden experiments.

Pea Plant

For every gene, different versions called alleles exist. Alleles control things like pea color or the presence of dimples on your face. Children inherit two alleles for each gene from their parents, one from the mother and one from the father.

The genotype refers to which two alleles an organism has. Sometimes both alleles are the same and sometimes they are different. The phenotype refers to the visible trait that results from the combination of alleles that are present. 

Parent Generation

Mendel began his experiments with true breeding strains, meaning plants that have offspring of only one phenotype when mated. In true breeding strains, both alleles are the same for a gene. Since there is only one kind of allele present, mating two plants from the same strain will produce offspring that have the same phenotype and genotype as their parents. Plants or animals with two identical alleles for a gene are said to be homozygous.

First Generation

Mendel first crossed two different true breeding strains together, one that produced yellow peas and one that produced green peas. We’ll use letters to represent alleles. Capital “A” will represent the yellow pea allele and lowercase “a” will represent the green pea allele.

The yellow pea phenotype has a genotype of AA.
The green pea phenotype has a genotype of aa.

AA x aa

When Mendel looked at the results of this mating, he saw that all of the offspring had yellow seeds. How did this happen? If one of the parent plants had green peas, why didn't a single one of the children plants have green peas? We can answer these questions and understand what's happening to the alleles in this crossing with the help of a Punnet Square.

Begin by writing the parents' genotypes along the top and side of the Punnet square.

Punnett Square, aa x AA

Next, fill in each cell with two alleles, one from the parent along the top and one from the parent along the side. The letters in the middle show you all possible combinations of alleles that can happen from mating these two genotypes.

Punnett Square, Aa all yellow

In this case, all offspring have the same genotype and phenotype. The order of the letters doesn’t make a difference in the phenotype (aA is the same as Aa) but the capital letter is usually written before the lowercase one. These offspring are said to be heterozygous, meaning that they have two different alleles for pea color.

Despite the fact that both alleles are present in the offspring, the traits did not blend together to result in yellowish-green peas. Instead, only one phenotype was visible and all peas were yellow. Because of this, the yellow pea phenotype is said to be dominant, meaning that it is visible in the heterozygous individual.

Aa Yellow

Second Generation

For the second generation, Mendel mated the heterozygous offspring from the first generation together.

Aa x Aa = 3/4 yellow, 1/4 green

When Mendel looked at the offspring from this mating, he noticed that 1/4 of the children plants had green seeds. Why did this happen? How was it possible for some of the offspring to have green seeds when both of the parent plants had yellow seeds? Let's once again use a Punnet square to answer these questions and understand what's happening to the alleles in this crossing.

Punnett Square, crossing 2 heterozygotes

By looking at the Punnett square, we see that there are three possible genotypes that could result from this crossing: AA, Aa, aa. The genotypes AA and Aa will result in the yellow pea phenotype because A is dominant. Only aa will produce the green pea phenotype.

Punnett Square, results of heterozygous cross

Now we see how it was possible for the green pea phenotype to skip a generation. The green pea allele was present in the F1 generation, but the phenotype was hidden by the yellow pea allele. The green pea phenotype is said to be recessive, meaning that it is only visible in the homozygous individual when the yellow allele is not present.


In the F2 generation, only 1 of the 4 boxes produced green peas. In other words, 25% of the offspring had green peas. This number tells you the probability, or likelihood, that an offspring will produce green or yellow peas.

We can use the probability to predict how many offspring are likely to have certain phenotype when mating plants or animals with different traits. Just take the probability of a phenotype and multiply it by the total number of offspring. Let's imagine there were 160 total offspring in Mendel's F2 generation. How many peas are likely to be green?

25% green peas x 160 total offspring = 40 green pea offspring

(Don't forget that 25% = 0.25)

Try It Yourself!

To learn more about Mendelian Genetics and the different ways that genes determine phenotype, play our Garden Gene Genius game. It is a fun way to learn about genetics and is a great way to learn how to solve Punnett squares.

Additional images from Wikimedia. Pea picture by Bill Ebbesen.

View Citation

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Bibliographic details:

  • Article: Punnett Squares
  • Author(s): Sabine Deviche
  • Publisher: Arizona State University School of Life Sciences Ask A Biologist
  • Site name: ASU - Ask A Biologist
  • Date published: July 20, 2010
  • Date accessed: July 15, 2024
  • Link:

APA Style

Sabine Deviche. (2010, July 20). Punnett Squares. ASU - Ask A Biologist. Retrieved July 15, 2024 from

American Psychological Association. For more info, see

Chicago Manual of Style

Sabine Deviche. "Punnett Squares". ASU - Ask A Biologist. 20 July, 2010.

MLA 2017 Style

Sabine Deviche. "Punnett Squares". ASU - Ask A Biologist. 20 Jul 2010. ASU - Ask A Biologist, Web. 15 Jul 2024.

Modern Language Association, 7th Ed. For more info, see
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Have you tried our genetics game? Garden Gene Genius is a fun way to learn about genetics and how to solve Punnett squares.

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