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Polygenic inheritance and environmental effects

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IST‑1.J (LO)
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IST‑1.J.3 (EK)
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SYI‑3.B (LO)
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SYI‑3.B.1 (EK)
Traits that are controlled by multiple genes and/or influenced by the environment. Penetrance and expressivity.

How is height inherited?

If what you're really interested in is human genetics, learning about Mendelian genetics can sometimes be frustrating. You'll often hear a teacher use a human trait as an example in a genetics problem, but then say, "that's an oversimplification" or "it's much more complicated than that." So, what's actually going on with those interesting human traits, such as eye color, hair and skin color, height, and disease risk?
As an example, let's consider human height. Unlike a simple Mendelian characteristic, human height displays:
  • Continuous variation. Unlike Mendel's pea plants, humans don’t come in two clear-cut “tall” and “short” varieties. In fact, they don't even come in four heights, or eight, or sixteen. Instead, it’s possible to get humans of many different heights, and height can vary in increments of inches or fractions of inchesstart superscript, 1, end superscript.
    Histogram showing height in inches of male high school seniors in a sample group. The histogram is roughly bell-shaped, with just a few individuals at the tails (60 inches and 77 inches) and many individuals in the middle, around 69 inches.
    The heights of a group of male high school seniors. Image modified from "Continuous variation: Quantitative traits," by J. W. Kimball (CC BY 3.0)
  • A complex inheritance pattern. You may have noticed that tall parents can have a short child, short parents can have a tall child, and two parents of different heights may or may not have a child in the middle. Also, siblings with the same two parents may have a range of heights, ones that don't fall into distinct categories.
Simple models involving one or two genes can't accurately predict all of these inheritance patterns. How, then, is height inherited?
Height and other similar features are controlled not just by one gene, but rather, by multiple (often many) genes that each make a small contribution to the overall outcome. This inheritance pattern is sometimes called polygenic inheritance (poly- = many). For instance, a recent study found over 400 genes linked to variation in heightsquared.
When there are large numbers of genes involved, it becomes hard to distinguish the effect of each individual gene, and even harder to see that gene variants (alleles) are inherited according to Mendelian rules. In an additional complication, height doesn’t just depend on genetics: it also depends on environmental factors, such as a child’s overall health and the type of nutrition he or she gets while growing up.
In this article, we’ll examine how complex traits such as height are inherited. We'll also see how factors like genetic background and environment can affect the phenotype (observable features) produced by a particular genotype (set of gene variants, or alleles).

Polygenic inheritance

Human features like height, eye color, and hair color come in lots of slightly different forms because they are controlled by many genes, each of which contributes some amount to the overall phenotype. For example, there are two major eye color genes, but at least 14 other genes that play roles in determining a person’s exact eye colorcubed.
Looking at a real example of a human polygenic trait would get complicated, largely because we’d have to keep track of tens, or even hundreds, of different allele pairs (like the 400 involved in height!). However, we can use an example involving wheat kernels to see how several genes whose alleles "add up" to influence the same trait can produce a spectrum of phenotypesstart superscript, 1, comma, 4, end superscript.
In this example, there are three genes that make reddish pigment in wheat kernels, which we’ll call A, B, and C. Each comes in two alleles, one of which makes pigment (the capital-letter allele) and one of which does not (the lowercase allele). These alleles have additive effects: the aa genotype would contribute no pigment, the Aa genotype would contribute some amount of pigment, and the AA genotype would contribute more pigment (twice as much as Aa). The same would hold true for the B and C genesstart superscript, 1, comma, 4, end superscript.
64-square Punnett square illustrating the phenotypes of the offspring of an AaBbCc x AaBbCc cross (in which each uppercase allele contributes one unit of pigment, while each lowercase allele contributes zero units of pigment).
Of the 64 squares in the chart:
1 square produces a very very dark red phenotype (six units of pigment)
6 squares produce a very dark red phenotype (five units of pigment)
15 squares produce a dark red phenotype (four units of pigment).
20 squares produce a red phenotype (three units of pigment)
15 squares produce a light red phenotype (two units of pigment)
6 squares produce a very light red phenotype (one unit of pigment)
1 square produces a white phenotype (no units of pigment)
Diagram based on similar diagram by W. P. Armstrongstart superscript, 5, end superscript.
Now, let’s imagine that two plants heterozygous for all three genes (AaBbCc) were crossed to one another. Each of the parent plants would have three alleles that made pigment, leading to pinkish kernels. Their offspring, however, would fall into seven color groups, ranging from no pigment whatsoever (aabbcc) and white kernels to lots of pigment (AABBCC) and dark red kernels. This is in fact what researchers have seen when crossing certain varieties of wheatstart superscript, 1, comma, 4, end superscript.
This example shows how we can get a spectrum of slightly different phenotypes (something close to continuous variation) with just three genes. It’s not hard to imagine that, as we increased the number of genes involved, we’d be able to get even finer variations in color, or in another trait such as height.

Environmental effects

Human phenotypes—and phenotypes of other organisms—also vary because they are affected by the environment. For instance, a person may have a genetic tendency to be underweight or obese, but his or her actual weight will depend on diet and exercise (with these factors often playing a greater role than genes). In another example, your hair color may depend on your genes—until you dye your hair purple!
One striking example of how environment can affect phenotype comes from the hereditary disorder phenylketonuria (PKU)start superscript, 6, end superscript. People who are homozygous for disease alleles of the PKU gene lack activity of an enzyme that breaks down the amino acid phenylalanine. Because people with this disorder cannot get rid of excess phenylalanine, it rapidly builds up to toxic levels in their bodiesstart superscript, 7, end superscript.
If PKU is not treated, the extra phenylalanine can keep the brain from developing normally, leading to intellectual disability, seizures, and mood disorders. However, because PKU is caused by the buildup of too much phenylalanine, it can also be treated in a very simple way: by giving affected babies and children a diet low in phenylalaninestart superscript, 8, end superscript.
If people with phenylketonuria follow this diet strictly from a very young age, they can have few, or even no, symptoms of the disorder. In many countries, all newborns are screened for PKU and similar genetic diseases shortly after birth through a simple blood test, as shown in the image above.
_Image credit: "Phenylketonuria testing," by Eric T. Sheler, USAF Photographic Archives (public domain)._

Variable expressivity, incomplete penetrance

Even for characteristics that are controlled by a single gene, it’s possible for individuals with the same genotype to have different phenotypes. For example, in the case of a genetic disorder, people with the same disease genotype may have stronger or weaker forms of the disorder, and some may never develop the disorder at all.
In variable expressivity, a phenotype may be stronger or weaker in different people with the same genotype. For instance, in a group of people with a disease-causing genotype, some might develop a severe form of the disorder, while others might have a milder form. The idea of expressivity is illustrated in the diagram below, with the shade of green representing the strength of the phenotype.
Narrow expressivity: all six squares are dark green.
Variable expressivity: the six squares are various shades of green.
The squares in each example are intended to represent individuals of the same genotype for the gene of interest.
Illustration modeled after similar image by Steven M. Carrstart superscript, 10, end superscript.
In incomplete penetrance, individuals with a certain genotype may or may not develop a phenotype associated with the genotype. For example, among people with the same disease-causing genotype for a hereditary disorder, some might never actually develop the disorder. The idea of penetrance is illustrated in the diagram below, with green or white color representing the presence or absence of a phenotype.
Complete penetrance: all six squares are dark green.
Incomplete penetrance: three of the squares are dark green, and three of the squares are white.
The squares in each example are intended to represent individuals of the same genotype for the gene of interest.
Illustration modeled after similar image by Steven M. Carrstart superscript, 10, end superscript.
What causes variable expressivity and incomplete penetrance? Other genes and environmental effects are often part of the explanation. For example, disease-causing alleles of one gene may be suppressed by alleles of another gene elsewhere in the genome, or a person's overall health may influence the strength of a disease phenotypestart superscript, 11, end superscript.

Want to join the conversation?

  • blobby green style avatar for user muhammad.aslam
    how environment causes pku?
    (8 votes)
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    • blobby green style avatar for user gfdesignlv
      The environment doesn't actually cause the PKU -- that is genetic. But the environment can cause it to express in the phenotype -- create symptoms -- based on the environment. The PKU gene simply causes a person to be unable to properly process phenylalanine (they lack an adequate amount of the necessary enzymes). If that person eats foods that are high in it, they can begin to express symptoms of that genetic mutation. If they limit or eliminate those foods, they often will have no symptoms.
      (35 votes)
  • leafers ultimate style avatar for user PB the SWAG
    What's the difference between polygenic and epistasis?
    It sounds like in both of them, multiple genes affect one trait.
    (7 votes)
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    • female robot grace style avatar for user tyersome
      While a polygenic phenotype can occur without epistasis, if you have epistasis you must be dealing with a polygenic phenotype.

      Polygenic just means that there are multiple genes involved in a phenotype.
      Epistasis refers to situations where one allele masks the phenotypic effect of one or more alleles of another gene.
      (17 votes)
  • duskpin ultimate style avatar for user Igor
    I'm trying to calculate the probability of getting 6 second to darkest wheat cores using combinatorics. The way I think about it is:
    the probability of getting AABBCc + AABbCC + AaBbCC,
    or 1/4*1/4*1/2 + 1/4*1/2*1/4 + 1/2*1/4*1/4 = 6/64, but what if we are dealing with much more than 3 alleles from each parent? The result are seemingly fall under "pascal's triangle" distribution but the intuitive sense of why it's the case isn't that straightforward..
    (6 votes)
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  • duskpin seedling style avatar for user _friedmanmichael
    Can a disaster, natural or man-made, affect human traits?
    (3 votes)
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    • winston baby style avatar for user Ivana - Science trainee
      Quite interesting question!

      I can think of radiation which causes mutations.

      Definitely causes of mutations can affect human traits and phenotype, but not in the form that it will favor survival. Nonetheless, future generations may be less adaptable and degenerated (recall Chernobyl nuclear plant disaster or Minamata disease in Japan (caused by excessive mercury due to chemical industry).


      My answer is definitely yes. Negative impact.
      (5 votes)
  • blobby green style avatar for user jeremy.dellomo
    how are we able to walk on the earth
    (1 vote)
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  • leaf red style avatar for user layaz7717
    Does anyone know anything about syndactyly and its genetic inheritance?
    (3 votes)
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  • duskpin ultimate style avatar for user RiverclanWarrior
    Does this mean that some genetic diseases are affected by environment? Like, can the environment improve or worsen the symptoms?
    (3 votes)
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  • blobby green style avatar for user amresharma1
    Does penetrance and expressivity can be determined with Hardy-Weinberg equation. how?
    (2 votes)
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  • purple pi purple style avatar for user Jay
    What happens if PKU isn't found at birth?
    (2 votes)
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  • piceratops sapling style avatar for user ALEXANDERN
    So I am very short for my age , yet my mom and dad are both tall but my mom is a little shorter than my dad . Why is that? Do i have a disease or something that affects my growth ?
    (2 votes)
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    • male robot donald style avatar for user Tybalt
      A short stature can be caused by a variety of causes. It could be genetic, a hormone known as growth hormone could be low in the body, or, in more serious cases, an underlying disease or condition may have contributed to your stature (I.E: tumors, malnutrition, mitochondrial disease). If you are otherwise healthy, it is most likely either genetic or hormonal.

      Does this help?
      (1 vote)