Homologous Chromosomes: Definition, History, Structure, Functions, Related Problems and Relevant Research

They are a set of a maternal and a paternal chromosome that pair within a cell during meiosis.

Homologues have the same genes at the same loci where they provide points along each chromosome that allow a pair of chromosomes to line up correctly with each other before separating during meiosis.

This is the basis of Mendelian inheritance that characterizes the inherited patterns of genetic material from an organism to its descendant parental developmental cell in the given time and area.


Chromosomes are linear arrangements of condensed deoxyribonucleic acid (DNA) and histone proteins, which form a complex called chromatin.

Homologous chromosomes are made up of pairs of chromosomes of approximately the same length, centromere position, and staining pattern, for genes with the same corresponding loci.

A homologous chromosome is inherited from the mother of the organism; the other is inherited from the father of the organism. After mitosis occurs within the daughter cells, they have the correct number of genes that are a mixture of the genes of the two parents.

In diploid (2n) organisms, the genome is made up of one set of each pair of homologous chromosomes, compared to tetraploid organisms that can have two sets of each pair of homologous chromosomes.

Alleles on homologous chromosomes can be different, resulting in different phenotypes of the same genes.

This mix of maternal and paternal traits is enhanced by crossover during meiosis, where the lengths of the chromosome arms and the DNA they contain within a pair of homologous chromosomes are swapped with each other.


In the early 1900s, William Bateson and Reginald Punnett were studying genetic inheritance and noted that some combinations of alleles appeared more frequently than others. That information and data were explored by Thomas Morgan .

Using cross-trial experiments, he revealed that, for a single parent, alleles of genes close to each other along the chromosome move together. Using this logic, he concluded that the two genes he was studying were on homologous chromosomes.

Later, during the 1930s, Harriet Creighton and Barbara McClintock studied meiosis in maize cells and examined the genetic loci on maize chromosomes.

Creighton and McClintock found that the new allele combinations present in the offspring and the crossing event were directly related. This demonstrated interchromosomal genetic recombination.

Structure of homologous chromosomes

Homologous chromosomes are chromosomes that contain the same genes in the same order along their chromosomal arms. There are two main properties of homologous chromosomes: the length of the chromosome arms and the location of the centromere.

The actual arm length, according to the gene locations, is critically important for proper alignment. The placement of the centromere can be characterized by four main arrangements, consisting of being metacentric, submetacentric, telocentric, or acrocentric.

Both properties are the main factors in creating a structural homology between chromosomes. Therefore, when there are two chromosomes of the exact structure, they can pair up to form homologous chromosomes.

Since homologous chromosomes are not identical and do not originate from the same organism, they are different from sister chromatids.

Sister chromatids are produced after DNA replication has occurred, and are therefore identical, they duplicate side by side.

In humans

Humans have a total of 46 chromosomes, but there are only 22 homologous autosomal chromosome pairs. The extra 23 pair are the sex chromosomes, X and Y.

If this pair is made up of an X and Y chromosome, then the chromosome pair is not homologous because their size and genetic content differ greatly.

The 22 pairs of homologous chromosomes contain the same genes but encode different traits in their allelic forms, since one was inherited from the mother and the other from the father.

So humans have two sets of homologous chromosomes in each cell, which means that humans are diploid organisms.


Homologous chromosomes are important in the processes of meiosis and mitosis. They allow the recombination and random segregation of genetic material from the mother and father into new cells.

In meiosis

Meiosis is a round of two cell divisions that results in four haploid daughter cells that contain half the number of chromosomes as the parent cell.

It halves the number of chromosomes in a germ cell by first separating the homologous chromosomes in meiosis I and then the sister chromatids in meiosis II.

The process of meiosis I is generally longer than meiosis II because it takes longer for chromatin to replicate and for homologous chromosomes to properly orient and secrete through the synchronization and synapse processes in meiosis I.

During meiosis, genetic recombination (by random segregation) and crossing produces daughter cells that contain different combinations of genes encoded by the mother and father.

This recombination of genes allows the introduction of new pairs of alleles and genetic variation. Genetic variation between organisms helps make the population more stable by providing a wider range of genetic traits for natural selection to operate.

Profase I

In prophase I of meiosis I, each chromosome lines up with its homologous pair and pairs completely. In prophase I, DNA has already been replicated, so each chromosome consists of two identical chromatids connected by a common centromere.

During the zygotene stage of prophase I, homologous chromosomes pair with each other. This pairing occurs by a synapse process where the synaptonemic complex – a protein scaffold – assembles and binds to homologous chromosomes along its length.

Cohesin crosslinking occurs between homologous chromosomes and helps them resist separation to anaphase. Genetic crossing, a type of recombination, occurs during the pachytene stage of prophase I.

In addition, another type of recombination frequently occurs, called synthesis-dependent chain annealing (SDSA).

Synthetic-dependent chain-pairing recombination involves information exchange between paired homologous chromatids, but not physical exchange. Synthesis-dependent chain-pairing recombination does not cause crossover.

In the process of crossing over, genes are exchanged by breaking and joining homologous parts of chromosome lengths. Structures called chiasmata are the site of the exchange.

The chiasmate physically connects the homologous chromosomes once the crossover occurs and throughout the chromosome segregation process during meiosis.

Both non-crossover and crossover types of recombination function as processes to repair DNA damage, particularly double-stranded breaks.

In the diplotene stage of prophase I, the synaptonemic complex disarms before the homologous chromosomes can separate, while the sister chromatids remain associated at their centromeres.

Metafase I

In metaphase I of meiosis I, homologous chromosome pairs, also known as bivalent or tetrads, line up in a random order along the metaphase plate. Random orientation is another way for cells to introduce genetic variation.

The meiotic spindles emanating from opposite poles of the spindle bind to each of the homologues (each pair of sister chromatids) in the kinetochore.

Anafase I

In anaphase I of meiosis, homologous chromosomes separate from each other. The homologs are cleaved by the enzyme separase to release the cohesin that holds the homologous chromosomal arms together.

This allows the chiasmate to break free and the homologues to move to opposite poles of the cell. Homologous chromosomes are now randomly secreted into two daughter cells that will undergo meiosis II to produce four haploid daughter germ cells.

Meiosis II

After the tetrads of the homologous chromosomes separate in meiosis I, the sister chromatids of each pair separate. Both haploids (because the chromosome # has been halved).

Previously, there were two sets of chromosomes, but now each set exists in two different daughter cells that have arisen from the single diploid parent cell by meiosis I) daughter cells resulting from meiosis undergo another cell division in meiosis II but without another round of replication chromosome.

The sister chromatids in the two daughter cells are separated during anaphase II by nuclear spindle fibers, resulting in four haploid daughter cells.

In mitosis

Homologous chromosomes do not function the same in mitosis as they do in meiosis. Before each mitotic division that a cell undergoes, the original cell’s chromosomes replicate.

Homologous chromosomes within the cell will ordinarily not pair up and will undergo  genetic recombination with each other.

Instead, the replicants, or sister chromatids, will line up along the metaphase plate and then separate in the same way as meiosis II, by separating at their centromeres by nuclear mitotic spindles.

If a cross between sister chromatids occurs during mitosis, it does not produce any new recombinant genotypes.

In somatic cells

Homologous pairing in most contexts will refer to germ line cells, however it also takes place in somatic cells.

For example, in humans, somatic cells have very tightly regulated homologous pairs (separated into chromosomal territories, and pairing at specific loci under the control of developmental signaling).

However, other species (especially Drosophila) exhibit homologous pairing much more frequently. Various functions of homologous pairing in somatic cells have been elucidated through high-throughput screens in the early 21st century.

Problems with homologous chromosomes

There are severe repercussions when chromosomes do not segregate properly. Faulty segregation can lead to fertility problems, embryonic death, birth defects, and cancer.

Although the mechanisms for matching and attaching homologous chromosomes vary between organisms, the correct functioning of these mechanisms is essential for the final genetic material to be correctly classified.

No disjunction

Adequate homologous chromosome separation in meiosis I is crucial for the separation of sister chromatids in meiosis II. A failure to separate properly is known as nondisjunction.

There are two main types of nondisjunction that occur: trisomy and monosomy. Trisomy is caused by the presence of an extra chromosome in the zygote compared to the normal number, and monosomy is characterized by the presence of one less chromosome in the zygote compared to the normal number.

If this uneven division occurs in meiosis I, then none of the daughter cells will have a proper chromosomal distribution and serious effects, including Down syndrome, can occur.

Unequal division can also occur during the second meiotic division. The nondisjunction that occurs at this stage can result in normal daughter cells and deformed cells.

Other uses

While the main function of homologous chromosomes is their use in nuclear division, they are also used in the repair of double-stranded DNA breaks.

These double-stranded breaks can occur in DNA replication and, most often, are the result of DNA’s interaction with harmful naturally-occurring molecules, such as reactive oxygen species.

Homologous chromosomes can repair this damage by lining up with chromosomes of the same genetic sequence.

Once the base pairs have been correctly paired and oriented between the two strands, the homologous chromosomes go through a process that is very similar to recombination, or they cross over as seen in meiosis.

Part of the intact DNA sequence overlaps with that of the damaged chromosome sequence. Replication proteins and complexes are recruited at the site of damage, allowing for proper replication and repair.

Through this operation, double-stranded breaks can be repaired and DNA can function normally.

Relevant research

Current and future research on the topic of homologous chromosomes is highly focused on the roles of various proteins during recombination or during DNA repair.

In an article recently published by Pezza et al. the protein known as HOP2 is responsible for both homologous chromosomal synapse and double-strand break repair by homologous recombination.

The elimination of HOP2 in mice has a great impact on meiosis. Other current studies are also focusing on specific proteins involved in homologous recombination.

There is ongoing research on the ability of homologous chromosomes to repair double-stranded DNA breaks. Researchers are investigating the possibility of exploiting this ability for regenerative medicine.

This drug could be very common in relation to cancer, as DNA damage is believed to contribute to carcinogenesis.

Manipulating the repair function of homologous chromosomes could improve a cell’s damage response system. While research has yet to confirm the effectiveness of such a treatment, it may become a useful therapy for cancer.