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Linked Genes

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Biology

Have you ever wondered why people with blonde hair also have blue eyes? Or why red-green color blindness is more common in males than females (Fig. 1)? These questions can be answered by understanding linked genes. While a great deal of focus has been put on Mendelian genetics, there are many exceptions in which genes do not follow the laws proposed by Mendel. In the following, we will explore the linked genes and sex-linked genes that defy Mendel's laws.

For a refresher on Mendel's genetics, look at our articles Mendelian Genetics and Mendel's Laws of Segregation. For more exceptions to Mendel's laws, see Non-Mendelian Genetics.

Linked Genes Defined

Linked genes, or linkage, refer to a set of genes that tend to be inherited together because the genes are positioned close to each other on the same chromosome. This positioning leads to these genes being inherited together at much greater frequencies than Mendel's law of independent assortment would predict. Recall that a key assumption for the law of independent assortment is that genes are located on different chromosomes or very distant from each other on the same chromosome. Therefore, linked genes positioned close to each other on the same chromosome are an exception to the law of independent assortment.

The law of independent assortment states that the alleles for different genes are sorted into gametes independently from each other.

Linked vs Unlinked Genes

To compare ratios between linked and unlinked genes, we should first look at the chromosome segregation that occurs during meiosis.

For unlinked genes, two heterozygous parents, AaBb, where A and B are genes located on different chromosomes, will produce four types of gametes found in equal proportions (Fig. 2). The four combinations of gametes are AB, Ab, aB, ab, each having a frequency of 25%. Importantly, note how each chromatid stays intact and is not separated during the entire process of meiosis (Fig. 3).

In contrast, linked genes are found in close proximity to each other on the same chromatid. Therefore, since chromatids tend to remain largely intact throughout meiosis, these genes are more likely to be inherited together into a gamete (Fig. 4). In other words, certain alleles are always packaged together.

For example, if Mendel's genes for pea color and pea shape were linked, green-colored and wrinkly peas may be frequently seen together, while yellow-colored and round peas may also be frequently seen together.

There is an exception to this rule called crossing over or homologous recombination. Recombination occurs during prophase I of meiosis to increase genetic diversity. During recombination, homologous chromosomes are separated and exchange fragments of their DNA with each other (Fig. 5). This leads to new alleles on the same chromosome.

For example, if a recombination event happens between the pea-color gene and the pea-shape genes that were normally linked, we might see green-colored round peas and yellow-colored wrinkly peas.

In the above example, alleles AB are linked on the blue chromosome, and alleles ab are linked on the red chromosome. Following recombination, the new possible gamete genotypes will be AB, Ab, aB, and ab, just like unlinked genes. However, the location of a recombination event on a chromosome is completely random; therefore, it is much more unlikely that Ab and aB alleles will be inherited together. Imagine that, instead of between genes A and B, a recombination event took place at the top of the chromosome. In this case, alleles AB and ab will still be inherited together.

For this reason, the original allele pairs, AB and ab, are called parental chromatids. While the less likely, Ab and aB alleles are called recombinant chromatids. The closer the two genes are, the less likely a recombination event will occur between them. In very tight linkage, the parental chromatids will almost always be seen, with few cases of recombinant chromatids.

Table 1. Differences between unlinked and linked genes.

Unlinked GenesLinked Genes
Position on the chromosome Genes are found on different chromosomes or far apart on the same chromosome.Genes are found close together on the same chromosome.
Frequency of alleles Follows the law of independent assortment. Equal frequencies (25%) of each of the four gamete combinations (AB, Ab, aB, and ab).Unequal frequencies with parental alleles (AB and ab) are produced more commonly than recombinant alleles (Ab and aB)
Affected by recombinationNo.Yes, if the recombination event occurs between the genes of interest.

Examples of Linked Genes

One example of linked genes includes hair color and eye color genes. While there is not just one gene that contributes to hair color and another gene that contributes to eye color, there is some evidence that two of the genes involved in hair color and eye color are linked. This is why we might see individuals with blue eyes also have blonde hair or why a person with red hair might also have light skin.

Linkage can also be useful for determining the position of genes on a chromosome. If we follow the law of independent assortment, we see that the parental chromatids will be found in the offspring 50% of the time. For example, if we have chromosome 1 with alleles AB and chromosome 2 with alleles ab, we expect to see 50% of the offspring have recombinant alleles, Ab and aB, and 50% have parental alleles, AB and ab. In the case of linkage, we should expect to see parental alleles much more commonly than recombinant alleles. Therefore, if we see this occur, we can assume that the two genes are linked and close together on the same chromosome. If this process is repeated for multiple different genes, a genetic map or linkage map can be generated.

A linkage map tries to position all known genes in their relative positions on a chromosome (Fig. 6).

Sex-linked Genes

Thomas Hunt Morgan originally found Sex-linked genes during his research of fruit fly genetics. He noticed that eye color in fruit flies did not follow typical Mendelian genetics. Instead, he noticed that when he crossed a red-eyed female with a red-eyed male, the offspring produced a 2:1:1 ratio of red-eyed females: red-eyed males: white-eyed males. Therefore, just like linked genes, sex-linked genes are another example that does not follow Mendelian genetics.

Genes are found on chromosomes; the X and Y sex chromosomes are no exception. Sex-linked genes are genes found on the X and Y chromosomes and therefore are biased, to be found in one sex over the other. Males have one X chromosome inherited from the mother and one Y chromosome inherited from the father. In contrast, females have two X chromosomes that are inherited from each parent. This difference makes the inheritance of traits different between males and females. Females can be homozygous or heterozygous for a specific X-linked gene; however, males will only have one copy of the X-linked gene. Therefore, if a male inherits a recessive allele from their mother, they will express that recessive trait.

Sex-linked genes are denoted by XB for dominant or Xb for recessive, where B is the gene of interest. The X represents that the gene is located on the X chromosome, while the superscript denotes the allele.

Practice Problems for Sex-linked Genes

Punnett Squares are very useful for tackling practice problems; remember to include X and Y to represent the X and Y chromosomes, respectively.

Red-green color blindness is a genetic disorder caused by a mutation for a photoreceptor gene found on the X chromosome. It is an X-linked recessive disorder. If a female carrier and a normal-visioned male have a child, what is the likelihood that the child will be colorblind? What are all the possible genotypes and phenotypes for their child?

"X-linked recessive" means that a female must have two copies of the recessive allele, XbXb, to be red-green colorblind. Since males only have one copy of the X chromosome, if a male inherits one recessive allele, Xb, they will be red-green colorblind. We can set up a Punnett square to show the cross (Fig. 7).

Overall, the child has a 25% chance of being colorblind. If the child is a biological female, they have a 0% chance of being color blind as both XBXB and XBXb have a normal-colored vision. However, if the child is a male, they have a 50% chance (XBY or XbY).

Linked Genes - Key Takeaways

  • Linked genes or linkage describes a set of genes that tend to be inherited together because the genes are positioned close to each other on the same chromosome.
  • Recombination is when homologous chromosomes split and exchange fragments of their DNA with each other to unlink linked genes.
  • Parental chromatids are chromatids that match the parent's alleles, while recombinant chromatids are chromatids that are produced after a recombination event.
  • Sex-linked genes are genes found on the X or Y chromosome.

Linked Genes

The X and Y chromosomes.

Genes that are found on the X and Y chromosome

Genes that are found close together on the same chromosome are likely to be inherited together because chromatids are intact during meiosis and recombination between closely positioned genes is less likely to occur. 

Yes, linked genes are found close together on the same chromosome.  

X-linked genes are genes that are found on the X chromosome. 

Final Linked Genes Quiz

Question

What are sex-linked genes?

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Answer

Genes found on the X or Y chromosome 

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What are linked genes?

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Answer

Genes that are found close together on the same chromosome and tend to be inherited together

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What is the difference between parental and recombinant chromatids?

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Answer

  • Parental chromatids are chromatids that match the parent's alleles while recombinant chromatids are chromatids that are produced after a recombination event.

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What is recombination?

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Answer

An event during meiosis where homologous chromosomes are cut and exchange fragments of their DNA with each other to unlink linked genes 

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When does recombination occur?

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Answer

Prophase I

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Question

If a two genes are found at the tip of two different chromosomes, they are ____.

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Answer

Unlinked

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If two genes are found together on either ends of the same chromosome, they are ____.

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Answer

Unlinked 

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If two genes are linked, offspring are much more likely to inherit ____ chromatids.

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Answer

Parental

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What might be a reason why people with red hair have light skin?

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Answer

The genes for red hair and light skin might be linked

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Question

Red-green color blindness is a genetic disorder caused by a mutation for a photoreceptor gene found on the X chromosome. It is an X-linked recessive disorder. If a female carrier and a normal-visioned male have a child, what is the likelihood that the child will be colorblind? 


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Answer

25% 

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Question

Red-green color blindness is a genetic disorder caused by a mutation for a photoreceptor gene found on the X chromosome. It is an X-linked recessive disorder. If a female carrier and a normal-visioned male have a male child, what is the likelihood that their male child will be colorblind? 


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Answer

50%

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Question

Red-green color blindness is a genetic disorder caused by a mutation for a photoreceptor gene found on the X chromosome. It is an X-linked recessive disorder. If a female carrier and a normal-visioned male have a female child, what is the likelihood that the female child will be colorblind? 


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Answer

0%

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Question

If two genes are unlinked, what is the frequency of the potential gametes? 

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Answer

Equal (25% each)


AB, Ab, aB, ab

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If two genes are linked, ___ gametes are more likely to be present than ___ gametes.

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Answer

parental, recombinant 

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True or False: A male with one copy of an X-linked recessive allele will express the recessive trait.  

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Answer

True 

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True or False: A female with one copy of an X-linked recessive allele will express the recessive trait.  

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False

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Question

The Chi-Square Test helps determine validity of data

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Answer

True

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What is a null hypothesis? 

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There is no significant difference occuring 

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How can we describe our results?

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Significantly significant and significantly insignificant 

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What does it mean if something was statistically insignificant?

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It means the results only happened by chance

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What are one-tailed hypotheses? 

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Hypotheses where change is based on a single factor and the type of change (ex. increase or decrease) is not specified 

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What are two-tailed hypotheses? 

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Hypotheses where the type of change is stated

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What are the criteria for a Chi-Square test?

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  • The sample size has to be large (>20).
  • The data must be categorical.
  • Only raw counts can be used – not ratios, rates, fractions, or percentages.
  • The comparison between theoretical (expected) and experimental (observed) results is being made.

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What are the assumptions for a Chi-Square test? 

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  • The comparisons are made on random samples.
  • The expected count of each cell is greater than one (>1).
  • No more than 20% of the cells have expected counts less than 5 (<5).

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What is the formula for the Chi-Square Test?

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The sum of the square of the difference between the observed and expected values, divided by the expected values 

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What are degrees of freedom? 

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The max number of values that have the freedom to vary

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What is a p-value? 

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The probability of having data still support the hypothesis despite the size of the Chi-Square being large or larger than the current experiment 

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What does it mean when the Chi-Square is larger than the critical value? 

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The results are signifcant

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Can we have patterns of inheritance that do not fit Mendelian ratios?

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Answer

Yes

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Question

What is statistical error? 

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Answer

The difference between a measured value and the actual value of the collected data. If the error value is more significant, the data will be considered less reliable. 

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What is categorical data? 

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Answer

Values that can be sorted into groups or categories. It can be further divided into nominal (values you can count but not order, e.g., eye color) and ordinal (values you can count and order e.g., house numbers).  

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