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Griffiths AJF, Miller JH, Suzuki DT, et al. An Introduction to Genetic Analysis. 7th edition. New York: W. H. Freeman; 2000.

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An Introduction to Genetic Analysis. 7th edition.

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Gene interaction and modified dihybrid ratios

Genetic analysis can identify the genes that interact in the determination of a particular biological property. The key diagnostic is that two interacting genes produce modified dihybrid ratios. There are various types of interactions, and they lead to a range of different modifications. An important distinction is between genes interacting in different biological pathways and those interacting in the same pathway.

Interacting genes in different pathways

A simple, yet striking, example of gene interaction is the inheritance of skin coloration in corn snakes. The natural color is a repeating black-and-orange camouflage pattern, as shown in Figure 4-11a. The phenotype is produced by two separate pigments, both of which are under genetic control. One gene determines the orange pigment, and the alleles that we shall consider are o+ (presence of orange pigment) and o (absence of orange pigment). Another gene determines the black pigment, with alleles b+ (presence of black pigment) and b (absence of black pigment). These two genes are unlinked. The natural pattern is produced by the genotype o+/– ; b+/–. A snake that is o/o ; b+/– is black because it lacks orange pigment (Figure 4-11b), and a snake that is o+/– ; b/b is orange because it lacks the black pigment (Figure 4-11c). The double homozygous recessive o/o ; b/b is albino, as shown in Figure 4-11d. Notice, however, that the faint pink color of the albino is from yet another pigment, the hemoglobin of the blood that is visible through this snake’s skin when the other pigments are absent. The albino snake also clearly shows that there is another element to the skin-pigmentation pattern in addition to pigment, and this element is the repeating motif in and around which pigment is deposited.

Figure 4-11. Analysis of the genes for skin pigment in the corn snake.

Figure 4-11

Analysis of the genes for skin pigment in the corn snake. The wild type (a) has a skin pigmentation pattern made up of a black and an orange pigment. The gene O determines an enzyme in the synthetic pathway for orange pigment; when this enzyme is deficient (more...)

Because there are two genes in this system, we obtain a typical dihybrid inheritance pattern, and the four unique phenotypes form a 9:3:3:1 ratio in the F2. A typical analysis might be as follows:

Image ch4e16.jpg

In summary, the 9:3:3:1 dihybrid ratio is produced because the mutations are in two parallel biochemical pathways.

Image ch4e17.jpg

Generally, interacting genes in two different pathways produce an F2 with four phenotypes corresponding to the four possible genotypic classes, as in the snake example. However, when the mutations are in one biological pathway, different ratios are seen. Usually there are only two or three phenotypes resulting from various combinations of the genotypic classes. Likewise, the F2 ratio is a modification of the 9:3:3:1 ratio, produced by grouping various components of the ratio. Examples are shown in the next section.

Interacting genes in the same pathway

For an example of a modified ratio produced by genes in the same pathways, we need only to return to the example of petal color in harebells.

Mutations with the same phenotype.  

The harebell anthocyanin pathway terminated in a blue pigment and the intermediates were all colorless. Two different white-petalled homozygous lines of harebells were crossed and the F1 was blue flowered, showing complementation. What will be the F2 resulting from crossing the F1 plants? The F2 shows both blue and white plants in a ratio of 9:7. How can these results be explained? The 9:7 ratio is clearly a modification of the dihybrid 9:3:3:1 ratio with the 3:3:1 combined to make 7. The cross of the two white lines and subsequent generations can be represented as follows:

Image ch4e18.jpg

The results show that homozygosity for the recessive mutant allele of either gene or both genes causes a plant to have white petals. To have the blue phenotype, a plant must have at least one dominant allele of both genes.

An important type of gene interaction at the molecular level is the interaction between a regulatory gene and the gene that it regulates (Figure 4-12). Such genes also show a type of complementation. A common situation is that the regulatory gene produces a regulatory protein that binds to the upstream regulatory site of the target gene, possibly facilitating the action of RNA polymerase (Figure 4-12a). In the absence of the regulatory protein, the target gene would be transcribed at very low levels, inadequate for cellular needs. This type of gene interaction can be followed in a situation in which a dihybrid is heterozygous for a null mutation of the regulatory gene (r+/r) and heterozygous for a null mutation—say, a translation-termination mutation (a+/a). Normally translation-termination codons are at the 3′ end of every mRNA, but mutation can introduce a termination codon within the coding sequence. In this position, it results in a short polypeptide. Assume that the mutation in the present example is close to the 5′ end of the protein-coding sequence. The possible genotypes are shown in Figure 4-12. The stop codon will lead to premature transcriptional termination—in this case, a protein of such small size that it is negligible. The r+/r ; a+/a dihybrid will give the following progeny:

Image ch4e19.jpg

Figure 4-12. Interaction between a regulating gene and its target.

Figure 4-12

Interaction between a regulating gene and its target.

Here then we see another mechanism for complementation, the cooperation of a regulatory and a regulated gene.

Mutations with different phenotypes.  

If one or more intermediates in a biochemical pathway is colored, then a different F2 ratio is produced. In this example, taken from the plant blue-eyed Mary (Collinsia parviflora), the pathway is as follows:

Image ch4e20.jpg

The w and m genes are not linked. If homozygous white and magenta plants are crossed, the F1 and F2 are as follows:

Image ch4e21.jpg

Complemention results in a wild-type F1. However, in the F2, a 9:3:4 phenotypic ratio is produced. This kind of interaction is called epistasis, which literally means “standing on”; in other words, an allele of one gene masks the expression of the alleles of another gene. In this example, the w allele is epistatic on m+ and m. Conversely, m+ and m can be expressed only in the presence of w+. Because a recessive allele is epistatic, this is a case of recessive epistasis. The state of the synthetic pathway in the various genotypes is illustrated in Figure 4-13.


Epistasis is inferred when an allele of one gene masks expression of alleles of another gene and expresses its own phenotype instead.

Figure 4-13. A molecular mechanism for recessive epistasis.

Figure 4-13

A molecular mechanism for recessive epistasis. Two representative genes encode enzymes catalyzing successive steps in the synthesis of a blue petal pigment. The substrates for these enzymes are colorless and pink, respectively, so null alleles of the (more...)

In general, every time one gene is higher, or upstream, in some biochemical pathway, we would expect there to be an epistatic effect of a defective allele on alleles of genes later in the sequence. Therefore, finding a case of epistasis (for example, by the 9:4:3 modified dihybrid ratio) can be a source of insight about the sequence in which genes act. This principle can be useful in piecing together biochemical pathways.

Another case of recessive epistasis well known to most people is the yellow coat color of Labrador retriever dogs. Two alleles, B and b, stand for black and brown coats, respectively, but the allele e of another gene is epistatic on these alleles, giving a yellow coat (Figure 4-14). Therefore the genotypes B/– ; e/e and b/b ; e/e are both of yellow phenotype, whereas B/– ; E/– and b/b ; E/– are black and brown, respectively. This case of epistasis is not caused by an upstream block in a pathway leading to dark pigment. Yellow dogs can make black or brown pigment, as can be seen in their noses and lips. The action of the allele e is to prevent deposition of the pigment in hairs. In this case, the epistatic gene is developmentally downstream; it represents a kind of developmental target that has to be of E genotype before pigment can be deposited.

Figure 4-14. Coat-color inheritance in Labrador retrievers.

Figure 4-14

Coat-color inheritance in Labrador retrievers. Two alleles B and b of a pigment gene determine (a) black and (b) brown, respectively. At a separate gene, E allows color deposition in the coat, and e/e prevents deposition, resulting in (c) the gold phenotype. (more...)


Epistasis points to interaction of genes in some biochemical or developmental sequence.


Another important type of gene interaction is suppression. A suppressor is an allele that reverses the effect of a mutation of another gene, resulting in the normal (wild-type) phenotype. For example, assume that an allele a+ produces the normal phenotype, whereas a recessive mutant allele a results in abnormality. A recessive mutant allele s at another gene suppresses the effect of a so that the genotype a/a · s/s will have wild-type (a+-like) phenotype. The phenotype of a suppressor alone (genotype a+/a+ · s/s) is sometimes wild type or near wild type; in other cases, the suppressor produces its own abnormal phenotype.

Suppressors also result in modified dihybrid ratios. Let’s look at a real example from Drosophila and consider a recessive suppressor su of the unlinked recessive purple eye color allele pd. A homozygous purple-eyed fly is crossed with a homozygous red-eyed stock carrying the suppressor.

Image ch4e22.jpg

The overall ratio in the F2 is 13 red:3 purple. This ratio is characteristic of a recessive suppressor acting on a recessive mutation. Both recessive and dominant suppressors are found, and they can act on recessive or dominant mutations. These possibilities result in a variety of different phenotypic ratios.

Suppression is sometimes confused with epistasis. However, the key difference is that a suppressor cancels the expression of a mutant allele and restores the corresponding wild-type phenotype. The modified ratio is an indicator of this type of interaction. Furthermore, often only two phenotypes segregate (as in the preceding example), not three, as in epistasis.

How do suppressors work at the molecular level? There are many possible mechanisms. A well-researched type is the nonsense suppressor, which acts on a mutation caused by a translation-termination (nonsense) codon within a coding sequence. Nonsense mutants produce premature amino acid chain termination. However, a mutation in a tRNA anticodon that allows the tRNA to insert an amino acid at a nonsense codon will suppress the effect of the mutation by allowing protein synthesis to proceed past the site of the mutation in the mRNA. Because tRNA genes are often present in several copies, a suppressor mutation in one of them will be perfectly viable. Another type of suppression is possible in protein–protein interactions. If two proteins normally fit together to provide some type of cellular function, when a mutation causes a shape change in one protein, no bonding occurs and hence no function (Figure 4-15). However, a compensatory shape change by mutation in the second protein can act as a suppressor to restore normal binding. Finally, in situations in which a mutation causes a block in a metabolic pathway, the suppressor finds some way of circumventing the block—for example, by channeling in substances beyond the block from related pathways.

Figure 4-15. A molecular mechanism for suppression.

Figure 4-15

A molecular mechanism for suppression.

Because of the demonstrable interaction of a suppressor with its target gene, geneticists deliberately seek suppressors as another way of piecing together a set of interacting genes that affect one biological process or structure. The approach is relatively easy because all that is necessary is to perform a large-scale mutation-induction experiment starting with a mutant line (say, genotype m) and simply look for rare individuals that are wild type. Most of these wild types will be m+ reverse mutations, but some will be suppressed (m · su) and distinguishable by the dihybrid ratios produced on crossing. This procedure can be very easily applied in haploid organisms. For example, if large numbers of cells of an arginine-requiring mutant (arg) are spread on a plate of growth medium lacking arginine, most cells will not grow, but reverse mutations to the true wild-type allele (arg+) and suppressed mutations (arg · su) will grow and announce their presence by forming visible colonies. The suppressed colonies can be detected by crossing to wild type because arginine-requiring progeny will be produced:

Image ch4e23.jpg


Suppressors cancel the expression of a mutant allele of another gene, resulting in normal wild-type phenotype.

Duplicate genes.  

Our final example of gene interaction in the same pathway is based on the idea that some genes may be present more than once in the genome. The example concerns the genes that control fruit shape in the plant called shepherd’s purse, Capsella bursa-pastoris. Two different lines have fruits of different shapes: one is “heart shaped”; the other, “narrow.” Are these two phenotypes determined by two alleles of a single gene? A cross between the two lines produces an F1 with heart-shaped fruit; this result is consistent with the hypothesis of determination by a pair of alleles. However, the F2 shows a 15:1 ratio of heart-shaped to narrow, and this ratio suggests a specific modification of the dihybrid 9:3:3:1 Mendelian ratio in which the 9, 3, and 3 are grouped. The genetic control of fruit shape can be explained by means of duplicate genes (Figure 4-16). Apparently, heart-shaped fruits result from the presence of at least one dominant allele of either gene. The two genes appear to be identical in function. (Contrast this 15:1 ratio with the 9:7 ratio where both dominant genes are necessary to produce a specific phenotype.)

Figure 4-16. Inheritance pattern of duplicate genes controlling fruit shape in shepherd’s purse.

Figure 4-16

Inheritance pattern of duplicate genes controlling fruit shape in shepherd’s purse. Either A1 or A2 can cause a heart-shaped fruit.


Duplicate genes provide alternative genetic determination of a specific phenotype.

The next two sections present examples of how more than two genes interact in determining some specific character. One example is from a plant and one from an animal.

By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

Copyright © 2000, W. H. Freeman and Company.
Bookshelf ID: NBK21850


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