Punnett Square


Punnett Square Definition

A Punnett square is a graphical representation of the possible genotypes of an offspring arising from a particular cross or breeding event. Creating a Punnett square requires knowledge of the genetic composition of the parents. The various possible combinations of their gametes are encapsulated in a tabular format. Therefore, each box in the table represents one fertilization event.

The inherent assumption is that each trait is determined by a single gene locus and that various traits assort independently from one another. Though this is true for many useful traits, especially when choosing characters for plant or animal breeding, there are many exceptions.

This tool was created in the twentieth century, much after Mendel’s seminal experiments on genetics. However, they are now commonly used to explain the results that Mendel obtained, especially when combined with our current knowledge of DNA, genes and chromosomes.

Common Terms in Genetics

Some terms are often used in the study of genetics and these are particularly useful in understanding the function of Punnett squares. Among these is the term ‘allele’ and is used to denote a variant of a gene. For example, a pea plant can have red or white flowers and the gene variants coding for each of these is called an allele.

When an organism contains two copies of the same allele, its genetic composition or genotype is said to be homozygous. These are also called true-breeding specimens. For instance, plants with white flowers are homozygous at the genetic loci coding for flower color.

Individuals who have two different alleles are said to be heterozygous at that locus. Many plants that have red flowers can have one allele for red color and another for white color. The externally observed characteristic of an individual is called the phenotype. The phenotype in a heterozygous individual is said to be the ‘dominant’ form of the gene and the trait that is suppressed is considered as the ‘recessive’ allele. In the example of flower color, the allele coding for red color is dominant over the one for white.

In a cross between a dominant homozygote and a recessive homozygote, all the offspring will have a heterozygous genotype and a dominant phenotype.

Some gene loci are on sex chromosomes and are called sex-linked traits, while all the others are said to be autosomal.

Functions of Punnett Squares

In large-scale experiments, such as those conducted by Mendel, Punnett squares can accurately predict the ratios of various observable traits as well as their underlying genetic composition. For instance, when a true-breeding tall pea plant is cross fertilized with pollen from a true-breeding short pea plant, the Punnett square can predict that all the offspring will be tall, and all of them will be heterozygous with both the allele for shortness and tallness. It can further predict that if these heterozygous plants are allowed to self-fertilize, approximately seventy-five percent of the second generation plants will be tall, and the remaining twenty-five percent will be short. Among the tall plants, one-third will remain true-breeding while the remaining two-thirds will be heterozygous. This tool is therefore used by plant and animal breeders to choose appropriate specimens in order to obtain offspring carrying a desired trait.

They are also used in genetic counseling to help couples make the decision about having children. For example, in cases where both parents are carriers for an autosomal recessive disease such as cystic fibrosis, there is a twenty-five percent chance of their child suffering from the illness and a fifty-percent chance that their offspring will be carriers. However, if one parent has the disease and the other is neither a carrier nor suffering from the illness, the couple can be reassured that their child will not develop cystic fibrosis since she will carry only one copy of the abnormal gene.

Types of Punnett Squares

Two types of Punnett squares are commonly used. The first is relevant when a single trait determined by one genetic locus is being observed. This is called a monohybrid cross and examples include some of Mendel’s original experiments, where he chose true-breeders for a single trait and crossed them with members carrying a different allele. For a monohybrid cross, these are 2X2 squares with four boxes, each representing one fertilization event between the parent gametes.

The second type is used to predict the outcome of breeding experiments where two traits are being followed and the Punnett square is larger, with sixteen boxes. The 4X4 square is necessary since each of the parents can produce four types of gametes, based on the distribution of the alleles of the two genes.

When more than two traits are being observed, a Punnett square becomes unwieldy and other tools are used to predict the outcomes of such crosses.

Examples of Punnett Squares

Most people are introduced to Punnett squares through the experiments of Mendel. Among the various traits of the common pea plant that he observed, one was the color of the peas. Other common examples used to elucidate the predictive power of this tool are the inheritance of blood types and eye color in humans.

Example #1: Seed Color in Common Pea Plant Pisum sativum

Mendel created true-breeding homozygous plants for both the alleles – yellow and green color seeds. When he cross pollinated these homozygotes, he found that all the offspring had yellow seeds. When he allowed these yellow offspring to undergo self pollination, he was surprised to find that nearly twenty-five percent of the second generation of pea plants contained green seeds. He concluded that the yellow allele was dominant over the green one. In order to better understand this phenomenon, he crossed some of the first generation plants with yellow seeds with a true-breeding green plant. This would later be known as a test cross.

In every Punnett square, an allele is represented by the first letter of the dominant phenotype. In this case, the dominant yellow color allele is denoted by the capital letter ‘Y’ and the recessive allele by the small letter ‘y’. Each allele is allowed to segregate independently into a gamete and the gametes are represented just outside the 2X2 table.

Punnett Square

Each of the boxes shows one possible genotype for the offspring. In this test cross, half the offspring have yellow seeds and are genotypically heterozygous. The other half are homozygous and have green seeds.

Example #2: Tail And Hair Color in Cats

When a homozygous short-tailed, white haired cat is mated with a long-tailed brown haired cat, all the offspring appear to inherit one trait from each parent. They all have short tails and brown hair, showing that brown color is dominant over white and the allele for a short tail is dominant over the one for a long tail.

Dihybrid cross

When members of this first generation mate with each other, a large majority of their offspring will have short tails and brown hair. Additionally, there is a three-in-sixteen probability that the parental combinations will reappear: short tail with white hair or long tail with brown hair. Finally there is a one-in-sixteen probability that a new combination could appear – long-tailed and white colored.

If an animal breeder was looking for a long-tailed, white-haired specimen, he would know that it would only appear in the second generation.

Limitations of Punnett Squares

While Punnett squares are a convenient tool to understand Mendelian genetics, they cannot be used in many situations involving complex genetic inheritance. For example, they are not effective in estimating the distribution of genotypes and phenotypes when there is linkage between two genes. Genetic linkage is a phenomenon where two genes exist close to each other on the same chromosome. Therefore, during gamete formation, the chances of these two traits being inherited together, in the same combination as that found in the parent, is high. One instance of this is the linkage between the locus of the gene causing Nail-patella Syndrome (NPS) and the one determining blood group. Analysis of one family whose members suffer from NPS found that it was often inherited along with a B-type blood group. These linkages will change the random distribution of the two traits among offspring, therefore making the Punnett square unreliable as a predictive device.

In addition, when a single trait is determined by multiple genes and the effect of each of these genes is graded, Punnett squares cannot accurately predict the distribution of phenotypes in the offspring. Human height is determined by over four hundred genes distributed across the genome. In addition, this trait is also influenced by environmental factors such as nutrition.

Finally, genes that are inherited completely from one parent, such as those in the mitochondria or on the Y-chromosome, as well as genotypes that are lethal to the foetus, confound the results from a Punnett square.

Related Biology Terms

  • Codominance – A situation where two alleles are neither dominant nor recessive towards each other and both are expressed as phenotype.
  • Diploid – A cell containing two sets of chromosomes, one set from each parent. Diploid cells contain two copies of nearly every gene.
  • Gametes – Mature, haploid germ cells from the male and female that can fuse with one another to form a zygote.
  • Haploid – A cell containing a single set of chromosomes.


1. Which of these is inherited completely from the mother?
A. Genes for eye color
B. Genes for cystic fibrosis
C. Genes from the Y-chromosome
D. Mitochondrial genes

Answer to Question #1

2. Which of these are assumptions in creating a Punnett square?
A. The alleles for each trait segregate during meiosis
B. Each trait assorts independently of the others
C. Only one gene locus is involved in a particular trait
D. All of the above

Answer to Question #2

3. How many rows and columns would be needed to create a Punnett square for a trihybrid cross?
A. 3X3
B. 6X6
C. 8X8
D. 9X9

Answer to Question #3

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