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The Complex Expression Patterns of Multiple Alleles

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Introductions and Goals

Mendel was able interpret the results of his genetic crosses because he took careful notes, made accurate counts, and chose traits that exhibited a clear dominant or recessive expression pattern. In fact, alleles that show simple dominant or recessive expression patterns are sometimes called "Mendelian traits."Many alleles, however, do not behave in such a simple Mendelian manner. This tutorial will explore more complex patterns of expression. By the end of this tutorial you should have a basic understanding of:

  • Genes with multiple alleles
  • The distinction between the three types of dominance
  • How genes can have multiple effects
  • How genes can affect the expression of other genesWhy some characters are controlled by more than one gene

Performance Objectives

  • Compare and contrast the different dominance relationships that alleles can show
  • Discuss the phenomenon of pleiotropy and its effect on an organism’s phenotype
  • Explain how epistasis affects the expression of genes
  • Describe polygenic inheritance

Incomplete Dominance

In Mendel's experiments, offspring always looked like one of two  phenotypes  due to the complete dominance of one allele over the other for characters that had two traits. This is not always the case because some genes display incomplete dominance. In this type of dominance relationship between two alleles, individuals who are heterozygous exhibit a phenotype intermediate between individuals who are homozygous. . For example, Figure 1 depicts the outcome of a cross between a snapdragon with red flowers and one with white flowers the offspring in the F1  have pink flowers. In this case neither of the alleles for flower color  is completely dominant over the other. Therefore, individuals  who are heterozygous have a phenotype unlike those with either set of homozygous alleles.

Figure 1. Incomplete dominance in snapdragon color. (Click image to enlarge).

As demonstrated in Figure 1, the Punnett square for this cross is like that for any other monohybrid cross. However, the ratio of phenotypes in the F2 generation is not 3:1 (dominant:recessive), as seen with completely dominant alleles, but rather a 1:2:1 ratio of red:pink:white flowers. In this example the alleles are  represented differently than in the previous examples. Since neither allele  is dominant over the other, the use of an uppercase and lowercase version of the same letter is not appropriate. In this example the character (flower color) is indicated by a letter (C), and the alleles encoding the trait (white or red) are listed as uppercase subscripts ( they are both uppercase because neither is dominant to the other). You may see other symbolic representations for incomplete dominance, but don't let this confuse you. The important thing to know is that some genes are expressed in an incomplete dominant manner.

At the following Web site, find the correct answer to the multiple-choice monohybrid or dihybrid cross questions. Work out each problem for yourself. To view an explanation of the problem, select the "TUTORIAL" button. After viewing the correct answer, close the Monohybrid Cross Problem Set or Dihybrid Cross window to return to this page. (note: These sites are a part of the Monohybrid and Dihybrid Problem Sets provided by The Biology Project at the University of Arizona.)

Problem 9: Incomplete dominance - This problem is a part of the Monohybrid Cross Problem Set.

Problem 10: Disappearance of parental phenotypes in the F1 generation - This problem is also a part of the Monohybrid Cross Problem Set.

Problem 11: Incomplete dominance in a dihybrid cross - This problem is a part of the Dihybrid Cross Problem Set.


We have examined complete dominance, in which one allele is clearly dominant over the other, and incomplete dominance, in which neither allele  is dominant over the other. In a third type of dominance, codominance, both alleles are expressed in the phenotype of individuals that have are heterozygous. The human MN Blood group, with alleles designated M and N is an example of codominance. Th This blood group is determined by the presence of a specific protein on the surface of red blood cells, such as those shown in this figure. Group M individuals have one variant (allele) of this proteins, group N have the other variant protein, and group MN individuals express both variants (alleles) of this protein. In the latter case, the heterozygous situation does not result in an intermediate phenotype; instead, the M and N proteins are both  expressed in the phenotype.

Figure 2. The MNS blood group system is similar to the molecules shown here on a cell's surface. (Click image to enlarge)

The Three Types of Dominance

Distinguishing between these three types of dominance is sometimes difficult.. Think of complete dominance, incomplete dominance, and codominance as a continuum of dominance relationships among alleles at a gene. At one end is complete dominance, in which the phenotype for only one of the two alleles is expressed in individuals that are heterozygous. At the other end is codominance, in which both alleles are equally expressed in individuals that are heterozygous. In between there are various levels of incomplete dominance, in which individuals that are heterozygous for the alleles display an intermediate phenotype. The key to understanding the difference between the three types is to look at the phenotype of the individuals with heterozygous alleles, then classify the relationship accordingly.

Multiple Alleles

So far we have only examined  characters with two traits that are controlled by two alleles. This is easy to visualize because diploid organisms can only  have two alleles. Within a population, however, more than two alleles can exist (although any given individual only has two alleles).

The human ABO blood group provides an example of multiple alleles, and structure of the cell surface antigens for the three blood type alleles is shown in Figure 3. There are four possible phenotypic blood types for this particular gene: A, B, AB, and O. The letters refer to two specific carbohydrate molecules on the surface of red blood cells. Individuals can have the A carbohydrate (blood type A), the B carbohydrate (blood type B), both the A and B carbohydrates (blood type AB), or neither carbohydrate (blood type O).

Please note that the molecules depicted above are not the same as those in the MN blood groups. In fact, MNS and ABO are just two of nearly thirty different blood group systems. Collectively, over 990 alleles  at approximately 39 genes control for the different surface proteins which determine the compatibility of one person’s blood with another’s. You can read more about the different blood group systems at the NCBI Blood Group Antigen Gene Mutation Database.

Figure 3. The difference in antigens for the human A and B blood type alleles in the ABO blood group system.  (Click image to enlarge)

Figure 4. Multiple alleles for the ABO blood groups. (Click image to enlarge)

The ABO blood groups are formed by various combinations of three different alleles; IA (codes for carbohydrate A), IB (codes for carbohydrate B), and i (codes for the lack of any carbohydrate). As shown in Figure 4, individuals with one or two IA alleles (the genotype) will have blood type A (the phenotype), those with one or two IB alleles will have blood type B, those with both the IA and IB alleles will have blood type AB, and those with the genotype ii will have blood type O.  What is the relationship of the O allele to the A and B alleles (hint:  look at the case of the letter used to represent that allele)?

The Punnett square can be used to predict the genotype frequencies resulting from multiple allele crosses. However, one cannot be certain of an individual's genotype if they are blood type A or B because there are two possible genotypes for each of these blood types. Therefore, many cross problems that examine blood types are similar to test crosses; that is, the parental genotype is uncertain. A few examples will aid in your understanding.

At the following Web sites, find the correct answer to the multiple-choice monohybrid cross questions. Work out each problem. To view an explanation of the problem, select the "TUTORIAL" button. After viewing the correct answer, close the Monohybrid Cross Problem Set window to return to this page. (These sites are a part of the Monohybrid Problem Sets provided by The Biology Project at the University of Arizona.)

Problem 11: Co-dominant alleles: The Human ABO markers - This problem is a part of the Monohybrid Cross Problem Set.

Problem 13: Predicting human blood types - This problem is also a part of the Monohybrid Cross Problem Set.


So far we have only considered genes that affect a single phenotypic character.  However, there are many examples showing that one gene can have multiple effects (pleiotropy) on the phenotype. For example, albino individuals lack pigment in their skin and hair, and also have crossed eyes at a higher frequency than pigmented individuals (Figure 5). This occurs because the gene that causes albinism can also cause defects in the nerve connections between the eyes and the brain. However, these two traits are not always linked, again showing the complexity of genetic interactions in determining phenotypes.

Figure 5. Pleiotropy in individuals with albinism. (Click image to enlarge)

Mendel also recognized this effect. He observed that pea plants with red flowers had red coloration where the leaf joined the stem, but that their seed coats were gray in color. Plants with white flowers had no coloration at the leaf-stem juncture and displayed white seed coats. These combinations were always found together, leading Mendel to conclude that they were likely controlled by the same hereditary factor (i.e., gene).


Sometimes one gene can affect the expression of another gene (epistasis). A good example of epistasis is the genetic interactions that produce coat color in horses and other mammals. In horses, brown coat color (B) is dominant over tan (b). However, how that gene is expressed in the phenotype is dependent on a second gene that controls the deposition of pigment in hair. The dominant gene (C) codes for the presence of pigment in hair, whereas the recessive gene (c) codes for the absence of pigment. If a horse is homozygous recessive for the second gene (cc), it will have a white coat regardless of its coat color genotype (B gene) because pigment is not deposited in the hair.  Figure 6 shows a Punnett square for this example. The white horses have a genotype specifying brown or tan coat color at the first gene, but are completely white because they are homozygous recessive for the gene controlling pigment deposition.

For another explanation of epistasis as it relates to coat color in mice, please view the following five-minute lecture segment from the Howard Hughes Medical Institute at the University of California, Irvine:

Figure 6. An example of epistasis. (Click image to enlarge)

At the following Web sites, find the correct answer to the multiple-choice dihybrid cross questions. Work out each problem yourself using paper and pencil. To view an explanation of the problem, select the "TUTORIAL" button. After viewing the correct answer, close the Dihybrid Cross Problem Set window to return to this page. (These sites are a part of the Dihybrid Problem Sets provided by The Biology Project at the University of Arizona.)

Problem 12: What is the genotype of the agouti parent? - This problem is a part of the Dihybrid Cross Problem Set.

Problem 13: AaBb dihybrid cross involving epistasis - This problem is also a part of the Dihybrid Cross Problem Set.

Please note that epistasis is distinct from polygenic inheritance. Epistasis is an interaction that occurs when one gene directly  affects the expression of another, while polygenic inheritance is the total influence of several genes on a single trait. While distinct, the terms are also not mutually exclusive; some polygenic inheritances may also show epistatic interactions.

Polygenic Inheritance

The characters that Mendel studied are sometimes referred to as discrete characters because they can only be classified on an "either-or" basis (e.g., purple or white flowers, green or yellow seeds). Many characters cannot be classified in this manner because they vary in a population across a continuum (gradient). For example, the figure above illustrates that skin color in humans is a quantitative character. Quantitative characters usually indicate that the character is controlled by more than one gene (polygenic inheritance).

Figure 7 shows a simplification of the genetics of skin color in humans, with three  genes interacting to determine the level of pigment in an individual's skin. The dominant alleles (A, B, and C) each contribute one "unit" of pigment to the individual, and their effects are cumulative such that individuals with more of these alleles will be darker than those with fewer alleles. The recessive alleles (a, b, and c) do not contribute any units of pigment. Therefore, skin color is related to the number of dominant alleles present in each individual's genotype.

A cross of two completely heterozygous parents produces seven phenotypes in their offspring, ranging from very light to very dark skin. The distribution of skin color in the offspring would resemble a bell-shaped curve because there would be more individuals with intermediate skin colors than either extreme. As the number of genes involved increases, the differences between the various genotypes become more subtle and the distribution fits the curve more closely. Other examples of polygenic inheritance in humans include height, hair color, and eye color. This helps to explain the  variations in these characters that we see in different individuals.

Figure 7. A simplified example of polygenic inheritance . (Click image to enlarge)


This tutorial explored the more complex expression patterns of alleles. These patterns of expression do not contradict the ideas and conclusions of Mendel,  but show that genes and their products can interact and/or be expressed in more complex ways. In all cases, these genes are still transmitted from generation to generation as distinct alleles on chromosomes that segregate independently during meiosis. The differences lie in how the gene product behaves within the cell, and the number of such products that contribute to a given character trait.

Some alleles can show incomplete dominance. In the snapdragon flower color we saw that three phenotypes could be traced to two alleles. In other words, two separate homozygous phenotypes resulted (as is usually seen with characters transmitted in a Mendelian manner) and a third phenotype associated with a heterozygous genotype (clearly different than the case observed with Mendelian traits, where the heterozygous phenotype is the same as the homozygous dominant genotype). How can two alleles yield three phenotypes? Consider the snapdragon. When a plant receives two alleles (a double dose) of the red allele, the flower is very red. These alleles encode for enzymes involved in the production of red pigment. The alternative alleles produce an enzyme that is nonfunctional and cannot participate in pigment synthesis. When a plant receives two copies of this nonfunctional alternative allele, pigment is not produced and the flower is white. When the plant receives one copy (a single dose) of the functional red allele, it can produce some pigment, but not as much as with two fully functional alleles, and so, the color is less red (pink).

In the example above, note that the reason for the phenotypic pattern was that one allele was nonfunctional and the other functional allele resulted in a phenotype that was dependent on there being one or two copies of the functional alleles. There is another situation, however, termed codominance, in which both alleles are functional and expressed. The M and N blood groups are examples of codominance. These alleles encode for proteins that are located on the surface of red blood cells. They are similar but not identical; they differ in four amino acids. If the individual is homozygous, then the phenotype is either M or N. If heterozygous, however, then both proteins are expressed on the surface of red blood cells.

So far we have considered fairly simple cases, where the number of alleles is limited to two. In fact, many genes have multiple alleles. This may seem impossible because in the diploid state there is only room for two alleles (one on the maternal chromosome and one on the paternal chromosome) of a gene. At the population level, however, many more allele forms are possible (although in any given diploid individual, only two occur at any given time). The ABO blood type is one example. We will discuss population genetics in Tutorial 36.

In some cases, genes and their alleles may be expressed in complex ways. That is, no single trait can be attributed to a given allele. Pleiotropy describes this situation, and includes the examples of pigmentation and crossed eyes in the case of albinism.

In the case where one gene product is used by (or dependent on) another product, epistasis can occur. This is fairly common because gene products do not function in isolation. In the example of fur color in mice, one can see that pigment synthesis and pigment deposition are two processes that must occur in order for a specific phenotype (i.e., color) to be observed.

Lastly, we considered the case of polygenic inheritance, whereby many genes and their alleles are involved in the expression of a given phenotype. If you think about it, you will likely recognize that polygenic inheritance and epistasis are related. In fact, many traits are determined by multiple genes, which makes the analysis of expression patterns complex.


After reading this tutorial, you should have a working knowledge of the following terms:

  • blood groups (ABO and MNS)
  • codominance
  • complete dominance
  • epistasis
  • incomplete dominance
  • multiple alleles
  • pleiotropy
  • polygenic inheritance
  • quantitative character

Case Study for The Complex Expression Patterns of Multiple Alleles

Your older brother has been hired to plan a landscaping project in a neglected area of his client’s yard. There are a group 45 Rose of Sharon (Hibiscus syriacus) shrubs that have naturalized in the area (i.e., these shrubs have been growing unattended for 25 years or more). These plants have flowers of three colors; purple, white, and lavender. Your brother tells you that he counted 11 white flowered plants, 25 lavender, and 9 purple flowered plants. Your brother has been instructed to remove the plants, but before doing so, the client would like some seeds that when germinated will give plants all having lavender flowers. Your brother tells the client he can’t do this because, after all, the plants have been crossing by themselves for years and show the range of flower types. You however have taken a biology course and know something about genetics.

  • Explain why your brother is incorrect and which cross he can make that will most likely yield seeds of all lavender plants.
  • Be sure to explain why your cross is likely to work (feel free to use a Punnet square as part of your answer).

Now that you have read this tutorial and worked through the case study, go to ANGEL and take the tutorial quiz to test your understanding.  Questions?  Either send your instructor a message through ANGEL or attend a weekly review session (the times and places are posted on ANGEL).