Interactions of Genes and the Environment

1Overview

Two plants grown from seeds of the same parent can end up very different if one sits in a sunny window and the other in a dark cupboard. Two people with similar DNA can differ in height, skin colour after a summer, or health outcomes. A gene is not a destiny. It is a set of instructions that works inside a living cell, in a body, in a particular environment. This lesson covers the official content item “interactions of genes and the environment”: how inherited information and surroundings combine to produce the traits seen in an organism.

2Genotype, phenotype and environment

The genotype is the set of alleles an organism carries. The phenotype is the set of observable traits that results: appearance, body chemistry, behaviour and health. The relationship can be summarized as:

phenotype = genotype + environment (and their interactions)

The environment here means everything that is not the DNA sequence itself. It includes outside factors such as nutrition, sunlight, temperature, exposure to chemicals and infections, and also internal factors such as hormones. Scientists often describe the combined influence as “nature and nurture.” Neither alone explains a trait, and the question for most traits is how much each contributes.

3A single-gene example: phenylketonuria (PKU)

Phenylketonuria is a clear example of how an environmental factor, in this case diet, can decide how a genotype is expressed. People with PKU have variants of the PAH gene that reduce or remove the activity of an enzyme, phenylalanine hydroxylase. This enzyme normally converts the amino acid phenylalanine into other compounds. Without it, phenylalanine builds up in the blood and tissues, and the nerve cells of the brain are especially sensitive to it.

PKU is inherited in an autosomal recessive pattern: a child must inherit two altered copies of the gene, and parents are typically carriers with one altered copy who show no signs. In many places, newborn babies are screened shortly after birth. When PKU is found early, a diet low in phenylalanine, which limits high-protein foods such as meat, dairy, nuts and tofu, is the main management. Without treatment, high levels of phenylalanine can cause intellectual disability, seizures and other problems.

The genotype is identical in the two situations in the diagram, but the phenotype is very different. This is a direct demonstration that changing the environment can change the outcome of a genetic condition. It also shows that a “genetic” disease is not always an “unavoidable” one. The same principle applies to mothers with PKU: if the diet is not followed during pregnancy, high phenylalanine levels can harm the developing fetus, even though the baby itself may not have PKU.

4Polygenic traits and the example of height

Most traits are not controlled by a single gene with two alleles. A polygenic trait is influenced by many genes, each contributing a small effect. Human eye colour involves at least eight genes, and height is a stronger example: more than 700 height-associated variants have been identified, with more expected, and some of them affect the cartilage in the growth plates where bones lengthen during childhood.

Scientists estimate that about 80 percent of height differences in a population are tied to inherited DNA variations. That figure is a statement about a population, not a rule for an individual, and it does not mean the environment does not matter. Nutrition, general health and activity all influence growth. Exposures during pregnancy, such as maternal nutrition, smoking and hazardous substances, can also affect a child’s height. Studies of immigrant families suggest that moving to a place with better nutrition and healthcare can raise the height of the next generation, which indicates that some differences between groups are not genetic.

Because many variants combine in many different ways, a child’s adult height is hard to predict. Children usually end up near their parents’ heights, but siblings can differ. Polygenic traits typically show continuous variation, a smooth spread of values, instead of a few distinct types as in Mendel’s peas.

5Genes that interact with other genes

The environment of a gene also includes the other genes in the cell. In epistasis, one gene suppresses or changes the expression of another. In mice, for example, one gene is required for any coat pigment to be made, so a mouse with two non-functional copies of that gene is albino regardless of which alleles it carries for coat colour at a second gene. Gene-gene interactions of this kind produce ratios of offspring that differ from the simple patterns taught in the next lessons.

6Epigenetics: the environment writes on the genome

The environment can affect gene activity directly. As explained in the gene expression lesson, epigenetic changes alter how strongly genes are switched on or off without changing the DNA sequence. Chemical tags are added to DNA (methylation, which usually silences genes) or to histone proteins (which loosen or tighten the packing of DNA).

Several features of epigenetic marks make them important for gene-environment interactions:

• They are reversible. The tags “are not permanent, but may be added or removed as needed.”
• They often persist through cell division, so that a cell’s pattern of gene activity is passed to its daughter cells.
• Diet and other environmental factors can alter patterns of DNA methylation.
• Some marks can be passed from one generation to the next. For instance, imprinted genes that are silenced during the development of one parent’s eggs or sperm remain silenced in the offspring.

The study of the full set of epigenetic changes in a genome is called epigenomics. It is an active research field, and many details of how the environment and epigenetic marks interact are still being worked out.

7Mutagens and the environment

Some environmental factors act on the DNA sequence itself. Ultraviolet radiation from the sun is listed as a cancer-causing exposure, because it can damage DNA. Cancer begins with changes in genes that alter how cells function. Some of these changes occur naturally when cells divide, and others result from environmental exposures that damage DNA. Being exposed to a carcinogen does not guarantee cancer: dose, how long the exposure lasts, and genetic background all influence risk. This topic is treated in detail in the lesson on mutation, but it shows that the gene-environment relationship goes both ways, since the environment can change genes and genes affect how the body copes with the environment.

8Complex diseases and the limits of prediction

Single-gene conditions such as cystic fibrosis follow predictable patterns, but they are the minority. In developed countries single-gene defects account for only about 5 percent of diseases. Common conditions such as heart disease and type 2 diabetes involve multiple genes and environmental factors such as diet, and they do not follow simple inheritance patterns.

This has practical consequences. A genetic test may reveal an increased risk, but it cannot say with certainty that a disease will occur. Lifestyle choices can lower risk for many conditions regardless of genotype, and a person with no known genetic risk can still develop the disease. For this reason, genetic information is best seen as one part of a picture that also includes family history, lifestyle and environment.

9Investigating gene-environment questions

The curriculum asks students to consider questions such as how to determine whether characteristics are genetically inherited, and how genetic data can be gathered to study traits. Careful reasoning is needed because a trait that runs in a family may be inherited, or the family may simply share an environment (such as diet). Evidence that helps separate the two includes:

1. Comparing relatives who share different proportions of genes and different environments.
2. Changing one factor at a time. In plants and animals, genetically identical individuals can be raised in different conditions, or different genotypes can be raised under the same conditions.
3. Looking for the gene. Genome studies can search for variants that are more common in people with a trait, as has been done for height.
4. Using large samples. Mendel’s work, like modern studies, relied on many individuals to avoid being misled by chance.

The following lessons turn to the patterns by which alleles are inherited, beginning with Mendel’s experiments. The role of the environment remains important throughout, because every pattern of inheritance describes only how alleles are passed on, not how they are expressed in every situation. More about how DNA works is in What is DNA?.

10Practice problems with solutions

Problem 1: interpreting a family result

Both parents of a child are carriers of PKU (Pp × Pp). What is the chance that the child has PKU, and what could be done after birth?

Solution. The Punnett square gives 1 PP : 2 Pp : 1 pp, so the chance of PKU is 1 in 4. Newborn screening can detect PKU shortly after birth. If it is present, a low-phenylalanine diet developed with a health care professional is the main way to keep phenylalanine in a safe range, so the phenotype depends on the environment as well as the genotype.

Problem 2: an experiment on a plant trait

A student wants to know whether leaf size in a plant is mostly genetic. A fair test grows cuttings from one plant (identical genes) in bright and dim light, and grows several different varieties together in the same light. If the cuttings differ between light levels, the environment matters. If different varieties differ under the same light, genes matter. Using many plants in each group reduces the effect of chance. If both comparisons show differences, both factors contribute.

Common points to remember

• A genotype can allow a range of phenotypes, and the environment influences where in that range an individual falls.
• A trait that is highly heritable in a population is not fixed for an individual, and a trait that is affected by the environment is not necessarily easy to change.
• Epigenetic marks can respond to diet and other exposures, and some can be passed to later generations.

Why the distinction matters

Public health depends on this reasoning. If a condition were purely genetic, only genetic counselling could address it. Because many conditions respond to environment, diet changes, sun protection, avoiding tobacco smoke and healthy pregnancy care can lower risk even for people with inherited susceptibility. Students evaluating a health claim can ask whether it describes a gene, an environmental exposure, or an interaction of the two.

?Quick check

Try each question first, then reveal the answer.