Linkage, as related to genetics and genomics, refers to the closeness of genes or other DNA sequences to one another on the same chromosome. The closer two genes or sequences are to each other on a chromosome, the greater the probability that they will be inherited together.
Linkage. Linkages, simply put, are the close location of genes or other DNA markers to each other on chromosomes. The closer the genes are to each other on a chromosome, the more likely they are linked or inherited together from parents to offspring. Closely linked genes are less likely to experience recombination or crossing over between them during meiosis, which is the production of sperm or egg cells. Less distance between two genes means there is less physical space on a chromosome for the biological process of the exchange of DNA to occur.  What does it mean to be linked? For a pair of hands, the above image may suggest a certain type of linkage. For genes, it might suggest that they are very hard to separate.
Genes that are located on the same chromosome are called linked genes. Alleles for these genes tend to segregate together during meiosis, unless they are separated by crossing-over.Crossing-over occurs when two homologous chromosomes exchange genetic material during meiosis I. The closer together two genes are on a chromosome, the less likely their alleles will be separated by crossing-over. At the following link, you can watch an animation showing how genes on the same chromosome may be separated by crossing-over:www.biostudio.com/d_%20Meioti...ed%20Genes.htm. Linkage explains why certain characteristics are frequently inherited together. For example, genes for hair color and eye color are linked, so certain hair and eye colors tend to be inherited together, such as blonde hair with blue eyes and brown hair with brown eyes. What other human traits seem to occur together? Do you think they might be controlled by linked genes?
Genes located on the sex chromosomes are called sex-linked genes. Most sex-linked genes are on the X chromosome, because the Y chromosome has relatively few genes. Strictly speaking, genes on the X chromosome are X-linked genes, but the term sex-linked is often used to refer to them. Sex-linked traits are discussed at http://www.youtube.com/watch?v=-ROhfKyxgCo (14:19).
Linkage can be assessed by determining how often crossing-over occurs between two genes on the same chromosome. Genes on different (nonhomologous) chromosomes are not linked. They assort independently during meiosis, so they have a 50 percent chance of ending up in different gametes. If genes show up in different gametes less than 50 percent of the time (that is, they tend to be inherited together), they are assumed to be on the same (homologous) chromosome. They may be separated by crossing-over, but this is likely to occur less than 50 percent of the time. The lower the frequency of crossing-over, the closer together on the same chromosome the genes are presumed to be. Frequencies of crossing-over can be used to construct a linkage map like the one in Figure below. A linkage map shows the locations of genes on a chromosome. Linkage Map for the Human X Chromosome. This linkage map shows the locations of several genes on the X chromosome. Some of the genes code for normal proteins. Others code for abnormal proteins that lead to genetic disorders. Which pair of genes would you expect to have a lower frequency of crossing-over: the genes that code for hemophilia A and G6PD deficiency, or the genes that code for protan and Xm?
Use these resources to answer the questions that follow.
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Blixt, S. Why didn't Gregor Mendel find linkage? Nature 256, 206 (1975) doi:10.1038/256206a0 (link to article) Bridges, C. B. Salivary chromosome maps with a key to the banding of the chromosomes of Drosophila melanogaster. Journal of Heredity 26, 60–64 (1935) ———. A revised map of the salivary gland X chromosome. Journal of Heredity 29, 1113 (1938) Hillers, K., & Villeneuve, A. Chromosome-wide control of meiotic crossing over in C. elegans. Current Biology 13, 1641–1647 (2003) doi:10.1016/j.cub.2003.08.026 Morgan, T. H. Random segregation versus coupling in Mendelian inheritance. Science 34, 384 (1911) Passarge, E., et al. Incorrect use of the term "synteny." Nature Genetics 23, 387 (1999) (link to article) Pierce, B. Genetics: A Conceptual Approach. (New York, W. H. Freeman & Co., 2005) Punnett, R. C. Linkage in the sweet pea (Lathyrus odoratus). Journal of Genetics 13, 101–123 (1923) ———. Linkage groups and chromosome number in Lathyrus. Proceedings of the Royal Society of London: Series B, Containing Papers of a Biological Character 102 236–238. (1927) Robbins, R. J. Introduction to sex-limited inheritance in Drosophila. Electronic Scholarly Publishing Foundations of Classical Genetics Project. http://www.esp.org/foundations/genetics/classical/thm-10a.pdf (2000) (accessed May 19, 2008) Sturtevant, A. H. The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association. Journal of Experimental Zoology 14, 43–59 (1913) Weiner, J. Time, Love, Memory: A Great Biologist and His Quest for the Origins of Behavior (New York, Random House, 1999)
Linked genes are genes that are likely to be inherited together because they are physically close to one another on the same chromosome. During meiosis, chromosomes are recombined, resulting in gene swaps between homologous chromosomes. If genes are close together, the chances of being recombined are higher than if they are far away from each other. It is impossible for linked genes to be on different chromosomes. Chromosomes are recombined during meiosis. During homologous recombination, the chromosomes can be “cut” at random points after which they are combined with another copy of a homologous chromosome that has been cut at the same point. This way, the DNA from one chromosome ends up in another homologous chromosome. Let’s take a closer look at this. Chromosomes are DNA strands containing hundreds or even thousands of genes. Most organisms that engage in sexual reproduction have two copies of each chromosome. Whereas both copies of each chromosome have the genes for the same feature (e.g. hair color), each copy of the chromosome may contain a different allele (e.g. one copy may code for black hair and the other copy for red hair). Two chromosomes with the same genes, even if they have different alleles, are called homologous chromosomes. There is however one type of cells that have only one copy of each chromosome instead of two: gametes (eggs and sperm in the case of humans). To form gametes, cells undergo meiosis, which consists in cell division whereby the daughter cells obtain one copy of each chromosome instead of two. It is during meiosis that homologous recombination occurs. The following figure shows how homologous recombination occurs during meiosis: In this figure, the cell on the left originally has two different copies (gray and pink) of two different chromosomes (large and small). Each copy has the same genes as the other copy but is very likely to have different alleles; that is why they are shown in different colors. The cell then makes an identical copy of each copy (second panel in the figure). There are now two pairs of homologous chromosomes, all of them attached to an identical copy. Each identical copy is also called sister chromatid. There are therefore four pairs of sister chromatids. In the third panel of the figure, we can see that each pair of sister chromatids gets aligned next to the other pair of sister chromatids, or in other words, homologous chromosomes are aligned. This is the time in which recombination occurs. Recombination takes place in the fourth panel of the figure: the DNA of two homologous sister chromatids are cut and rejoined. This step is also illustrated and can be seen more clearly here: One chunk of the DNA has been swapped between homologous chromosomes, resulting in a new combination of alleles. Importantly, the site at which this DNA cut occurs is mostly random. Furthermore, meiosis occurs every time new gametes are formed; therefore, the cut is in a different location along the DNA, leading to numerous possible combinations. In the next step (fifth panel in the figure), the cell divides into two, with the two daughter cells receiving two copies of each chromosome, each copy carrying different alleles and also the recombined DNA. In the last step (sixth panel), the two daughter cells divide again without replicating their DNA, leading to four daughter cells, each with one copy of each chromosome. Notice how the recombined DNA makes the daughter cells different from one another. It is essential to understand homologous recombination to comprehend linked genes. Now that we know that the chromosomes are cut at random places during homologous recombination, we can see how linked genes are inherited together. Let’s take a real example to better understand it: freckles and red hair. It is very common to find people with freckles and red hair. In fact, this occurs way more often than it would by chance; otherwise, many blonde or brunette people would have freckles more often, and fewer red-haired people would have freckles. This happens because the genes that code for freckles and the genes that code for red hair sit close together on the same chromosome. When homologous recombination occurs, it is very unlikely that the DNA will be cut in between the two genes. Although homologous recombination happens numerous times, these two features are inherited together most of the time because the chances that the DNA coding for these two genes is split up are very low, consequently leading to the genes being inherited together most of the time. Scientists have developed ways to figure out where the genes are located based on the frequencies of recombination. This is done by analyzing the offspring of an organism such as fruit flies (Drosophila melanogaster). If two different genes are on two separate chromosomes, then the offspring will inherit the four alleles (two alleles for each gene) in equal percentages: 25% will inherit allele A of chromosome 1 and allele A of chromosome 2, 25% will inherit allele B of chromosome 1 and allele A of chromosome 2, 25% will inherit allele A of chromosome 1 and allele B of chromosome 2, and 25% will inherit allele B of chromosome 1 and allele B of chromosome 2. The way it is usually calculated is in terms of the alleles shared with the parent organisms. In this case, 50% would inherit the parental genes, and the other 50% would inherit a combination of the parental genes. If, on the other hand, the two different genes sit on the same chromosome, then the offspring will inherit the four alleles in different percentages. The percentage of offspring inheriting the parental genes will be larger than 50%, whereas the percentage of offspring inheriting a combination of the parental genes will be lower than 50%. If the percentage is lower but still close to the expected 50% of combined parental genes, then the genes are on the same chromosome but far apart, perhaps one on each side of the chromosome so that it is very likely that the DNA in between them will be cut during recombination. If the percentage of the offspring having combined parental genes instead of parental genes is very low, e.g. 4%, then the genes sit very close together on the chromosome. 1. What are linked genes? D is correct. Linked genes that sit on the same chromosome and are likely to be inherited together because they are usually not separated during recombination. 2. Why are linked genes inherited together? C is correct. During homologous recombination, the DNA is cut at random places and the genes are swapped between sister chromatids. If the genes sit very close together on the same chromosome, they are very unlikely to be split up when this happens. References
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What is it called when two genes are linked?
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