7.5: Observing an individual’s phenotype is not sufficient for determining its genotype.

Things are not always as they appear. Take skin coloration, for example. Humans and many other animals have a gene that contains the information for producing melanin, one of the chemicals responsible for giving our skin its coloring (FIGURE 7-11). This gene is one of many that influence skin color. Unfortunately, there is also a defective, non-functioning version of the melanin gene that is passed along through some families. An individual who inherits two copies of the defective version of the gene cannot produce pigment and has a condition known as albinism, a disorder characterized by little or no pigment in the eyes, hair, and skin. But it is impossible to tell whether a normally pigmented individual carries one of these defective alleles just by looking at his or her appearance—we would need to get a genetic analysis done to discover this information.

The inability to deduce an individual’s genetic makeup through simple observation is a general problem in genetics: physical appearances don’t necessarily reflect the underlying genes. A normally pigmented individual may carry two copies of the pigment-producing allele or may have just one. In either case, the individual will look the same. The outward appearance of an individual is called its phenotype. A phenotype includes features visible to the naked eye such as flashy coloration, height, or the presence of antlers. A phenotype also includes less easily visible characteristics such as the chemicals an individual produces to clot blood or digest lactose. An individual’s phenotype even includes the behaviors it exhibits.

Underlying the phenotype is the genotype. This is an organism’s genetic composition. We usually speak of an individual’s genotype in reference to a particular trait. For example, an individual’s genotype might be described as “homozygous for the recessive allele for albinism,” meaning that the person has two recessive alleles of the gene. Another individual’s genotype for the melanin gene might be described as “heterozygous” (a recessive allele and a dominant allele.) Occasionally, the word “genotype” is also used as a way of referring to all of the genes an individual carries.

When an organism exhibits a recessive trait, such as albinism, we know with certainty what its genotype is for the melanin gene. When it shows the dominant trait, on the other hand, it’s impossible to distinguish whether the organism carries two copies of the dominant allele (homozygous dominant) or carries one copy of the dominant allele and one of the recessive (heterozygous). Because it’s not possible to discern the genotypes of two individuals with the same phenotype just by looking at them, much of genetic analysis must make use of clever experiments and careful record-keeping.

To analyze and predict the outcome of crosses, first we must assign symbols to represent the different variants of a gene. Generally we use an uppercase letter for the dominant allele and lowercase letter for the recessive allele. In the case of pigmentation/albinism, we use the letter “m” because the trait is caused by the gene carrying instructions for production of the pigment melanin. We represent the genotype of the albino giraffe as mm, because that individual must carry two copies of the recessive allele, m. A giraffe that is pigmented must have the genotype MM or Mm. If we don’t know which of the two possible genotypes the pigmented individual has, we can write M_ where _ is a placeholder for the unknown second allele.

We can trace the possible outcomes of a cross between two individuals using a handy tool called the Punnett square. In FIGURE 7-12 we illustrate the cross between a true-breeding pigmented individual, MM, and an albino, mm. Along the top of the square we list, individually, the two alleles that one of the parents produces, and along the left side of the square we list the two alleles that the other parent produces. We split up an individual’s two alleles in this way because, although the individual carries two alleles, only one of the alleles is contained in each sperm or egg cell that it produces. The two gametes that come together at fertilization produce the genotype of the offspring.

In the four cells of the Punnett square, we enter the genotypes of all the possible offspring resulting from our cross. Each cell contains one allele given at the head of the column and one allele at the left of the row. In Cross 1 illustrated in Figure 7-12, every possible offspring would be heterozygous and would be normally pigmented, because it receives a dominant allele from the pigmented parent and a recessive allele from the albino parent.

In the bottom half of Figure 7-12 (Cross 2), we trace the cross between two heterozygous individuals. Note that each parent produces two kinds of gametes, one with the dominant allele and one with the recessive allele. This cross has three possible outcomes: one-quarter of the time the offspring will be homozygous dominant (MM), one-quarter of the time the offspring will be homozygous recessive (mm), and the remaining half of the time the offspring will be heterozygous (Mm). Phenotypically, three-quarters of the offspring will be normally pigmented (MM or Mm) and one-quarter will be albino (mm).