Structural Variations in Chromosomes | Genetics

The following point highlight the five main types of structural variation in chromosomes. The types are: 1. Deletion or Deficiency 2. Duplications 3. Translocations 4. Inversions 5. B-Chromosomes.

Type # 1. Deletion or Deficiency:

A deficiency means deletion of a small portion of a chromosome resulting in loss of one or more genes. A deficiency originates from breakage occurring at random in both chromatids of a chromosome (called chromosome break), or only in one chromatid (chromatid break).

The breakage may be caused by various agents such as radiation, chemicals, drugs or viruses at any time during the cell cycle, either in somatic or in germ cells. Depending upon its location, a deletion may be terminal when a single break occurs near the end of the chromosome; or interstitial when two breaks occur in a middle portion of the chromosome.

Each break produces two raw ends which may behave in one of following three ways:

(a) There might be reunion of the broken ends called restitution so that the original chromosome structure is restored;

(b) The broken ends may not unite giving rise to a chromosomal segment without a centromere which is eventually lost during cell division;

(c) If two single breaks occur in two different chromosomes in a cell, the deleted segment of one chromosome may unite with the raw broken end on the other chromosome; this is called exchange union.

Fate of a Deleted Fragment:

If the fragment does not have a centromere (acentric), then at metaphase it will not be able to get attached to spindle fibres and move towards a pole with other centric chromosomes. It will remain at the centre of the cell and will not be included within any of the two daughter nuclei. It will be free in the cytoplasm and will eventually be lost (Fig. 12.1). In this way, the cell will lose one or more genes contained in the deleted fragment.

A diploid cell has a homologue of the chromosome which has lost a segment. The corresponding segment of the intact homologue will have alleles of the genes that the cell has lost. Such a cell is said to be heterozygous for a deficiency. A very small deficiency in the heterozygous state is viable, but if homozygous it is lethal. When a deletion is large it is lethal even in the heterozygous state.

If a deletion occurs in cells of the germ line, then 50% of the gametes formed will have a deleted chromosome and 50% gametes would be normal. This would result in half the offspring with phenotypic abnormalities related to the genes carried on a small deleted fragment.

If the deficiency occurs in a developing embryo, some cells would have normal chromosomes and other cells would have the deficiency. This could produce a mosaic individual with two different phenotypes.

Detection of Deficiency:

The occurrence of a deficiency can sometimes be inferred from the results of a genetic cross when a rare recessive phenotype unexpectedly appears in the progeny. Consider a cross between two parents DD and dd where D controls the dominant expression of a trait, and d is the recessive allele. The F1 is expected to show the dominant trait and have the genotype Dd.

If on the contrary, some F1 individuals show the recessive phenotype, one explanation could be sought in a deletion of the chromosomal segment bearing gene D. Since other interpretations are also possible, it is best to confirm the occurrence of deficiency from a cytological study of the chromosomes as described below.

Deficiencies are best observed in preparations of homologously paired chromosomes at meiotic prophase either in large sized plant chromosomes or in polytene chromosomes. Normally during pachytene homologous chromosomes are intimately synapsed throughout their length.

If one of the homologues is deficient over a small length, the corresponding portion of the second homologue has nothing to pair with. It therefore, forms a loop (Fig. 12.1), which is clearly visible in cytological preparations and is clear-cut proof that deficiency has occurred.

Suppose further that the deleted segment carries the dominant gene D. The recessive allele d is still present in the other homologue and expresses itself even in the single dose because the dominant allele D which normally suppresses it is absent. Such a phenomenon whereby a single recessive allele expresses itself in absence of the dominant allele is called pseudo-dominance.

This also explains the results of the cross described above. Pseudo-dominance is similar to the hemizygous condition found exclusively in males where a recessive gene or a single X chromosome is expressed. Pseudo-dominance effect is observed in autosomal genes.

Due to the fact that deficiencies can produce unique phenotypic effects and the ease with which they can be identified by loop formation, they are important cytological tools for mapping genes.

In Drosophila this method has been used to locate a number of genes on the banded polytene chromosome. In general it can be stated that each band represents a distinct gene. Since there are 5000 bands in D. melanogaster it is believed that there are about 5,000 genes in this species.

Deficiencies also produce phenotypic abnormalities in man. The cat-cry syndrome (cri- du-chat) where the baby cries like a cat is due to a deletion in the short arm of chromosome 5. A deletion in the long arm of chromosome 22 (Ph 1 or Philadelphia chromosome) leads to chronic granulocytic leukemia.

In plants deficiencies are not easily transmitted to the progeny because their presence in developing pollen grains leads to pollen sterility. Nevertheless they have been observed in some plants.

In maize Creighton and McClintock have found that small deficiencies are viable even in the homozygous state. A special kind of single break occurs through the centromere of a metacentric chromosome giving rise to two isochromosomes with terminal telomeres. Such an event is also called misdivision of centromere (Fig. 12.2).

Type # 2. Duplications:

A duplication involves attachment of a chromosomal fragment resulting in addition of one or more genes to a chromosome. Whenever there is a duplication in a chromosome, there is a corresponding deletion in another chromosome.

Following types of duplications are known (Fig. 12.3: the diagrams are self-explanatory):

The phenotypic effect produced by a duplication is illustrated by the attached-X females in Drosophila. Consider such flies which are homozygous for some recessive sex-linked traits. It is found that when a fly receives a fragment of an X chromosome carrying the wild type allele from its male parent, then only the dominant phenotype is expressed.

The recessive alleles of the same gene although present in the homozygous condition, are not able to express themselves. Evidently the presence of a single dominant allele in a duplication is enough to produce the wild type phenotype.

The origin of duplications can be traced to unequal crossing over during meiosis. Normally homologous chromosomes are paired in a perfect manner so that identical loci lie exactly opposite each other.

The mechanism ensures that after crossing over between non-sister chromatids, equal exchange products are formed. If paired chromosomes are misaligned, it is not possible for exchange to take place between exactly opposite locations on two chromatids.

Instead, exchange occurs between adjacent points on two chromatids so that one resulting chromatid will have a duplication, the other a deletion. Such an exchange is called unequal crossing over. A gamete that receives a chromosome with a duplication will be diploid for some genes. When it fertilises a normal gamete, the zygote will have three sets of those genes that are present in the duplicated segment.

Bar eyes is a dominant X-linked trait in Drosophila females which provides a range of interesting phenotypes resulting from duplication. In a homozygous wild type female there is a large oval compound eye (non-bar) with about 779 facets.

The Bar trait reduces the eye to a vertical bar with very few facets. Bridges analysed the salivary gland chromosomes of Drosophila and found that the Bar gene (B) was present on a region designated 16A of the X chromosome.

When the band in the 16A region is present in duplicate in one X chromosome of the female (i.e. heterozygous for the duplication B/X), it results in an elongated Bar-shaped eye, smaller than the wild type (+/+) due to the presence of only 358 facets.

When a female is homozygous for the duplication (B/B), the Bar-shaped eye is further reduced in size and has 68 facets. If there is unequal crossing over in a female homozygous for Bar (B/B), it results in one chromatid where the 16A region (Bar locus) is present in triplicate, and the second chromatid with only one Bar locus.

Such a heterozygous triplicate condition produces a pheno­type known as ultra-bar (B^u) with only 45 facets. If the triplicate condition becomes homozygous (B^U/B^U), the result is a very small eye with only 25 facets (Fig. 12.4). Unequal crossing over is also responsible for a rare human haemoglobin known as haptoglobin.

The Bar locus in Drosophila provides an explanation for position effect. According to this phenomenon the expression of a gene becomes altered when the position of the gene is physically changed. Cytologically, a duplication is identified by the same method as deficiency, since in the heterozygous condition the extra fragment forms a loop in one of the two homologues.

Type # 3. Translocations:

Sometimes a segment of a chromosome becomes detached and unites with another non-homologous chromosome. Such an inter-chromosomal rearrangement is called translocation.

The rearrangements are of following types (Fig. 12.5):

a. Simple Translocation:

A single break occurs in a chromosome, and the broken fragment becomes attached to the end of another chromosome. However, due to the presence of “non-sticky” telomeres at the unbroken ends of a chromosome, such a terminal attachment of a segment does not take place.

b. Shifts:

In this type three breaks are involved. Two breaks occur in a chromosome to produce an interstitial fragment. This fragment becomes inserted into one of the arms of another non-homologous chromosome in which a single break has produced two “sticky” ends.

c. Reciprocal Translocations:

These are the most frequent and extensively studied translocations. A single break occurs in each of the two non-homologous chromosomes followed by a mutual exchange of the broken fragments. This results in two new chromosomes each having one segment of the other chromosome.

Rarely, two breaks occur in each of the two chromosomes followed by exchange of intercalary segments. If the centromere containing segment of one chromosome is joined to the acentric piece of the other non-homologue, the exchange is called eucentric. But if two centric pieces from two non-homologues join to form a dicentric chromosome, it is called aneucentric.

In the next division the dicentric chromosome will form a bridge and the acentric fragment will be lost. Therefore aneucentric exchange unions are usually lethal. The eucentric reciprocal translocations produce viable gametes if both pairs of non-homologous chromosomes exchange segments.

Reciprocal exchange of segments involves no loss of genetic material. There is a qualitative change in the sequence of genes which is transmitted during mitosis and meiosis. Reciprocal translocations represent an important group of inter-chromosomal structural aberrations in chromosomes.

d. Multiple Translocations:

Sometimes more than two pairs of non-homologous chromosomes may be involved in a translocation as observed Drosophila and Oenothera. In 1930 Stern studied a multiple translocation system in Drosophila in which a segment of the Y chromosome became attached to the X chromosome. At the same time a reciprocal translocation occurred between the X and chromosome IV. This resulted in a female with 9 chromosomes instead of 8.

e. Half Translocations:

When the nucleus containing two broken chromosomes is small, the broken ends are not widely separated in space and have better chance of undergoing reciprocal exchange. This is true for the small compact nucleus in the head of a sperm.

In oocytes, on the contrary, due to the large nuclear volume the distance between the broken ends of non-homologous chromosomes may be so great that the chance for an exchange union is relatively small. In such a case only one exchange union may take place, leaving the other two broken ends free. This is called half translocation.

Cytology of Reciprocal Translocations:

In translocation homozygotes meiosis is normal with regular bivalent formation at pachytene. At anaphase, movement to the poles is normal and viable gametes are produced. On the contrary in translocation heterozygotes pairing is complicated due to segments that have been exchanged between non-homologous chromosomes.

Instead of bivalents therefore, cross-shaped configurations of quadrivalents are formed at Metaphase I because of synapsis between homologous segments. Such interchange figures are more easily recognised in plant species with large chromosomes.

A translocation heterozygote has two normal and two interchange chromosomes. Following the rules of pairing these four chromosomes will form a cross-shaped interchange configuration shown in Fig. 12.6. The fate of chromosomes and the type of gametes that will be produced depend upon the frequency and distribution of chiasmata.

The chance that one or more chiasmata are formed in a certain segment depends on three factors: the length of the segment, the amount of exchange in the given organism, and characteristic properties of the segment that relate to chiasma formation.

The formation of chiasma in the separate segments determines the frequencies of the different metaphase configurations. Conversely from the latter frequencies it is possible to estimate the chance that each segment has one or more chiasmata, or the intensity of crossing over in the segment.

When two opposite segments in the cross have a chiasma each, it results in two rod bivalents. If chaismata occur in two adjacent terminal segments, a trivalent and a univalent are formed. However, the ring and chain quadrivalents are the most common translocations.

Sometimes two heterozygous reciprocal translocations may occur in the same cell. When there is one chromosome common to both, a multivalent of chromosomes is formed (hexavalent). When two interchanges occur in the same two chromosomes a quadrivalent can result.

It is possible to determine whether or not two translocations share a chromosome. This is done by making a double heterozygote and by observing whether two quadrivalents, a hexavalent, or a single quadrivalent are formed. In plants like barley, Datura, maize, rye and some others, a series of interchanges are known, involving all chromosomes at least once.

The chromosomes involved in an interchange can be determined when the interchange is hybridised successively with all interchanges of the series, called a tester set. In one case a quadrivalent will be observed at meiosis; the known interchange and the one to be analysed have both chromosomes in common.

In two cases a hexavalent is formed (the known and unknown interchange share one chromosome); and in the remaining cases two quadrivalents are observed. This is an efficient method of determining which chromosomes are involved in an unknown interchange.

In each of the four arms of the cross-shaped quadrivalent one chiasma is usually formed. At diakinesis two events take place: repulsion between homologues causing their separation, and terminalisation (movement) of chiasmata towards the distal end of the arms. At metaphase therefore, the interchange figure becomes oriented to form an open ring or a twisted, zigzag configuration (Fig. 12.7).

In case chiasma does not form in one of the four arms, the cross- shaped complex opens up to form a chain. Anaphasic movement of chromosomes towards the poles takes place in one of the three different ways described below (Fig. 12.8).

a. Alternate Segregation:

The twisted orientation ensures perfect disjunction so that both translocated chromosomes 1′ and 2′ go to one pole, and both un-translocated chromosomes 1 and 2 go to the other pole. Thus all the remaining gametes will receive a full complement of genes and would give rise to viable individuals.

b. Adjacent-1 Segregation:

This will take place in the open ring configuration whereby one translocated and one un-translocated chromosome will go to the same pole, in this way chromosome 1 and 2′ will go to one pole whereas 1’ and 2 will go to the other pole.

c. Adjacent-2 Segregation:

Again in the open ring configuration, two homologous chromosomes 1 and 1′ will go to one pole, the other two homologues 2 and 2′ go to the other pole. It is evident that both the adjacent types of segregation will give rise to gametes with duplications and deficiencies which would cause semi-sterility. The proportion of inviable gametes produced would be determined by the frequency of germ line cells having ring configuration.

In animals gametes with duplication deficiency genomes are viable, but the zygote does not survive. Homozygous translocations can give rise to viable individuals if the paired homologues have normal crossing over and segregation at meiosis.

The site in the cross-shaped figure where crossing over occurs is important in estimating sterility. With respect to crossing over, each arm has a distinct interstitial segment which lies between the centromere and the break point of the translocation; the second is called pairing segment which represents portions of the arms of the cross beyond interstitial segments.

Crossing over in the pairing segments has no effect on the segregation pattern as only homologous are exchanged. The ring and zigzag arrangements obtained are in fact due to crossovers in the pairing segments. If crossing over occurs in the interstitial segment then non-homologous portions are exchanged leading to the production of unbalanced gametes.

Genetic Methods of Detecting Translocations:

Translocations can be detected by performing genetic crosses and observing gene segregation. When translocation heterozygotes are selfed or crossed with each other, the progeny is of three types: normal homozygotes, interchange heterozygotes, and interchange homozygotes in the ratio 1:2:1 (Fig. 12.9 A, B).

If there are two reciprocal translocations in a cell that do not share any chromosome, then there is independent segregation.

But if two translocations share a common chromosome there can be two consequences:

(a) The same homologue of the common chromosome is involved in both translocations. The resulting balanced gametes are of two types, one with both translocations, the other with none. Alternate segregation is necessary to produce them. Thus when heterozygotes are selfed the progeny is in the ratio: 1 homozygous for both, 2 heterozygous for both, and 1 homozygous normal.

(b) There is one chromosome shared by two translocations, but here one homologue is involved in one, the other homologue in the other translocation as indicated below.

This happens normally when two independently formed translocations are combined in one individual by hybridisation. Here also only two types of gametes are formed: one type having one translocation and the third chromosome normal; the other having the other translocation and also one chromosome of the three normal.

When heterozygotes are now selfed they produce one homozygote for one translocation and also for one normal chromosome; two double heterozygotes and the normal types are formed due to crossing over in the different segment.

Translocations affect linkage relationships between genes in two ways:

(a) In the homozygote linkage is changed; the genes in the translocated segment are not linked with the genes in the chromosome where they originally belonged; they are now linked to other genes. Study of this change in linkage can be used to detect a translocation and identify the involved chromosome.

(b) In the translocation heterozygote all the genes on all the involved chromosomes are linked. This is because usually only balanced gametes take part in fertilisation or only balanced zygotes survive. Balanced gametes arise when either all interchange chromosomes or all normal chromosomes are present in one gamete.

Recombination between genes on different chromosomes, that is, between the gene and translocation takes place between the interchange breakpoint and the locus. The percentage crossing over between a locus and the break point can be calculated. The translocation can be detected from mitotic chromosomes.

The heterozygotes can be located from multivalents at meiosis. The two homozygous types, the normal and interchange are not distinguishable from each other as both produce bivalents. An easier method of identifying heterozygotes is through their semi-sterility. The simplest analysis between the gene and translocation using heterozygotes can be done by a test cross which yields a 1: 1 segregation for the translocation and also for the gene.

Translocation in Oenothera:

The various species of the plant Oenothera (Onagraceae) are heterozygous for multiple translocations and show rings of chromosomes at meiosis. There are 14 chromosomes in the diploid cell of which some or all may be involved in translocations.

On this basis the species of Oenothera form a graded series. O. hookeri is distinct in having 7 pairs of chromosomes and no translocations. The other species form rings of 6, 8, 10, 12 or 14 chromosomes at meiosis (Fig. 12.10). O. lamarckiana has a ring of 12 chromosomes and one bivalent pair. In O. muricata all the 14 chromosomes are united to form a giant ring. O. biennis shows one ring of 8 and another of 6 chromosomes.

Similar instances of interchange heterozygosity are also known in some other plants such as Rhoeo discolor (Commelinaceae), Isotonia (Lobeliaceae), Hypericum (Hypericaceae) and 6 more genera of the family Onagraceae besides Oenothera. It is rare in animals.

A few genera of scorpions like Isometrus, Buthus and Tityus show translocation heterozygosity and ring of chromosomes at meiosis. There are certain genetic mechanisms which enforce permanent translocation heterozygosity in Oenothera. The cytogenetics of Oenothera has been worked out extensively.

Type # 4. Inversions:

Inversions result when there are two breaks in a chromosome and the detached segment becomes reinserted in the reversed order. They are classified into two types depending upon the inclusion or absence of the centromere within the inverted segment.

Thus when both breaks occur in one arm of the chromosome it leads to a paracentric inversion; when a break occurs in each of the two arms, the centromere is included in the detached segment and leads to a pericentric inversion.

Meiosis is normal in inversion homozygotes. In heterozygotes pairing between homologous chromosomes is affected in the region of the inverted segment. Consequently, there is a suppression of recombination and fertility is impaired.

Paracentric Inversions:

This type of inversion is identified in the heterozygote by formation of a pairing loop at pachytene. If the size of the loop is large enough, chiasma formation will take place within it. When a single chiasma forms between an inverted and a normal segment, the two chromatids involved will produce one dicentric chromatid and one acentric fragment after exchange (Fig. 12.11). The other two chromosomes will be normal.

At anaphase I the dicentric chromosome will be pulled towards both poles, it will form a bridge that will ultimately break. The acentric fragment due to its inability to move would be eventually lost.

Consequently, of the resulting four gametes, two would be normal and two deficient in chromosome segments. In plants deficient gametes are not viable (pollen grains that are deficient usually abort and are nonfunctional). In animals such gametes take part in fertilisation but either the zygote or the embryo aborts.

In an individual heterozygous for a paracentric inversion therefore, viable offspring are produced only by two of the four chromatids which did not have chiasma formation between them in the region of the loop.

In each chromatid the gene sequence in the inversion segment will be of the non-recombinant, parental type. Consequently, none of the offspring would be recombinants for genes present within the inverted segment. In this way a paracentric inversion suppresses recombination throughout its length.

In some insects and in Drosophila, individuals heterozygous for an inversion do not show reduction in fertility. In fact paracentric inversions occur frequently in natural populations of Drosophila. There are two explanations for this. One is absence of crossing over in male meiosis.

The second is occurrence of four products of female meiosis in linear order of which the middle two egg nuclei have the deficiency; the peripheral two nuclei are functional and fertilised. They produce viable offspring of the parental type.

Pericentric Inversions:

In an individual heterozygous for a pericentric inversion, the centromere is present within the loop. When chiasma formation takes place within the inverted segment the chromatids resulting after exchange do not form a dicentric and acentric fragment as in a paracentric inversion heterozygote.

Instead, they have one centromere each, but are deficient for some segments whereas other segments are duplicated (Fig. 12.12). The exchange segments produce inviable gametes and offspring. As in the case of pericentric inversions, the two chromatids not involved in crossing over only produce viable offspring with parental combination of genes present in the inverted segment.

Due to the suppression of recombination the genes present in the inverted segment segregate as a single unit called supergene within a population. Inversions are easy to identify in the banded polytene chromosomes of Drosophila larvae and have been extensively studied.

Type # 5. B-Chromosomes:

In addition to the normal chromosome complement, a number of plant and animal species have extra chromosomes called B-chromosomes (normal complement in such cases is designated A). They are smaller than the A chromosomes, they do not pair with any A chromosome during meiosis, and apparently do not serve any vital function in the organism.

However, they persist in the population without conferring any obvious advantages. Their number is variable within species and among individuals within a population, in others they may be lacking.

As they are not required for normal growth and reproduction, they have been considered to be genetically inert and dispensable. However, the recent work on corn and rye has shown that they have a few active genes and they perform certain functions.

B-chromosomes have been extensively studied in plants of Zea mays (maize) and Secale cereale (rye). They behave abnormally during mitotic division in the uninucleate pollen grains which gives rise to a small generative cell and a large vegetative cell. At anaphase of mitosis, the daughter chromatids of B-chromosomes fail to separate even though the centromeres have divided.

Due to nondisjunction both chromatids move together toward the pole which forms the generative nucleus. Later on when the generative nucleus divides to form two male gametes, B-chromosomes segregate normally. There is preferential fertilisation of eggs by male gametes which carry B-chromosomes.