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24.1: Gene Mapping and Chromosomal Karyotypes

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    Genes provide instructions to build living organisms and each specific gene maps to the same chromosome in every cell. This physical gene location within the organism's chromosomes is called the gene loci. If two genes are found on the same chromosome, especially when they are in close proximity to one another, they are said to be linked.

    Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Two genetic markers that are physically near to each other are unlikely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be more linked than markers that are far apart. In other words, the nearer two genes are on a chromosome, the lower the chance of recombination between them, and the more likely they are to be inherited together. Markers on different chromosomes are perfectly unlinked.

    Genetic linkage is the most prominent exception to Gregor Mendel's Law of Independent Assortment. The first experiment to demonstrate linkage was carried out in 1905. At the time, the reason why certain traits tend to be inherited together was unknown. Later work revealed that genes are physical structures related by physical distance.

    The typical unit of genetic linkage is the centimorgan (cM). A distance of 1 cM between two markers means that the markers are separated to different gametes on average once per 100 meiotic product, thus once per 50 meioses. A linkage map (also known as a genetic map) is a table for a species or experimental population that shows the position of its known genes or genetic markers relative to each other in terms of recombination frequency, rather than a specific physical distance along each chromosome. Linkage maps were first developed by Alfred Sturtevant, a student of Thomas Hunt Morgan (Fig. 24.1.1).

    Figure: This gene linkage map shows the relative positions of allelic characteristics on the second Drosophila chromosome. The alleles on the chromosome form a linkage group due to their tendency to form together into gametes. The distance between the genes (map units) are equal to the percentage of crossing-over events that occurs between different alleles. This diagram is also based on the findings of Thomas Hunt Morgan in his Drosophila cross. (CC BY-SA 4.0 International; Twaanders17 via Wikipedia

    A linkage map is a map based on the frequencies of recombination between markers during crossover of homologous chromosomes. The greater the frequency of recombination (segregation) between two genetic markers, the further apart they are assumed to be. Conversely, the lower the frequency of recombination between the markers, the smaller the physical distance between them. Historically, the markers originally used were detectable phenotypes (enzyme production, eye color) derived from coding DNA sequences; eventually, confirmed or assumed noncoding DNA sequences such as microsatellites or those generating restriction fragment length polymorphisms (RFLPs) have been used.

    Linkage maps help researchers to locate other markers, such as other genes by testing for genetic linkage of the already known markers. In the early stages of developing a linkage map, the data are used to assemble linkage groups, a set of genes which are known to be linked. As knowledge advances, more markers can be added to a group, until the group covers an entire chromosome. For well-studied organisms the linkage groups correspond one-to-one with the chromosomes.

    Traditional studies used to physically map genes onto specific chromosomes were painstaking and involved using restriction enzymes to fragment the genome of an organism and then clone the fragments into YACs or BACs creating a DNA library. The library could then be screened with specific genetic probes to determine which fragment contained a gene of interest. The fragments would then need to be sequenced and reassembled using overlapping patterns. Today, the sequencing of entire genomes from nearly any organism is possible and relatively easy in comparison. Thus, a traditional genetic map can more readily be overlayed on the physical chromosomal map of an organism. This was one of the overarching goals for the human genome project (Fig. 24.1.2)

    Figure from: The National Institutes of Health

    The entire chromosome set of a species is known as a karyotype, which can be thought of as a global map of the nuclear genome. Karyotyping is the process by which the condensed chromosomes of an organism are stained and photographed using light microscopy. Karyotyping can be used to determine the chromosome complement of an individual, including the number of chromosomes and any abnormalities.

    Karyotypes describe the chromosome count of an organism and what these chromosomes look like under a light microscope. Attention is paid to their length, the position of the centromeres, banding pattern, any differences between the sex chromosomes, and any other physical characteristics. The preparation and study of karyotypes is part of the larger field of cytogenetics. The field of cytogenetics is interested in studying inheritance in relation to the structure and function of chromosomes. Thus, karyotyping is a fundamental process within this field.

    The study of whole sets of chromosomes is sometimes known as karyology. The chromosomes are depicted (by rearranging a photomicrograph) in a standard format known as a karyogram or idiogram: in pairs, ordered by size and position of centromere for chromosomes of the same size (Fig. 24.1.3). The basic number of chromosomes in the somatic cells of an individual or a species is called the somatic number and is designated 2n. In the germ-line (the sex cells) the chromosome number is n (humans: n = 23). Thus, in humans 2n = 46. In normal diploid organisms, autosomal chromosomes are present in two copies. There may, or may not, be sex chromosomes. Polyploid cells have multiple copies of chromosomes and haploid cells, usually gametes, have single copies. Karyotypes can be used for many purposes; such as to study chromosomal aberrations, cellular function, taxonomic relationships, medicine and to gather information about past evolutionary events (karyosystematics).

    Figure from: The National Cancer Institute

    During the chromosomal staining processes used to produce a karyotype, the staining intensity along the chromosome can vary due to localized sequence and structural differences. These banding patterns are an inherent characteristic of a chromosome and can be utilized as a diagnostic tool. Typically, karyotypes are prepared from cells that are actively undergoing mitosis. The mitotic progression is blocked in prometaphase or metaphase when chromosomes exist in their most condensed state. The cells are lysed, but the nuclei are retained intact and are subsequently treated with a chemical fixing agent. Once fixed, a number of different types of stains can be used to visualize the chromosomes.

    One of the first types of chromosomal staining procedures developed was known as Q-banding, which was developed in 1970 by Torbjorn Caspersson. This technique uses the DNA-alkylating dye, quinacrine, which forms a covalent link with the DNA. Researchers noted that the staining patterns resulting from this technique were consistent and repeatable, demonstrating that banding patterns can be used to identify and characterize individual chromosomes. Giemsa dye, as shown in Figure 24.3, is more commonly used today, as it can be used with bright field microscopy and produces high detail banding patterns. A specific technique, called G-banding uses Giemsa staining following the treatment of mitotic chromosomes with the protease, trypsin. Pre-treating the sample with trypsin prior to staining causes the partial breakdown of chromosomal proteins leading to chromosomal relaxation. This allows more thorough staining of the chromosomes when treated with Giemsa dye. When the chromosomal region is more tightly packed into heterochromatin, it tends to stain more darkly with the Giemsa dye, than the more lightly packaged euchromatic regions. Heterochromatic regions tend to have higher A-T content and don't contain as many gene regions as euchromatic regions. Euchromatic regions stain more lightly with G-banding. Other types of staining with Giemsa, include R-banding or Reverse-banding, which involves heating the DNA prior to staining. This is thought to cause the melting of A-T rich regions, reducing the Giemsa staining, when compared to G-C rich, gene-containing regions of the chromosomes.

    When visualizing a karyotype, the chromosomal images are aligned so that heterologous chromosomes are paired together and positioned such that the p-arm (short arm) is on top and the q-arm (long arm) points downward. Karyotypes can be used to quickly identify gross chromatic abnormalities that are larger than a few megabases in difference. This includes abnormalities such as aneuploidy (the addition or absence of an entire chromosome), or translocations (the transfer of part of a chromosome to a neighboring chromosome), as shown in Figure 24.1.4 and 24.1.5.

    Figure 24.1.4 Female Down Syndrome Karyotype Demonstrating Trisomy 21. (Karyotype prepared by Fatma Soylemez). Image from: Soylemez, F. (2014) Chapter in Health Problems in Down Syndrome.

    Figure 24.1.5 Karyotype of a Translocation (A) G-banding karyotype of a patient with t(15;22) translocation. Chromosome 22 monosomy with an unbalanced translocation is observed. The red arrows indicate the abnormal chromosomes. X indicated total monosomy. Original magnification, x110. (B) Ideogram and partial G-banding karyotype showing a more defined image of the translocation of the q-arm of chromosome 22 to chromosome 15. Image from: Gug, C., et al (2018) Exp & Ther Med 16(4) 6609

    The telomeric regions of chromosomes can also be identified using fluorescent staining techniques, as shown in figure 24.1.6. The structure of telomeric chromosomal regions is described in section 24.3.

    Figure 24.1.6 Telomere Staining. Image from: U.S. Department of Energy Human Genome Program

    More recently, techniques such as chromosome painting, use fluorescently labeled probes to hybridize with specific chromosomes or even specific gene regions of a chromosome. Karyotypes originating from this technique are called spectral karyotypes. This technique can be especially useful in identifying translocations that have occurred in human cells, as shown in Figure 24.1.7.

    Figure 24.1.7 Spectral karyotyping (SKY) analysis of a fibroblast cell line derived from lung tissue (WI-38T) Different strains of WI-38T were developed and two showed high proliferation rates typical of premalignant state. (A) shows SKY analysis for WI-38T and the two high proliferation strains. Both high proliferation strains show translocations of chromosome 17 to the X chromosome. (B) shows specific staining of WI-38T(HP-1) for the 17q25 region of chromosome 17 (pink) which is visible of both copies of chromosome 17 and also on one of the X chromosomes, indicating the translocation. (C) shows a graphic image of the translocation. Image from: Buganim, Y., et al (2010) PLoS ONE 5(3) e9657


    Wikipedia contributors. (2021, May 23). Genetic linkage. In Wikipedia, The Free Encyclopedia. Retrieved 00:19, July 23, 2021, from

    Wikipedia contributors. (2021, July 6). Karyotype. In Wikipedia, The Free Encyclopedia. Retrieved 01:16, July 23, 2021, from

    24.1: Gene Mapping and Chromosomal Karyotypes is shared under a CC BY-SA 4.0 license and was authored, remixed, and/or curated by Henry Jakubowski.