Changes within chromosomes

Can occur within a chromosome or between non-homologous chromosomes

Types of changes

- deletions

- duplications

- inversions

- translocations

Chromosome deletions

- Loss of a piece of an arm or the lose of an arm from a chromosome

Types:- terminal, from the end of a chromosome- intercalary or intersitial, from within the chromosome

Chromosome deletions

Origin of deletions:- movement of transposible elements- radiation- genetically induced- product of recombination events with heterozygous inversions- product of meiosis with heterozygous translocations

Movement of transposible elements

- It is speculated that when a conservative transposible element moves a section of the chromosome that the element is leaving can be lost.

- This loss can either result in a terminal deletion or a intercalary deletion

transposible element

reconnection does not occur

terminal piece lost

Radiation:

High energy radiation can cause a physical break in the chromosome resulting in a deletion

Deletions caused by radiation can be either terminal or intercalary

Terminal deletion by radiation

Intercalary deletion by radiation

Protocol for producing deletions by radiation

- radiate pollen of dominant genotype

- pollinate recessive genotype

- screen progeny for recessive phenotype

- plants showing recessive phenotype could be the result of a deletion

Genetically inducing deletions

In certain interspecific crosses it was found that the presence or absence of a chromosome from one of the species could induce deletions

The genes that induce the deletions are called gametocidal genes because the deletions may lead to non-functional gametes

Behavior of deletions in meiosis

- reduced chromosome pairing

- as the deletion size increases pairing frequency decreases

- result is a decrease in the amount of recombination

- terminal deletions breed true

indicating restoration of telomeres

Determining the location of chromosomes using deletions

- molecular

- Southern blot

- PCR

Set of deletion lines

A A A a a a gene

expression

Set of deletion lines

location of gene

A A A a a a gene

expression

Southern blot analysis

- presence or absence of a marker would determine the chromosome and chromosome location of the molecular marker

- if the marker was linked to a gene then the gene location would now be known

Dis

om

ic

Nu

lli

1A

Nu

lli

1B

Nu

lli

1D

Tel

o 1

DS

Tel

o 1

DL

Del

1D

S-1

Del

1D

S-2

Del

1D

S-3

Southern blot results with marker used as a probe – what is the chromosome location of the probe?

Dis

om

ic

Nu

lli

1A

Nu

lli

1B

Nu

lli

1D

Tel

o 1

DS

Tel

o 1

DL

Del

1D

S-1

Del

1D

S-2

Del

1D

S-3

Gene is on the short arm of chromosome1D in the region covered by deletion 1DS-3

PCR approach

Have primers for a marker, EST or gene of interest

Identify chromosome, chromosome arm and deletions by the absence of product

Dis

om

ic

Nu

lli

4A

Nu

lli

4B

Nu

lli

4D

Tel

o 4

BS

Tel

o 4

BL

Del

4B

L-1

Del

4B

L-2

Del

4B

L-3

PCR results with primers - what is the chromosome location of the probe?

Dis

om

ic

Nu

lli

4A

Nu

lli

4B

Nu

lli

4D

Tel

o 4

BS

Tel

o 4

BL

Del

4B

L-1

Del

4B

L-2

Del

4B

L-3

PCR results with primers indicate the product is located on chromosome 4BL in the region of deletion 2.

Chromosome duplications

Regions of a chromosome that are repeated resulting in an increased dosage (number) of some genes

example: isochromosome, one arm duplicated and one arm is missing

A B AA

Normal chromosome Isochromosome

Types if duplications

- intra-arm where the duplication is in the same arm

- inter-arm where the duplication is in the other arm of the

chromosome

- non-homologous duplication where the duplication is on a different chromosome

Origin of duplications

natural

- oblique synapsis (unequal crossing-over)

- inversions

- translocations

induced

- radiation

- chemicals

Inversions

A chromosome inversion is a change of the linear sequence of genes on a chromosome

Two types of inversions can occur:

- paracentric where the inversion does not involve the centromere- pericentric where the inversion does involve the centromere

Formation of a paracentric inversion

B

D

C

C

A

D

B

A

Formation of a pericentric inversion

An inversion in theory may not be detrimental since no genes are gained or lost due to the inversion

Gene function could be affected if the break occurs in the middle of a gene or in its promoter region

Gene function could be affected by moving into or away from a region of heterochromatin

inverted

normal

In individuals heterozygous for an inversion recombination is reduced especially for the genes close to the breakpoints

This can play a role in speciation by allowing genes within the inversion to be inherited as a block of genes

The reason for the low level of recombination of genes within the inversion for individuals heterozygous for the inversion are the problems caused when crossing-over occurs

Crossing-over within the inversion can lead to duplication and deletions

In the case of paracentric inversions such a cross-over can result in dicentric and acentric chromosomes in meiosis

X

Prophase I – paracentric inversion

*showing only the chromatids involved in the cross-over

dicentricbridge

acentricfragment

Early anaphase I

dicentricbridge breaks

acentricfragmentlost

Late anaphase I

dicentricbridge breaks

acentricfragmentlost

Late anaphase I

The presence of chromosomes with duplications and deletions leads to non-viable gametes

If two of the four chromatids are involved in the cross-over then 50% of the gametes will be non-viable

The presence of partial sterility is one method for identifying individuals that are heterozygous for an inversion

To get proper pairing of the complimentary regions a loop structure has to form

If a cross-over occurs within the looped area (region with the inversion) then duplications and deletions can be produced

• Would we get any acentric fragments in pericentric (where centromere is involved in the cross over) inversion ?

X

Prophase I – pericentric inversion

*showing only the chromatids involved in the cross-over

A B C D E

A B C D E

F G H I J

F G H I J

A B C D E E D C B A

F G H I JJ I H G F

Late anaphase I

While there are no dicentric bridges or acentric fragments two of the chromosomes will have duplications and deletions

An interesting affect of the inversion is that genes within the inversion would be inherited as a block of genes because only chromatids not involved in the cross-over would result in a viable gamete

The inheritance of blocks of genes and the partial sterility found in individuals heterozygous for the inversion can lead to speciation

For speciation to occur it would require the presence of several inversions

With each additional inversion the probability of viable gametes in a hybrid between a normal by an inversion genotype decreases while fertility of individuals having two normal or two inversion parents stays at 100%

Combine the increased sterility with the inheritance of blocks of genes and differences between the two genotypes becomes great enough that they can not successfully mate and produce fertile hybrids (i.e. become two species)

An example of this is tomato and diploid potato

Based on molecular marker studies it was shown that the genes for the two species were generally on the same chromosomes but the gene order was inverted on several of the chromosomes when the two species were compared