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    Genetic linkage & mapping (article)

    What it means for genes to be linked. How to determine recombination frequency for a pair of genes.

    Non-Mendelian genetics

    Genetic linkage & mapping

    What it means for genes to be linked. How to determine recombination frequency for a pair of genes.

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    Key points:

    When genes are found on different chromosomes or far apart on the same chromosome, they assort independently and are said to be unlinked.

    When genes are close together on the same chromosome, they are said to be linked. That means the alleles, or gene versions, already together on one chromosome will be inherited as a unit more frequently than not.

    We can see if two genes are linked, and how tightly, by using data from genetic crosses to calculate the recombination frequency.

    By finding recombination frequencies for many gene pairs, we can make linkage maps that show the order and relative distances of the genes on the chromosome.


    In general, organisms have a lot more genes than chromosomes. For instance, we humans have roughly

    19, 19, 19, comma 000 000 000 genes on 23 23 23

    chromosomes (present in two sets)

    ^1 1

    start superscript, 1, end superscript

    . Similarly, the humble fruit fly—a favorite subject of study for geneticists—has around

    13, 13, 13, comma 000 000 000 genes on 4 4 4

    chromosomes (also present in two sets)

    ^2 2 squared .

    The consequence? Each gene isn't going to get its own chromosome. In fact, not even close! Quite a few genes are going to be lined up in a row on each chromosome, and some of them are going to be squished very close together.

    Does this affect how genes are inherited? In some cases, the answer is yes. Genes that are sufficiently close together on a chromosome will tend to "stick together," and the versions (alleles) of those genes that are together on a chromosome will tend to be inherited as a pair more often than not.

    This phenomenon is called genetic linkage. When genes are linked, genetic crosses involving those genes will lead to ratios of gametes (egg and sperm) and offspring types that are not what we'd predict from Mendel's law of independent assortment. Let's take a closer look at why this is the case.

    What is genetic linkage?

    When genes are on separate chromosomes, or very far apart on the same chromosomes, they assort independently. That is, when the genes go into gametes, the allele received for one gene doesn't affect the allele received for the other. In a double heterozygous organism (AaBb), this results in the formation of all

    4 4 4

    possible types of gametes with equal, or

    25\% 25% 25, percent , frequency.

    Why is this the case? Genes on separate chromosomes assort independently because of the random orientation of homologous chromosome pairs during meiosis. Homologous chromosomes are paired chromosomes that carry the same genes, but may have different alleles of those genes. One member of each homologous pair comes from an organism's mom, the other from its dad.

    As illustrated in the diagram below, the homologues of each pair separate in the first stage of meiosis. In this process, which side the "dad" and "mom" chromosomes of each pair go to is random. When we are following two genes, this results in four types of gametes that are produced with equal frequency.

    When genes are on the same chromosome but very far apart, they assort independently due to crossing over (homologous recombination). This is a process that happens at the very beginning of meiosis, in which homologous chromosomes randomly exchange matching fragments. Crossing over can put new alleles together in combination on the same chromosome, causing them to go into the same gamete. When genes are far apart, crossing over happens often enough that all types of gametes are produced with

    25\% 25% 25, percent frequency.

    When genes are very close together on the same chromosome, crossing over still occurs, but the outcome (in terms of gamete types produced) is different. Instead of assorting independently, the genes tend to "stick together" during meiosis. That is, the alleles of the genes that are already together on a chromosome will tend to be passed as a unit to gametes. In this case, the genes are linked. For example, two linked genes might behave like this:

    Now, we see gamete types that are present in very unequal proportions. The common types of gametes contain parental configurations of alleles—that is, the ones that were already together on the chromosome in the organism before meiosis (i.e, on the chromosome it got from its parents). The rare types of gametes contain recombinant configurations of alleles, that is, ones that can only form if a recombination event (crossover) occurs in between the genes.

    Source : www.khanacademy.org

    Genetics Chapter 5 HW Flashcards

    Genetics Chapter 5 HW Learn with flashcards, games, and more — for free.

    Genetics Chapter 5 HW

    5.0 1 Review

    When two genes fail to assort independently, the term normally applied is....?

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    Assume that a cross is made between AaBb and aabb plants and all the offspring are either AaBb or aabb. These results are consistent with the following circumstance...?

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    complete linkage

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    1/22 Created by pshafer

    Genetics Chapter 5 HW

    Terms in this set (22)

    When two genes fail to assort independently, the term normally applied is....?


    Assume that a cross is made between AaBb and aabb plants and all the offspring are either AaBb or aabb. These results are consistent with the following circumstance...?

    complete linkage

    Assume that a cross is made between AaBb and aabb plants and the offspring are equal number of AaBb, Aabb, aaBb, aabb. These results are consistent with the following circumstance...?

    independent assortment

    The phenomenon in which one crossover increases the likelihood of crossovers in nearby regions is called?

    negative interference

    Methods for determining the linkage group and genetic map in humans involve which of the following?

    syntenic testing and lod score determination.


    Mitotic crossing over is more frequent than meiotic crossing over.

    False T/F

    Linkage (viewed from the result of typical crossed) occurs when two loci are on the same chromosome.

    True T/F

    Positive interference occurs when a crossover in one region of a chromosome interferes with crossovers in nearby regions.

    True T/F

    In Drosophila, the frequency of crossing over in males is about equal to the frequency of crosing over in females.

    False T/F

    If two gene loci are on nonhomologous chromosomes, genes at these loci are expected to assort independently.


    In a testcross for two genes, what type of gametes are produced with:

    A) a complete linkage

    B) an independent assortment

    C) an incomplete linkage

    A) non-recombinant gametes

    B) 50% recombinant, 50% non-recombinant

    C) 50% non-recombinant, 50% recombinant

    Why do calculated recombination frequencies between pairs of loci that are located far apart underestimate the true genetic distance between loci?

    The farther apart the two loci are, the more likely the double crossovers between them. unless there are marker genes between the loci, such double crossovers will be undetected because the double crossovers and non-recombinants give the same phenotype. The calculated recombination frequency will underestimate the true crossover frequency because the double crossover progeny are not counted as recombinants.

    What does the interference tell us about the effect of one crossover on another?

    A positive interference value results when the actual number of double crossovers observed is less than the number of double crossovers expected from the single crossover frequencies. Thus, positive interference indicates that a crossover inhibits or interferes with the occurrence of a second crossover nearby. Conversely, a negative interference suggests that a crossover event can stimulate additional crossover events in the same region of the chromosome.

    A) In a three-point mapping experiment, what three general classes of offspring are expected (assuming crossover has happened)?

    B) How many different types of genotypes are expected?

    A) Non-crossovers, single cross-over, double cross-over

    B) 8

    What advantage does BUdR have in the study of chromosome structure and recombination?

    Chromatids stained with BUdR in both DNA strands are distinguishable from those with BUdR in only one strand of the double helix.

    What is the relationship between the degree of crossing over and the distance between two genes?

    It is direct; as the distance between linked gene increases, the frequency of recombination increases.

    At what stage of the meiotic cycle and during what chromosomal configuration does crossing over occur?

    At the four-strand stage of meiosis, after synapsis of homologous chromosomes, and before the end of prophase I.

    A plant of genotype ABab is testcrossed to abab. If the two loci are 10m.u. apart, what proportion of progeny will be ABab?

    1)Cross between AB/ab and ab/ab and the two genes are 10 m.u. apart.

    Among their progeny, 10% would be recombinant (Ab/ab and aB/ab) and 90% would be parental (AB/ab and ab/ab). Therefore, AB/ab would represent ½ of the parentals or 45%.

    The A and the D locus are so closely linked that no recombination is ever observed between them. If AdAd is crossed to aDaD and the F1 is intercrossed, what phenotypes will be seen in F2 and in what proportions?

    P: Ad/Ad x aD/aD F1: Ad/aD

    F2: 1 Ad/Ad phenotype Ad

    2 Ad/aD phenotype AD

    1 aD/aD phenotype aD

    If AABB is crossed to aabb and the F1 is testcrossed, what percent of the testcross progeny will be aabb if the two genes are

    A) unlinked

    B) completely linked

    C) 10 map units apart

    D) 24 m.u. apart

    3) The cross between two homozygous parents will result in all heterozygous F1 generation (all will be AaBb). The cross in question is AaBb x aabb (test cross is always to homozygous recessive).

    Source : quizlet.com

    Genetic Recombination and Gene Mapping

    Soon after Gregor Mendel’s laws were rediscovered, opportunities arose for scientists to use Mendel’s principles to explain the inheritance of various traits they were studying in their laboratories. However, work from multiple labs found that Mendelian principles were not always sufficient to explain the behavior of certain characteristics. One such lab was that of biologist Thomas Hunt Morgan. This lab’s research regarding gene linkage and recombination challenged the principle of independent assortment and led to a basic understanding of gene mapping.

    In 1911, while studying the chromosome theory of heredity, biologist Thomas Hunt Morgan had a major breakthrough. Morgan occasionally noticed that "linked" traits would separate. Meanwhile, other traits on the same chromosome showed little detectable linkage. Morgan considered the evidence and proposed that a process of crossing over, or recombination, might explain his results. Specifically, he proposed that the two paired chromosomes could "cross over" to exchange information. Today, we know that recombination does indeed occur during prophase of meiosis (Figure 1), and it creates different combinations of alleles in the gametes that result (i.e., the F1 generation; Figure 2).

    Figure 1: Recombination and gamete production.

    A comparison of nonrecombination (left) with recombination (right), shows how recombination affects the way chromosomes are passed into gametes in Meiosis II. On the right, a single crossover event produces half nonrecombinant gametes and half recombinant gametes.

    © 2014 Nature Education Adapted from Pierce, Benjamin. , 2nd ed. All rights reserved.

    Figure Detail

    When proposing the idea of crossing over, Morgan also hypothesized that the frequency of recombination was related to the distance between the genes on a chromosome, and that the interchange of genetic information broke the linkage between genes. Morgan imagined that genes on chromosomes were similar to pearls on a string (Weiner, 1999); in other words, they were physical objects. The closer two genes were to one another on a chromosome, the greater their chance of being inherited together. In contrast, genes located farther away from one another on the same chromosome were more likely to be separated during recombination. Therefore, Morgan correctly proposed that the strength of linkage between two genes depends upon the distance between the genes on the chromosome. This proposition became the basis for construction of the earliest maps of the human genome.

    Figure 2: Allele recombination.

    Recombination is the sorting of alleles into new combinations. Following the formation of gametes over two generations shows how recombination can produce new allelic combinations (lower right) or stay the same (lower left).

    © 2014 Nature Education Adapted from Pierce, Benjamin. , 2nd ed. All rights reserved.

    Figure Detail

    Sturtevant Uses Crossing-Over Data to Construct the First Genetic Map

    Soon after Morgan presented his hypothesis, Alfred Henry Sturtevant, a 19-year-old Columbia University undergraduate who was working with Morgan, realized that if the frequency of crossing over was related to distance, one could use this information to map out the genes on a chromosome. After all, the farther apart two genes were on a chromosome, the more likely it was that these genes would separate during recombination. Therefore, as Sturtevant explained it, the "proportion of crossovers could be used as an index of the distance between any two factors" (Sturtevant, 1913). Collecting a stack of laboratory data, Sturtevant went home and spent most of the night drawing the first chromosomal linkage map for the genes located on the X chromosome of fruit flies (Weiner, 1999).

    Figure 3: Sturtevant's gene map.

    In Sturtevant's gene map, six traits are arranged along a linear chromosome according to the relative distance of each from trait B. Traits include yellow body (B), white eyes (C, O), Vermillion eyes (P), miniature wings (R), and rudimentary wings (M).

    © 2013 Nature Education Adapted from Pierce, Benjamin. , 2nd ed. All rights reserved.

    When creating his map, Sturtevant started by placing six X-linked genes in order. B was a gene for black body color. C was a gene that allowed color to appear in the eyes. Flies with the P gene had vermilion eyes instead of the ordinary red, and flies with two copies of the recessive O gene had eyes that appeared a shade known as eosin. The R and M factors both affected the wings. Sturtevant placed C and O at the same point because they were completely linked and were always inherited together — in other words, he never saw any evidence for recombination between C and O. Sturtevant then placed the remainder of the genes in the order shown in Figure 3 (Sturtevant, 1913). Crossover events were tracked by examining the F2 progeny in crosses for "new" phenotypes.

    Figure 4: Phenotypes used in Sturtevant's cross.

    Sturtevant crossed flies with long wings (M) and vermillion eyes (p) with flies with rudimentary wings (m) and red eyes (P). These traits are X-linked.

    © 2008 Nature Education All rights reserved.

    For example, to find the distance between P (vermilion eyes) and M (long wings), Sturtevant performed crosses between flies that had long wings and vermilion eyes and flies that had small wings and red eyes. These crosses resulted in F1 flies that either had long wings and red eyes or long wings and vermilion eyes. Sturtevant then crossed these two types of F1 flies and analyzed the offspring for evidence of recombination. Unexpected phenotypes observed in the male F2 progeny from this cross were then examined. (Because very little recombination occurs in the male germ line of , only the female F1 chromosomes are considered for predicting phenotypes [Figure 4].) Sturtevant noted four classes of male flies in this F2 generation, as shown in Table 1.

    Source : www.nature.com

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