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Genetics

Contents of this Section

Some Phenotypes and Their Explanations

 

The Link Between Genotype and Phenotype

It is often difficult to understand the terms genotype and phenotype. These are new words, unique to genetics. They sound somewhat similar to each other, and each refers to a concept, rather than to something concrete that we can see, touch, and feel. What may be most confusing, however, is that we often don't see the link between genotype and phenotype until much later in our study of biology. Here, we provide some information that should help us make that link.

First, the terminology:

  • Genotype: the genes in the individual. When considering a single trait and a single gene, genotype refers to an individual's alleles of that gene. This is fairly easy to remember by thinking of genotype as "the type of genes" carried by an individual.
  • Phenotype: in the simplest definition, phenotype is what an individual looks like. This is the individual's traits, or characteristics. Usually, we refer to an individual's appearance; but many genes affect biochemical characteristics that we can't actually see by eye, and other genes affect behavior. A more broad definition might be "what an individual is like." When considering a particular trait, we usually refer just to that trait when we describe the individual's phenotype.

Mendel's Peas

In his experiments, Gregor Mendel worked with a number of different characteristics, or traits, of pea plants. In the population of pea plants grown at the monastery, there was rather little genetic variation; each of the traits he studied had only two versions. This probably reflects the fact that a single pea plant can pollinate its own flowers, so all of the offspring from that plant carry only the two alleles of the parent plant. Whatever the reason, this provided Mendel with fairly simple inheritance patterns--unlike the inheritance of brown hair color that we observe in human families.

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Pod Color

The pod is the structure that holds the seeds. Technically, this is the fruit of the pea plant. With snow peas and sugar-snap peas, we often harvest immature pods and eat them either fresh or cooked (as we do with green beans). Usually, however, we remove the peas from the pods, and eat just the seeds.

As with the peas themselves, Mendel's plants displayed two possible colors: yellow and green. The underlying explanations are the same.

Trait
Explanation for Trait

Green

The genes for chlorophyll production are active in cells of the pod. The green pigment (chlorophyll) is produced in the pod.

Yellow

The genes for chlorophyll productions are not active in the pod, so chlorophyll is not produced. The yellow color results from yellow pigments that are produced independently of chlorophyll (and are present in green pods also).

 

Genotype

(the alleles)

Phenotype

(the appearance)

Explanation for Phenotype
green/green green pods The genes for chlorophyll production are active.
yellow/yellow yellow pods The genes are not active, so chlorophyll is not made.
yellow/green green pods The green allele activates the genes for chlorophyll production. Once the genes have been activated, the green pigment is produced.

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Flower Color

Mendel's plants had either white flowers or purple flowers. The underlying reasons for the presence or absence of the purple pigment are similar to the reasons for presence or absence of green pigment in seeds and pods.

Trait
Explanation for Trait

Purple

The genes for production of a purple pigment (anthocyanin) are active in cells of the flower, so the pigment is made.

White

The genes for pigment production are inactive, so pigment is not made.

 

Genotype

(the alleles)

Phenotype

(the appearance)

Explanation for Phenotype
purple/purple purple flowers The genes for pigment production are active.
white/white white flowers The genes are not active, so purple pigment is not made.
purple/white purple flowers The purple allele activates the genes for pigment production, so the purple pigment is produced.

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Round and Wrinkled Seeds

In most plants, seeds go through a process of drying before they are released from the mother plant. As the mother plant absorbs water from the seed, the seed shrinks in size. The final size of the seed is determined by the quantity of nutrients that the seed has stored (which it does in order to provide food for the embryo to use as it first starts to grow). Most of that food is starch, a chemical that is produced by assembling glucose molecules into long fibers.

There are many enzymes involved in the production of starch in seeds. Any of these genes can be inactivated by mutation, which interferes with starch accumulation in the seed. It requires mutations in several of these genes to prevent starch accumulation altogether.

In Mendel's pea plants, some carried a mutant allele of one of these starch-assembly enzymes. With less starch in the seed, the drying process results in a final seed size that is smaller than normal. But since the seed coat is normal size, the seed coat shrinks and wrinkles during drying of the seed.

note: This is the same process that we see in corn, where "field corn" is normal, "sweet corn" is wrinkled, and "super sweet corn" is severely shrunken. This is described below.

Trait
Explanation for Trait

Round

Normal amounts of starch are produced in the seed.

Wrinkled

An allele of one of the genes for starch accumulation is at least partly inactive, so less starch is produced than normal. The seed shrinks during drying, and the seed coat wrinkles.

 

Genotype

(the alleles)

Phenotype

(the appearance)

Explanation for Phenotype
round/round round seeds The seed accumulates normal amounts of starch.
wrinkled/wrinkled wrinkled seeds An allele of one of the genes for starch accumulation is at least partly inactive, so less starch is produced than normal. The seed shrinks during drying, and the seed coat wrinkles.
round/wrinkled round seeds The fully-active allele for the starch-assembling enzyme is functional, and assembles glucose into starch. The inactive allele for this enzyme does not prevent the active enzyme from working, so starch accumulates to near-normal levels. The seed does not shrink and wrinkle.

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Seed Color

The round peas that we eat are the seeds of the plant. In our gardens, we often harvest peas before the seeds are fully mature, so they are still soft and moist. If we were to rely on peas as an important source of food during the winter, then we would allow the plants to reach maturity, and harvest the seeds after they have dried (as we do with beans).

The seeds of Mendel's peas came in two colors, yellow and green. In his genetic crosses, Mendel found that yellow is dominant to green. This contrasts with the yellow vs green colors of pea pods, where green is dominant to yellow. Pod color is easily explained by the production of green pigment, as described above. How can the opposite dominance relationship be explained?

Armstead et al. (Science 317:73 [2007]) recently found that the gene responsible for the green vs yellow color of pea seeds is responsible for chlorophyll degradation. That is, the normal development of pea seeds involves production of the green pigment followed by its degradation.

Trait
Explanation for Trait

Yellow

The genes for chlorophyll degradation are active in cells of the seed. The previously-produced green pigment (chlorophyll) is broken down. The yellow color results from yellow pigments that are produced independently of chlorophyll (and are present in green seeds also).

Green

The genes for chlorophyll degradation are not active in the seed, so the previously-produced chlorophyll remains.

 

Genotype

(the alleles)

Phenotype

(the appearance)

Explanation for Phenotype
yellow/yellow yellow seeds The chlrophyll-degradation genes are active, so chlorophyll is destroyed.
green/green green seeds The chlrophyl-degradation genes are inactive, so chlorophyll remains.
yellow/green yelow seeds The yellow allele activates the genes for chlorophyll degradation. Once the genes have been activated, the green pigment is destroyed.

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Flower Color in Snapdragons

Many pigments in plants and animals show a different behavior than Mendel's peas in the particular example described above. The particular genetic behavior depends on the particular genes involved and the particular DNA sequence changes that produce the alleles being studied. Snapdragons are a classic example of alleles that do not show strict dominance.

Trait
Explanation for Trait

Red

The genes for production of a red pigment are active in cells of the flower, so the pigment is made.

White

An allele of one of the genes for pigment production is inactive, so pigment is not made.

 

Genotype

(the alleles)

Phenotype

(the appearance)

Explanation for Phenotype
red/red

red flowers

The genes for production of a red pigment are active in cells of the flower, so the pigment is made.
white/white

white flowers

An allele of one of the genes for pigment production is inactive, so pigment is not made.
red/white

pink flowers

The fully-active allele for the pigment-producing enzyme functions, and produces red pigment. But, the inactive allele produces an enzyme that does not function, so the total enzyme activity is low. Therefore, less red pigment is made, and the flowers appear pink.

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Field Corn, Sweet Corn, and Super Sweet Corn

As described above for pea seeds, the portion of the corn plant that we eat is the seed. As the seed develops after pollination of the flower, it accumulates starch as its primary food reserve for the embryo to use during its first stages of growth. Several enzymes are involved in starch accumulation in the seed; mutations in any one of these can cause less starch to accumulate. Mutations are required in several of these genes at the same time to prevent starch accumulation altogether.

Corn seed cells absorb glucose from the sap of the plant, which produces glucose in its leaves by photosynthesis. Glucose, of course, is a sugar. If glucose is not assembled into starch in the developing seed, it remains glucose--or is converted to sweet fructose and sucrose. Therefore, immature seeds of plants that carry inactive alleles of the starch-assembly genes are much sweeter than are immature seeds of normal plants.

The majority of corn grown in the US is normal in its accumulation of starch. The seeds are allowed to reach maturity, and to dry out at the end of summer. The dry seeds (or "kernels") are harvested, stored, and eventually used for animal feed (about 80% of the crop), or for production of corn oil and high-fructose corn syrup (most of the rest of the crop), or for production of cornmeal, corn flakes, corn chips, and other similar products (very little of the crop overall). The varieties of corn used in this way are collectively called "field corn."

The corn that most of us know as corn-on-the-cob is immature corn seeds, harvested before the maturation of the seeds. The seeds are still moist and soft--and sweet. Immature field corn is not as sweet as the US public likes, however. Most of the glucose is converted to starch, which is flavorless. There are a number of other varieties of corn that we prefer. These carry mutations in the genes for the starch-assembly enzymes. As immature seeds, eaten as corn-on-the-cob, these seeds look normal, but taste much sweeter than field corn. When they mature, however, their lack of starch causes them to shrink and wrinkle, in much the same way as Mendel's wrinkled peas.

Trait
Explanation for Trait

Field Corn

Normal amounts of starch are produced in the seed.

Sweet Corn

An allele of one of the genes for starch accumulation is at least partly inactive, so less starch is produced than normal. The seed shrinks during drying, and the seed coat wrinkles.

The immature seeds are sweeter than normal, because the glucose that is not assembled into starch ends up as sweet fructose and sucrose.

The mutation is in the gene named sugary.

Super-Sweet Corn

In addition to the inactive allele of Sweet Corn, Super-Sweet varieties also carry an inactive allele of another one of the genes for starch accumulation. Far less starch is produced than normal. The seed shrinks severly during drying, and the seed coat wrinkles until is is almost empty.

The immature seeds are extremely sweet, because most of the glucose ends up as fructose and sucrose.

These kernels carry mutations in two genes, sugary and shrunken2.

When growing sweet corn or super-sweet corn, it is important to pollinate each variety exclusively with pollen from plants of the same variety. The sweet and super-sweet phenotypes are recessive, for the reasons described above for Mendel's round and wrinkled peas.

Below is a photograph of normal seeds (A), sugary seeds (B), shrunken seeds (C) , and seeds of the double-mutant, sugary shrunken (D) , from John Laughnan's original publication describing these mutations [Genetics 38:485 (1953)].

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Human Hair Color

As described in the preceding sections, human hair color varies tremendously. There are several different genes involved, including:

  • genes for production of the brown pigment (melanin)
  • genes that regulate production of the brown pigment
  • genes for assembly of the pigment into pigment granules
  • genes for modification of the pigment (producing red pigment)

All of these genes work together to produce the final hair color. Some of these same genes also influence eye color and skin color (hence the common association of light hair, light skin, and blue eyes, vs dark hair, dark skin, and brown eyes). In many animals, there are various alleles of the genes that regulate pigment production, resulting in different patterns of dark and light-colored hair. In humans, there are few, if any, such alleles that create color patterns; most of the alleles of these genes affect the overall quantity of pigment, resulting in darker or lighter hair.

Therefore, among the many shades of brown, there are contributions from multiple alleles of multiple genes. In general, however, we can make two statements relating the genotype to phenotype:

  • The more pigment the hair cells produce, the darker the hair color.
  • Darker hair-color alleles tend to be dominant over lighter alleles.

These two rules apply generally to these different shades of brown:

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Cystic Fibrosis

Cystic Fibrosis (CF) is a genetic condition usually recognized as a lung disorder. Untreated, the condition can cause death during childhood. Modern treatment methods enable CF sufferers to survive into early adulthood. There are many different degrees of the condition, reflecting the large number of different alleles that confer CF, and on other genetic factors that influence the presentation of the disease.

The gene, named CFTR, encodes a protein that is embedded in the plasma membrane of many cell types. The protein functions as a channel through which chloride ions are transported across the membrane (typically Cl- ions are exported from cells). The protein also interacts with other membrane proteins and affects their function. [CFTR stands for Cystic Fibrosis Transport Regulator.]

The medical condition of CF occurs only in individuals who carry two disease-causing alleles of the CFTR gene. The medical condition is thus recessive.

Like most heritable characteristics, however, CFTR does not show complete, strict dominance. Individuals who are heterozygous for a single disease-causing allele (and are referred to as CF "carriers") exhibit differences in chloride ion transport compared to individuals carrying two non-disease-causing alleles. This fact reflects (and explains) the geographic variation in the occurrence of CF in different human populations.

CF is very rare in equatorial Africa. In this hot climate, it is common to sweat during the day in order to maintain normal body temperature. Sweat is salty--containing sodium chloride, NaCl. CF carriers lose more salt while sweating than do non-carriers, and are thus susceptible to heat stroke and death. That is, the hot climate selects against CF disease-causing alleles, because heterozyous individuals are at a severe disadvantage.

In Europe, CF is much more common. Indeed, roughly 1000 different CFTR alleles are now known. The various alleles have been characterized extensively, both clinically and at the level of DNA sequence and the effect of DNA sequence changes on protein structure. The following is a summary figure that illustrates the locations of individual DNA sequence changes (mutations) of different types in the CFTR gene. Click on the figure or the link below it for additional information about these different alleles.

from the Cystic Fibrosis Mutation Database

In Europe, disease-causing alleles if CFTR are apparently not selected against by salt loss during sweating. Europe is colder than equatorial Africa, and sweating is not always necessary. But sweating sometimes is necessary during the summer; one would think this would select against disease-causing alleles. But the frequency of disease-causing alleles is much higher than would be expected if salt-loss during sweating were the entire heterozygous phenotype. What else differs in CF carriers, compared to non-carriers?

Severe diarrheal disease, such as Cholera, rapidly flushes sodium chloride from the body. The resulting electrolyte imbalance is one of the factors that can lead to death from such diseases. The mechanism by which diarrhea is produced involves transport of chloride ions (and sodium ions) into the colon, which impedes water uptake from the colon, and makes the colonic contents watery. The CFTR protein is a part of the system for transporting these ions into the colon. CF carriers transport less chloride into the colon when suffering from severe diarrheal disease. Thus, they lose less salt when sick with Cholera and similar diseases, and are more likely to survive.

In short, Cholera and similar diseases select for CFTR mutations when they are heterozygous. This selection would tend to increase the frequency of CFTR mutations in the population, despite the deadly homozygous phenotype.

For many centuries, European cities were beset by plagues--typhoid, Cholera, etc. Epidemic diseases were common. Especially common were food-borne and wate-borne bacterial diseases that cause severe diarrhea. Antibiotics had not yet been discovered, so there were no methods for curing the disease. One either pulled through somehow, or died.

Today in Europe these diseases are relatively rare. Antibiotics prevent them from reaching epidemic proportions when they do occur. Nonetheless, Europeans and many of us in the US who have European ancestry, carry the disease-causing CFTR alleles that helped our ancestors survive these disease epidemics.

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Drosophila melanogaster, the Fruit Fly: a Model System for Studying Genetics