13.1C: Identification of Chromosomes and Karyotypes - Biology

13.1C: Identification of Chromosomes and Karyotypes - Biology

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A karyotype depicts the number, size, and any abnormalities of the chromosomes in an organism.

Learning Objectives

  • Describe a normal human karyotype and discuss the various abnormalities that can be detected using this technique

Key Points

  • A normal human karyotype contains 23 pairs of chromosomes: 22 pairs of autosomes and 1 pair of sex chromosomes, generally arranged in order from largest to smallest.
  • The short arm of a chromosome is referred to as the p arm, while the long arm is designated the q arm.
  • To observe a karyotype, cells are collected from a blood or tissue sample and stimulated to begin dividing; the chromosomes are arrested in metaphase, preserved in a fixative and applied to a slide where they are stained with a dye to visualize the distinct banding patterns of each chromosome pair.
  • A karyotype can be used to visualize abnormalities in the chromosomes, such as an incorrect number of chromosomes, deletions, insertions, or translocations of DNA.

Key Terms

  • autosome: any chromosome other than sex chromosomes
  • karyotype: the observed characteristics (number, type, shape etc) of the chromosomes of an individual or species
  • translocation: a transfer of a chromosomal segment to a new position, especially on a nonhomologous chromosome

Identification of Chromosomes

The isolation and microscopic observation of chromosomes forms the basis of cytogenetics and is the primary method by which clinicians detect chromosomal abnormalities in humans. A karyotype is the number and appearance of chromosomes. To obtain a view of an individual’s karyotype, cytologists photograph the chromosomes and then cut and paste each chromosome into a chart, or karyogram, also known as an ideogram.

In a given species, chromosomes can be identified by their number, size, centromere position, and banding pattern. In a human karyotype, autosomes or “body chromosomes” (all of the non–sex chromosomes) are generally organized in approximate order of size from largest (chromosome 1) to smallest (chromosome 22). However, chromosome 21 is actually shorter than chromosome 22. This was discovered after the naming of Down syndrome as trisomy 21, reflecting how this disease results from possessing one extra chromosome 21 (three total). Not wanting to change the name of this important disease, chromosome 21 retained its numbering, despite describing the shortest set of chromosomes. The X and Y chromosomes are not autosomes and are referred to as the sex chromosomes.

The chromosome “arms” projecting from either end of the centromere may be designated as short or long, depending on their relative lengths. The short arm is abbreviated p (for “petite”), whereas the long arm is abbreviated q (because it follows “p” alphabetically). Each arm is further subdivided and denoted by a number. Using this naming system, locations on chromosomes can be described consistently in the scientific literature.

Although Mendel is referred to as the “father of modern genetics,” he performed his experiments with none of the tools that the geneticists of today routinely employ. One such powerful cytological technique is karyotyping, a method in which traits characterized by chromosomal abnormalities can be identified from a single cell. To observe an individual’s karyotype, a person’s cells (like white blood cells) are first collected from a blood sample or other tissue. In the laboratory, the isolated cells are stimulated to begin actively dividing. A chemical called colchicine is then applied to cells to arrest condensed chromosomes in metaphase. Cells are then made to swell using a hypotonic solution so the chromosomes spread apart. Finally, the sample is preserved in a fixative and applied to a slide.

The geneticist then stains chromosomes with one of several dyes to better visualize the distinct and reproducible banding patterns of each chromosome pair. Following staining, the chromosomes are viewed using bright-field microscopy. A common stain choice is the Giemsa stain. Giemsa staining results in approximately 400–800 bands (of tightly coiled DNA and condensed proteins) arranged along all of the 23 chromosome pairs. An experienced geneticist can identify each chromosome based on its characteristic banding pattern. In addition to the banding patterns, chromosomes are further identified on the basis of size and centromere location. To obtain the classic depiction of the karyotype in which homologous pairs of chromosomes are aligned in numerical order from longest to shortest, the geneticist obtains a digital image, identifies each chromosome, and manually arranges the chromosomes into this pattern.

At its most basic, the karyotype may reveal genetic abnormalities in which an individual has too many or too few chromosomes per cell. Examples of this are Down Syndrome, which is identified by a third copy of chromosome 21, and Turner Syndrome, which is characterized by the presence of only one X chromosome in women instead of the normal two. Geneticists can also identify large deletions or insertions of DNA. For instance, Jacobsen Syndrome, which involves distinctive facial features as well as heart and bleeding defects, is identified by a deletion on chromosome 11. Finally, the karyotype can pinpoint translocations, which occur when a segment of genetic material breaks from one chromosome and reattaches to another chromosome or to a different part of the same chromosome. Translocations are implicated in certain cancers, including chronic myelogenous leukemia.

During Mendel’s lifetime, inheritance was an abstract concept that could only be inferred by performing crosses and observing the traits expressed by offspring. By observing a karyotype, today’s geneticists can actually visualize the chromosomal composition of an individual to confirm or predict genetic abnormalities in offspring, even before birth.

A universal chromosome identification system for maize and wild Zea species

Maize was one of the first eukaryotic species in which individual chromosomes can be identified cytologically, which made maize one of the oldest models for genetics and cytogenetics research. Nevertheless, consistent identification of all 10 chromosomes from different maize lines as well as from wild Zea species remains a challenge. We developed a new technique for maize chromosome identification based on fluorescence in situ hybridization (FISH). We developed two oligonucleotide-based probes that hybridize to 24 chromosomal regions. Individual maize chromosomes show distinct FISH signal patterns, which allow universal identification of all chromosomes from different Zea species. We developed karyotypes from three Zea mays subspecies and two additional wild Zea species based on individually identified chromosomes. A paracentric inversion was discovered on the long arm of chromosome 4 in Z. nicaraguensis and Z. luxurians based on modifications of the FISH signal patterns. Chromosomes from these two species also showed distinct distribution patterns of terminal knobs compared with other Zea species. These results support that Z. nicaraguensis and Z. luxurians are closely related species.

Keywords: Chromosome identification FISH Karyotype Maize Oligo-FISH.

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Evolution of Sex Chromosomes and Complex Sex Chromosome Systems

Sex Chromosome Differentiation

Sex chromosomes have evolved independently many times across the tree of life, including in insects. Sex chromosomes are derived from originally homologous autosomes that acquired a master-switch sex-determining gene ( Bull 1983, see Figure 2). This creates sex chromosomes with a sex-determining function but an otherwise identical gene content and which recombine over most of their length (homomorphic sex chromosomes). The accumulation of sexually antagonistic mutations (i.e., mutations that are good for one sex, but bad for the other) close to the sex-determining region creates selective pressures to reduce or eliminate recombination between the proto-X/Y or proto-Z/W chromosomes, to ensure that such a sexually antagonistic allele is preferentially transmitted through the sex that it benefits. A restriction of recombination allows the sex chromosomes to diverge functionally and morphologically, and to evolve into heteromorphic sex chromosomes ( Bachtrog 2013). The sex chromosome present in the homomorphic sex (the X in male heterogametic systems, the Z in female heterogametic systems) can still recombine in the homogametic sex, and typically maintains most of its ancestral gene content. The sex-limited chromosome (the Y or W chromosome), however, will be completely sheltered from recombination. The lack of recombination decreases the efficacy of natural selection on the Y/W chromosome, and may lead to the accumulation of deleterious mutations at many or most of its original genes. Over long evolutionary time periods, the Y or W chromosome might degenerate entirely, and this loss in gene function is often associated with a simultaneous accumulation of repetitive DNA on the Y or W chromosome ( Bachtrog 2003). In the extreme case the Y or W chromosome may loose all essential genes and disappear entirely, leading to the evolution of XO or ZO sex determination ( Blackmon and Demuth 2014, 2015b).

Sex chromosome differentiation and origination of complex sex chromosomes. Sex chromosomes evolve from ordinary autosomes, after the emergence of a sex-determining locus. A restriction of recombination allows for differentiation, and Y/W chromosomes degenerate by an accumulation of deleterious mutations, and may be entirely lost (XO or ZO systems). Both fusions and fissions between sex chromosomes and autosomes can lead to the evolution of complex sex chromosomes (such as X1X2Y and XY1Y2 or Z1Z2W and ZW1W2 systems). Note that fusions are associated with a decrease in total chromosome number, while fissions increase the chromosome count.

Sex chromosome differentiation and origination of complex sex chromosomes. Sex chromosomes evolve from ordinary autosomes, after the emergence of a sex-determining locus. A restriction of recombination allows for differentiation, and Y/W chromosomes degenerate by an accumulation of deleterious mutations, and may be entirely lost (XO or ZO systems). Both fusions and fissions between sex chromosomes and autosomes can lead to the evolution of complex sex chromosomes (such as X1X2Y and XY1Y2 or Z1Z2W and ZW1W2 systems). Note that fusions are associated with a decrease in total chromosome number, while fissions increase the chromosome count.

Complex Sex Chromosomes

Complex sex chromosome systems, where a species harbors multiple X or Y or Z or W chromosomes can evolve relatively easily from an XY or ZW system by fusions between the ancestral sex chromosomes and autosomes, or fissions of the ancestral sex chromosome pair ( Figure 2 Kitano and Peichel 2012 Blanco et al. 2013). For example, a fusion between an X and an autosome can lead to a system containing multiple Y chromosomes, where the second Y chromosome corresponds to the unfused homolog of the autosome that fused to the X. This second Y can undergo similar degeneration as the ancestral Y, leading to the possession of two degenerate Y’s (and an XY1Y2 sex chromosome system). On the other hand, a fusion between an autosome and a Y chromosome can result in the evolution of an X1X2Y system. Similar sex chromosome—autosome fusions in ZW systems can also produce complex sex chromosomes, with autosome-Z fusions creating a ZW1W2 karyotype, and autosome-W fusions generating a Z1Z2W karyotype. Chromosomal fusions can also lead to the gain of new Y or W chromosomes in species that had ancestrally lost them (i.e., transitions from XO to XY or ZO to ZW systems), and is believed to have occurred within Lepidoptera ( Traut et al. 2008 Marec et al. 2010). Chromosomal fusions leading to complex sex chromosomes can be selected for if the fused autosome contains sexually antagonistic variation, analogous to the forces selecting for restricted recombination on the ancestral sex chromosomes, but they can also drift to fixation neutrally ( Charlesworth and Charlesworth 1980), or may in fact be slightly deleterious ( Pennell et al. 2015).

Complex sex chromosome systems can also derive from chromosomal fissions of the ancestral sex chromosomes ( Figure 2). For example, a fission of the ancestral X chromosome will result in an X1X2Y system while a fission of the Y will generate a XY1Y2 sex chromosome system. Similar, a Z chromosome fission will create Z1Z2W sex chromosomes and a W fission will result in a ZW1W2 karyotype. Chromosomal fissions are thought to be less common than simple chromosomal fusions, since each chromosomal fragment requires a centromere for proper segregation during meiosis. Indeed, it has been suggested that the relative importance of chromosomal fissions and fusions differs among species groups that possess either monocentric chromosomes (i.e., a single centromere on each chromosome), or holocentric chromosomes (where localized centromeres are absent, and each chromosome fragment can segregate successfully during meiosis Melters et al. 2012). Other chromosomal rearrangements, such as translocations, can also create complex sex chromosomes.

Most data that are available on sex chromosomes in insects are based on morphological differentiation from cytogenetic studies, that is, they are based on whether the X and the Y (or Z and W) appear distinct under a light microscope. Differentiation at the DNA sequence level is often accompanied by morphological differentiation, and sex chromosomes that appear morphologically similar are termed “homomorphic sex chromosomes,” and those that are distinct at the morphological level are termed “heteromorphic sex chromosomes.” While this distinction based on morphology often captures real differences in the underlying sequence divergence between sex chromosomes, systems that are classified as homomorphic may in fact be highly divergent at the DNA sequence level, yet show similar morphological features ( Vicoso et al. 2013). In fact, sequencing of 37 species of Diptera showed that despite relatively homogenous karyotypes the species exhibited 12 distinct sex chromosome configurations ( Vicoso and Bachtrog 2015). Thus, our classification based on morphological attributes is certainly an underestimate of sex chromosome occurrence and change, but provides an important first step in quantifying the diversity of sex chromosomes across insects, which we do below.

Identification of a balanced complex chromosomal rearrangement involving chromosomes 3, 18 and 21 with recurrent abortion: case report

Background: Complex chromosome rearrangements (CCRs) are constitutional structural rearrangements involve more than two breakpoints on two or more chromosomes. Balanced CCR carriers are often phenotypically normal but associated with high risk of spontaneous abortion and having abnormal offspring with unbalanced karyotype. Here, we report a new familial case of complex chromosome structural aberrations involving chromosomes 3, 18 and 21 and four breakpoints.

Results: Cytogenetic investigations showed a complex chromosomal chromosome rearrangement involving chromosomes 3, 18 and 21 with four breakpoints. 2 of 4 breakpoints were within the long arm of chromosome 18. Three-color fluorescence in situ hybridization (FISH) confirmed the complexity of the rearrangement and showed the derivative 21 to be composed of 3 distinct segments derived from chromosomes 21, 18, and 3. The karyotype of CCR carrier was determined as 46,XX,t(32118)(3pter → 3q12::18q23 → 18qter21pter → 21q22.1::18q21.1 → 18q23::3q12 → 3qter 18pter → 18q21.1::21q22.1 → 21qter).

Discussion: A new complex balanced CCR was characterized using conventional high resolution banding and molecular cytogenetic analysis. The results provided an explanation of recurrent abortion and abnormal child for balanced CCR carriers. Genetic counselling and prenatal diagnosis for couples with a balanced CCR is necessary since they have a high risk of having a child with unbalanced karyotype. Additional studies to reveal the molecular mechanism of CCRs would help reveal the rule of inherited CCRs in offspring.

Keywords: Complex chromosomal rearrangements (CCRs) Fluorescence in situ hybridization Genetic counseling Recurrent spontaneous abortions.

13.1C: Identification of Chromosomes and Karyotypes - Biology

A scientific group from the National Center for Human Genome Research in Bethesda, MD has recently published a modification to traditional karyotyping that permits rapid identification of chromosomal alterations. These findings are of import because the ability to detect altered chromosomes is increasingly important for pre- and postnatal diagnostics and in cancer and other diseases.

The traditional process for karyotyping involves adding a dye to metaphasic chromosomes. Different dyes that affect different areas of the chomosomes are used for a range of identification purposes. One common dye used is Giemsa That process is known as G-banding (see the G-banded chromosomes in the image to the left). This dye is effective because it markedly stains the bands on a chromosome Each chromosome can then be identified by its banding pattern, but the resuls is similar overall gray values for each chromosome.

The new karyotyping methods introduced by Schrock et al use fluorescent dyes that bind to specific regions of chromosomes. By using a series of specific probes each with varying amounts of the dyes, different pairs of chromosomes have unique spectral characteristics. A unique feature of the technology is the use of an interferometer similar to ones used by astronomers for measuring light spectra emitted by stars. Slight variations in color, undetectable by the human eye, are detected by a computer program that then reassigns an easy-to-distinguish color to each pair of chromosomes. The result is a digital image rather than film, in full color. Pairing of the chromosomes is simpler because homologous pairs are the same color, and abberrations and cross-overs are more easily recognizable. In additional, the spectral karyotype has been used to detect translocations not recognizable by traditional banding analysis.

A summary of the spectal karyotyping methods.

The paper:
Multicolor Spectral Karyotyping of Human Chromosomes
S CIENCE 26 Jul 1996 273 (5274):494 (in Reports)
E. Schröck, S. du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini, T. Ried

CYTOGENETICS: New Methods for Expanding the Chromosomal Paint Kit
S CIENCE 26 Jul 1996 273 (5274):430 (in Research News)

Similarities Between Male and Female Karyotypes

  • Male and female karyotypes are two types of complete sets of chromosomes of the two genders of humans.
  • The two types of chromosomes in both types of karyotypes are the autosomal and sex chromosomes. Generally, both male and female karyotypes contain autosomal chromosome pairs similar in both number and appearance.
  • Both of them allow the determination of the number and appearance of each chromosome in the nucleus of a somatic cell.
  • Also, both types of karyotypes allow the identification of the length of chromosomes, the position of the centromere, and the banding pattern. Also, they allow the determination of the physical characteristics of chromosomes.
  • Besides, both are important in the identification of chromosome abnormalities.

This research was supported by National Natural Science Foundation of China (Key Program, No.31430075) and National Natural Science Foundation of China (No. 31471872). The funding agencies provided funding to the research projects, but played no role in the design of study, collection and analysis, and interpretation of data and in writing the manuscript.


State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China

Qinzheng Zhao, Yunfei Bi, Yufei Zhai, Xiaqing Yu, Chunyan Cheng, Panqiao Wang, Ji Li, Qunfeng Lou & Jinfeng Chen

Institue of Horticulture, Zhejiang Academy of Agriculture Sciences, Hangzhou, 310021, China

Root tip chromosome karyotype analysis of hyacinth cultivars

Karyotype analysis in plants helps to reveal the affinity relationships of species and their genetic evolution. The current study aimed to observe chromosome karyotypes and structures of Hyacinthus orientalis. Twenty hyacinth cultivars were introduced from Holland, and their water-cultivated root tips were used as experimental samples. A solution of colchicine (0.02%) and 8-hydroxyquinoline (0.02 M) was used as a 20-h pre-treatment. Subsequently, Carnot I was used for fixation and 45% acetic acid was used for dissociation. The squash method was selected to prepare chromosome spreads for microscopic observation. The basic chromosome number of the hyacinth cultivar was 8, and the number of chromosomes in the diploid, triploid, tetraploid, and aneuploid cultivars was 16, 23, 24, 31, and 32, respectively. The L-type chromosome was predominant in the chromosomal composition. The hyacinth satellite was located on the short arm in numbers equivalent to the ploidy. This satellite is located on the middle-sized chromosome in the fourth group of chromosomes, demonstrating that Hyacinthus has a more primitive evolution than Lilium and Polygonatum. Among 20 hyacinth cultivars, 'Fondant' had the highest level of evolution and a maximum asymmetric coefficient of 61.69%. Moreover, the ratio between the shortest and longest chromosomes in this cultivar was 4.40, and its karyotype was type 2C. This study may elucidate long-term homonym and synonym phenomena. It may also provide a method of cytological identification as well as direct proof of the high outcross compatibility between hyacinth cultivars.