Not all genes independently assort

In the module on Basic Heredity, we discussed Mendel’s Second Law: Independent Assortment. You’ll recall that Mendel observed that the heredity of separate traits (seed shape vs seed color, for example) was independent of one another.

But Mendel got a bit lucky: the seven traits he chose are on separate chromosomes. Some genes, though, located close together on the same chromosome, do not independently assort. These genes are said to be linked, and linked alleles tend to be inherited together during meiosis. This phenomenon gives geneticists a tool to map genes to particular loci on a chromosome (the singular of loci is locus, meaning location).

Remember: during meiosis 1, homologous chromosomes pair along the metaphase plate of the cell. The pairing of maternal vs paternal chromosomes is random, contributing to the independent assortment of genes on different chromosomes (Figure 3). In addition, crossing over occurs between homologous chromosomes, resulting in recombinant chromosomes, or chromosomes that are a combination of both maternal and paternal sequences. This recombination allows the independent assortment of genes that are on the same chromosome, but very far apart.

Diagram of how chromosome pairs can be arranged during metaphase I of meiosis. On the top is an illustration of a cell with two pink and two blue chromosomes. The two pink chromosomes are both aligned to the left of the metaphase plate. On the bottom is a cell with one pink and one blue chromosome aligned to the left and one blue and one pink chromosome aligned to the right.
Figure 3 During metaphase I, the random arrangement of the homologous pairs results in the independent assortment of genes on separate chromosomes. In the top meiotic cell, both pink chromosomes will be inherited together, as will the blue chromosomes. On the bottom, each daughter cell will inherit one blue and one pink chromosome.
Illustration of crossing over showing that one segment of a pink chromatid has been exchanged for one segment of a blue chromatid.
Figure 4 Crossing over between homologous pairs contributes to the independent assortment of genes far apart on the same chromosome, like Genes A and B in this image. Genes B and C are very close together, and so a crossing over event will happen only infrequently between genes B and C. Genes B and C are linked and do not independently assort.

Linked genes are readily distinguished from independently assorting genes in a controlled cross. In the unit on Basic Heredity, we observed that a dihybrid testcross (AaBb x aabb) should always give a 1:1:1:1 ratio of offspring with phenotypes AB, ab, Ab, and aB. The gametes contributing to that ratio are shown in Figure 5. This is assuming independent assortment. In Figure 5, the genotypes Ab and aB are said to be parental, because these are the exact chromosomes the parental cells contributed to the dihybrid. The genotypes AB and ab are recombinant, since the original parental cells did not have that combination of alleles.

But if the genes are linked, two classes of offspring will be overrepresented, and two classes of offspring will be underrepresented. An extreme example of that is shown in Figure 6. In Figure 6, there is no recombination between genes A and B. Thus, the parental chromosomes Ab and aB are inherited intact. AB and ab genotypes are recombinant chromosomes, but recombinant chromosomes can occur only rarely if two genes are very close together (and not at all in Figure 6)

Illustration showing independent assortment of genes on separate chromosomes during the production of gametes, regardless of whether alleles were inherited from the same parent.
Figure 5 In this image, a dihybrid inherited alleles A and b from one parent and a and B from another. Those alleles are randomly redistributed when the dihybrid produces gametes, as shown on the right of the image.
Illustration showing no independent assortment of genes on the same chromosomes during the production of gametes. Alleles of genes A and B are inherited together because they are linked on the same chromosome.
Figure 6

Because the rate of recombination depends on how far apart two genes are, the recombination frequency was historically used to estimate map distances on a chromosome. Let’s take a look at some examples.

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