Classical Genetics

In module 2 we studied molecular genetics. Here we are concerned with classical genetics, which is the study of inheritance of characteristics at the whole organism level. It is also known as transmission genetics or Mendelian genetics, since it was pioneered by Gregor Mendel.

Gregor Mendel  [back to top]

Mendel (1822-1884) was an Austrian monk at Brno monastery. He was a keen gardener and scientist, and studied at Vienna University, where he learnt statistics. He investigated inheritance in pea plants and published his results in 1866. They were ignored at the time, but were rediscovered in 1900, and Mendel is now recognised as the “Father of Genetics”. His experiments succeeded where other had failed because:

• Mendel investigated simple well-defined characteristics (or traits), such as flower colour or seed shape, and he varied one trait at a time. Previous investigators had tried to study many complex traits, such as human height or intelligence.
• Mendel use an organism whose sexual reproduction he could easily control by carefully pollinating stigmas with pollen using a brush. Peas can also be self-pollinated, allowing self crosses to be performed. This is not possible with animals.
• Mendel repeated his crosses hundreds of times and applied statistical tests to his results.
• Mendel studied two generations of peas at a time.

A typical experiment looked like this: 

Mendel made several conclusions from these experiments:

1.       There are no mixed colours (e.g. pink), so this disproved the widely-held blending theories of inheritance that characteristics gradually mixed over time.

2.       A characteristic can disappear for a generation, but then reappear the following generation, looking exactly the same. So a characteristic can be present but hidden.

3.       The outward appearance (the phenotype) is not necessarily the same as the inherited factors (the genotype) For example the P1 red plants are not the same as the F1 red plants.

4.       One form of a characteristic can mask the other. The two forms are called dominant and recessive respectively.

5.       The F2 ratio is always close to 3:1. Mendel was able to explain this by supposing that each individual has two versions of each inherited factor, one received from each parent. We’ll look at his logic in a minute.

6.       Mendel’s factors are now called genes and the two alternative forms are called alleles. So in the example above we would say that there is a gene for flower colour and its two alleles are “red” and “white”. One allele comes from each parent, and the two alleles are found on the same position (or locus) on the homologous chromosomes. With two alleles there are three possible combinations of alleles (or genotypes) and two possible appearances (or phenotypes):

The Monohybrid Cross  [back to top]

A simple breeding experiment involving just a single characteristic, like Mendel’s experiment, is called a monohybrid cross. We can now explain Mendel’s monohybrid cross in detail.

 At fertilisation any male gamete can fertilise any female gamete at random. The possible results of a fertilisation can most easily be worked out using a Punnett Square as shown in the diagram. Each of the possible outcomes has an equal chance of happening, so this explains the 3:1 ratio (phenotypes) observed by Mendel.

This is summarised in Mendel’s First Law, which states that individuals carry two discrete hereditary factors (alleles) controlling each characteristic. The two alleles segregate (or separate) during meiosis, so each gamete carries only one of the two alleles.

The Test Cross

You can see an individual’s phenotype, but you can’t see its genotype. If an individual shows the recessive trait (white flowers in the above example) then they must be homozygous recessive as it’s the only genotype that will give that phenotype. If they show the dominant trait then they could be homozygous dominant or heterozygous. You can find out which by performing a test cross with a pure-breeding homozygous recessive. This gives two possible results:

• If the offspring all show the dominant trait then the parent must be homozygous dominant.

• If the offspring are a mixture of phenotypes in a 1:1 ratio, then the parent must be heterozygous.

How does Genotype control Phenotype?

Mendel never knew this, but we can explain in detail the relation between an individual’s genes and its appearance. A gene was originally defined as an inherited factor that controls a characteristic, but we now know that a gene is also a length of DNA that codes for a protein. It is the proteins that actually control phenotype in their many roles as enzymes, pumps, transporters, motors, hormones, or structural elements. For example the flower colour gene actually codes for an enzyme that converts a white pigment into a red pigment:

• The dominant allele is the normal (or “wild-type”) form of the gene that codes for functioning enzyme, which therefore makes red-coloured flowers.
• The recessive allele is a mutation of the gene. This mutated gene codes for non-functional enzyme, so the red pigment can’t be made, and the flower remains white. Almost any mutation in a gene will result in an inactive gene product (usually an enzyme), since there are far more ways of making an inactive protein than a working one.

Sometimes the gene actually codes for a protein apparently unrelated to the phenotype. For example the gene for seed shape in peas (round or wrinkled) actually codes for an enzyme that synthesises starch! The functional enzyme makes lots of starch and the seeds are full and rounded, while the non-functional enzyme makes less starch so the seeds wrinkle up.

This table shows why the allele that codes for a functional protein is usually dominant over an allele that codes for a non-function protein. In a heterozygous cell, some functional protein will be made, and this is usually enough to have the desired effect. In particular, enzyme reactions are not usually limited by the amount of enzyme, so a smaller amount will have little effect.

Sex Determination [back to top]

In module 2 we saw that sex is determined by the sex chromosomes (X and Y). Since these are non-homologous they are called heterosomes, while the other 22 pairs are called autosomes. In humans the sex chromosomes are homologous in females (XX) and non-homologous in males (XY), though in other species it is the other way round. The inheritance of the X and Y chromosomes can be demonstrated using a monohybrid cross:

This shows that there will always be a 1:1 ratio of males to females. Note that female gametes (eggs) always contain a single X chromosome, while the male gametes (sperm) can contain a single X or a single Y chromosome. Sex is therefore determined solely by the sperm. There are techniques for separating X and Y sperm, and this is used for planned sex determination in farm animals using IVF.

Sex Linkage

The X and Y chromosomes don’t just determine sex, but also contain many other genes that have nothing to do with sex determination. The Y chromosome is very small and seems to contain very few genes, but the X chromosome is large and contains thousands of genes for important products such as rhodopsin (a protein in the membrane of a photoreceptor cell in the retina of the eye, basically a light absorbing pigment), blood clotting proteins and muscle proteins. Females have two copies of each gene on the X chromosome (i.e. they’re diploid), but males only have one copy of each gene on the X chromosome (i.e. they’re haploid). This means that the inheritance of these genes is different for males and females, so they are called sex linked characteristics.

The first example of sex linked genes discovered was eye colour in Drosophila fruit flies. Red eyes (R) are dominant to white eyes (r) and when a red-eyed female is crossed with a white-eyed male, the offspring all have red eyes, as expected for a dominant characteristic (left cross below). However, when the opposite cross was done (a white-eye male with a red-eyed female) all the male offspring had white eyes (right cross below). This surprising result was not expected for a simple dominant characteristic, but it could be explained if the gene for eye colour was located on the X chromosome. Note that in these crosses the alleles are written in the form X^R (red eyes) and X^r (white eyes) to show that they are on the X chromosome.

Males always inherit their X chromosome from their mothers, and always pass on their X chromosome to their daughters.

Another well-known example of a sex-linked characteristic is colour blindness in humans. 8% of males are colour blind, but only 0.7% of females. The genes for green-sensitive and red-sensitive rhodopsin are on the X chromosome, and mutations in either of these lead to colour blindness. The diagram below shows two crosses involving colour blindness, using the symbols X^R for the dominant allele (normal rhodopsin, normal vision) and X^r for the recessive allele (non-functional rhodopsin, colour blind vision).

Other examples of sex linkage include haemophilia, premature balding and muscular dystrophy.

Codominance  [back to top]

In most situations (and all of Mendel’s experiments) one allele is completely dominant over the other, so there are just two phenotypes. But in some cases there are three phenotypes, because neither allele is dominant over the other, so the heterozygous genotype has its own phenotype. This situation is called codominance or incomplete dominance. Since there is no dominance we can no longer use capital and small letters to indicate the alleles, so a more formal system is used. The gene is represented by a letter, and the different alleles by superscripts to the gene letter.

A good example of codominance is flower colour in snapdragon (Antirrhinum) plants. The flower colour gene C has two alleles: C^R (red) and C^W (white). The three genotypes and their phenotypes are:

In this case the enzyme is probably less active, so a smaller amount of enzyme will make significantly less product, and this leads to the third phenotype. The monohybrid cross looks like this:

Note that codominance is not an example of “blending inheritance” since the original phenotypes reappear in the second generation. The genotypes are not blended and they still obey Mendel’s law of segregation. It is only the phenotype that appears to blend in the heterozygotes.

Another example of codominance is sickle cell haemoglobin in humans. The gene for haemoglobin Hb has two codominant alleles: Hb^A (the normal gene) and Hb^S (the mutated gene). There are three phenotypes:

Other examples of codominance include coat colour in cattle (red/white/roan), and coat colour in cats (black/orange/tortoiseshell).

Lethal Alleles  [back to top]

An unusual effect of codominance is found in Manx cats, which have no tails. If two Manx cats are crossed the litter has ratio of 2 Manx kittens to 1 normal (long-tailed) kitten. The explanation for this unexpected ratio is explained in this genetic diagram:

 The gene S actually controls the development of the embryo cat’s spine. It has two codominant alleles: S^N (normal spine) and S^A (abnormal, short spine). The three phenotypes are:

Many human genes also have lethal alleles, because many genes are so essential for life that a mutation in these genes is fatal. If the lethal allele is expressed early in embryo development then the fertilised egg may not develop enough to start a pregnancy, or the embryo may miscarry. If the lethal allele is expressed later in life, then we call it a genetic disease, such as muscular dystrophy or cystic fibrosis.

Multiple Alleles  [back to top]

An individual has two copies of each gene, so can only have two alleles of any gene, but there can be more than two alleles of a gene in a population. An example of this is blood group in humans. The red blood cell antigen is coded for by the gene I (for isohaemaglutinogen), which has three alleles I^A, I^B and I^O. (They are written this way to show that they are alleles of the same gene.) I^A and I^B are codominant, while I^O is recessive. The possible genotypes and phenotypes are:

 The cross below shows how all four blood groups can arise from a cross between a group A and a group B parent.

Other examples of multiple alleles are: eye colour in fruit flies, with over 100 alleles; human leukocyte antigen (HLA) genes, with 47 known alleles.

Multiple Genes

So far we have looked at the inheritance of a single gene controlling a single characteristic. This simplification allows us to understand the basic rules of heredity, but inheritance is normally much more complicated than that. We’ll now turn to the inheritance of characteristics involving two genes. This gets more complicated, partly because there are now two genes to consider, but also because the two genes can interact with each other. We’ll look at three situations:

• 2 independent genes, controlling 2 characteristics (the dihybrid cross).

• 2 independent genes controlling 1 characteristic (polygenes)

• 2 interacting genes controlling 1 characteristic (epistasis)

The Dihybrid Cross

Mendel also studied the inheritance of two different characteristics at a time in pea plants, so we’ll look at one of his dihybrid crosses. The two traits are seed shape and seed colour. Round seeds (R) are dominant to wrinkled seeds (r), and yellow seeds (Y) are dominant to green seeds (y). With these two genes there are 4 possible phenotypes:

Mendel’s dihybrid cross looked like this:

All 4 possible phenotypes are produced, but always in the ratio 9:3:3:1. Mendel was able to explain this ratio if the factors (genes) that control the two characteristics are inherited independently; in other words one gene does not affect the other. This is summarised in Mendel’s second law (or the law of independent assortment), what states that alleles of different genes are inherited independently.

We can now explain the dihybrid cross in detail.

The gametes have one allele of each gene, and that allele can end up with either allele of the other gene. This gives 4 different gametes for the second generation, and 16 possible genotype outcomes.

Dihybrid Test Cross  [back to top]

There are 4 genotypes that all give the same round yellow phenotype. Just like we saw with the monohybrid cross, these four genotypes can be distinguished by crossing with a double recessive phenotype. This gives 4 different results:

Polygenes   [back to top]

Sometimes two genes at different loci (i.e. separate genes) can combine to affect one single characteristic. An example of this is coat colour in Siamese cats. One gene controls the colour of the pigment, and black hair (B) is dominant to brown hair (b). The other gene controls the dilution of the pigment in the hairs, with dense pigment (D) being dominant to dilute pigment (d). This gives 4 possible phenotypes:

The alleles are inherited in exactly the same way as in the dihybrid cross above, so the same 9:3:3:1 ratio in the F2 generation is produced. The only difference is that here, we are looking at a single characteristic, but with a more complicated phenotype ratio than that found in a monohybrid cross.

A more complex example of a polygenic character is skin colour in humans. There are 5 main categories of skin colour (phenotypes) controlled by two genes at different loci. The amount of skin pigment (melanin) is proportional to the number of dominant alleles of either gene:

 Some other examples of polygenic characteristics are: eye colour, hair colour, and height. The important point about a polygenic character is that it can have a number of different phenotypes, and almost any phenotypic ratio

Epistasis   [back to top]

In epistasis, two genes control a single character, but one of the genes can mask the effect of the other gene. A gene that can mask the effect of another gene is called an epistatic gene (from the Greek meaning “to stand on”). This is a little bit like dominant and recessive alleles, but epistasis applies to two genes at different loci. Epistasis reduces the number of different phenotypes for the character, so instead of having 4 phenotypes for 2 genes, there will be 3 or 2. We’ll look at three examples of epistasis.

 1. Dependent genes. In mice one gene controls the production of coat pigment, and black pigment (B) is dominant to no pigment (b). Another gene controls the dilution of the pigment in the hairs, with dense pigment (D) being dominant to dilute pigment (d). This is very much like the Siamese cat example above, but with one important difference: the pigment gene (B) is epistatic over the dilution gene (D) because the recessive allele of the pigment gene is a mutation that produces no pigment at all, so there is nothing for the dilution gene to affect.  This gives 3 possible phenotypes: 

  2. Enzymes in a pathway. In a certain variety of sweet pea there are two flower colours (white and purple), but the F2 ratio is 9:7. This is explained if the production of the purple pigment is controlled by two enzymes in a pathway, coded by genes at different loci.        

Gene P is epistatic over gene Q because the recessive allele of gene P is a mutation that produces inactive enzyme, so there is no compound B for enzyme Q to react with. This gives just two possible phenotypes:

3. Duplicate Genes. This occurs when genes at two different loci make enzyme that can catalyse the same reaction (this can happen by gene duplication). In this case the coloured pigment is always made unless both genes are present as homozygous recessive (ppqq), so the F2 ratio is 15:1.

So epistasis leads to a variety of different phenotype ratios.

Expected ratios, observed ratios and the chi-squared test  [back to top]

In the monohybrid cross, the F₂ ratio was 3:1, and with the dihybrid cross the ratio was 9:3:3:1.  These are expected ratios, calculated from genotypes of the parental generation - assuming independent assortment, no sex linkage, or codominance.  In real crosses the offspring produced depends on chance fusion of gametes (fertilisation), leading to observed ratios.  There are differences between expected and observed rat