1. Changes within chromosomes
Can occur within a chromosome or between non-homologous chromosomes
Types of changes
- deletions
- duplications
- inversions
- translocations

2. 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

3. 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

4. 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

5. transposible element
reconnection does not occur
terminal piece lost

6. 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

7. Terminal deletion by radiation
Intercalary deletion by radiation

8. 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

9. 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

11. 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

12. Determining the location of chromosomes using deletions
- molecular
- Southern blot
- PCR

13. Set of deletion lines
A A A a a a gene expression

14. Set of deletion lines
location of gene
A A A a a a gene expression

15. 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

16. Del 1DS-1
Del 1DS-2
Del 1DS-3
Telo 1DS
Telo 1DL
Disomic
Nulli 1A
Nulli 1B
Nulli 1D
Southern blot results with marker used as a probe – what is the chromosome location of the probe?

17. Gene is on the short arm of chromosome
Del 1DS-1
Del 1DS-2
Del 1DS-3
Telo 1DS
Telo 1DL
Disomic
Nulli 1A
Nulli 1B
Nulli 1D
Gene is on the short arm of chromosome
1D in the region covered by deletion 1DS-3

18. PCR approach
Have primers for a marker, EST or gene of interest
Identify chromosome, chromosome arm and deletions by the absence of product

19. Del 4BL-1
Del 4BL-2
Del 4BL-3
Telo 4BS
Telo 4BL
Disomic
Nulli 4A
Nulli 4B
Nulli 4D
PCR results with primers - what is the chromosome location of the probe?

20. Del 4BL-1
Del 4BL-2
Del 4BL-3
Telo 4BS
Telo 4BL
Disomic
Nulli 4A
Nulli 4B
Nulli 4D
PCR results with primers indicate the product is located on chromosome 4BL in the region of deletion 2.

21. 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

22. A B A A
Normal chromosome
Isochromosome

23. 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

24. Origin of duplications
natural
- oblique synapsis (unequal crossing-over)
- inversions
- translocations
induced
- radiation
- chemicals

27. 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

29. Formation of a paracentric inversionB A D B C A D
Formation of a paracentric inversion

30. Formation of a pericentric inversion

31. 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

33. normal
inverted

35. 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

36. 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

37. Prophase I – paracentric inversionX
*showing only the chromatids involved in the cross-over

38. Early anaphase I
acentric
fragment
dicentric
bridge

39. Late anaphase I
acentric
fragment
lost
dicentric
bridge breaks

40. Late anaphase I
acentric
fragment
lost
dicentric
bridge breaks

42. 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

43. 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

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

45. Prophase I – pericentric inversionX
*showing only the chromatids involved in the cross-over

46. While there are no dicentric bridges or
Late anaphase I
A B C D E
F G H I J
A B C D E
E D C B A
J I H G F
F G H I J
A B C D E
F G H I J
While there are no dicentric bridges or
acentric fragments two of the chromosomes will have duplications and deletions

47. 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

48. 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%

49. 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

50. 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