1. Prepared by Malcolm D. Schug University of North Carolina Greensboro
Powerpoint to accompany
Genetics: From Genes to Genomes
Third Edition
Hartwell ● Hood ● Goldberg ● Reynolds ● Silver ● Veres
Chapter 5
Prepared by Malcolm D. Schug
University of North Carolina Greensboro
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2. Linkage, Recombination, and the Mapping of Genes on Chromosomes
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3. Outline of Linkage, Recombination, and the Mapping of Genes on Chromosomes
Linkage and meiotic recombination
Genes linked together on the same chromosome usually assort together.
Linked genes may become separated through recombination.
Mapping
The frequency with which genes become separated reflects the physical distance between them.
Mitotic recombination
Rarely, recombination occurs during meiosis.
In eukaryotes mitotic recombination produces genetic mosaics.
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4. Independent assortment Genes on different chromosomesB A B a b a b
Gametes a B A b
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5. Linkage Two genes on same chromosome segregate together.B b
Gametes
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6. Crossing over and linkage Lead to separation of linked genesB b
Gametes x
Parental
Recombinant
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7. Some genes on the same chromosome assort together more often than not.
In dihybrid crosses, departures from a 1:1:1:1 ratio of F1 gametes indicate that the two genes are on the same chromosome.
How we determine if two genes are on the same chromosome can be demonstrated by the white and yellow genes on the X chromosome of Drosophila.
yellow (y+) – yellow body color
white (w+) – white eye color
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8. Linkage at a sex-linked gene
Deviation from 1:1:1:1 ratio of phenotypes for males
Draw traits on chromosomes and work through the cross
Figure 5.2
Fig. 5.2
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9. Designations of “parental” and “recombinant” relate to past history.
Parental and recombinant classes are opposite of one another in these two crosses.
Similar percentages of recombinant and parental types show that the frequency of recombination is independent of the arrangement of alleles.
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10. Linkage in an autosomal gene
Genotypes of F1 female revealed by test cross
Parental class outnumbers recombinant class demonstrating linkage.
Figure 5.5
Fig. 5.4
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11. Chi square test pinpoints the probability that ratios are evidence of linkage.
Transmission of gametes is based on chance events.
Deviations from 1:1:1:1 ratios can represent chance events OR linkage.
Ratios alone will never allow you to determine if observed data are significantly different from predicted values.
The larger your sample, the closer your observed values are expected to match the predicted values.
Chi square test measures “goodness of fit” between observed and expected (predicted) results.
Accounts for sample size, or the size of the experimental population
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12. Applying the chi square test
Framing a hypothesis
Null hypothesis – observed values are not different from the expected values
For linkage studies – no linkage is null hypothesis
Expect a 1:1:1:1 ratio of gametes.
Alternative hypothesis – observed values are different from expected values
For linkage studies – genes are linked.
Expect significant deviation from 1:1:1:1 ratio.
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13. Applying the chi square test to a linkage study
Genotype
Experiment 1
Experiment 2
A B 17 34
a b 14 28
A b 8 16 11 22
Total 50
100
Class
Observed/Expected
Parentals
Recombination
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14. Chi Square – Experiment 1 & 2
c2 = S (observed – expected)2
number expected
c2 = S (31 – 25)2 + (19 – 25)2
25 25
= 2.88
Experiment 1
Experiment 2
c2 = S (62 – 50)2 + (38 – 50)2
50 50
= 5.76
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15. Chi square table of critical values
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16. Recombination results when crossing-over during meiosis separates linked genes.
1909 – Frans Janssens observed chiasmata, regions in which nonsister chromatids of homologous chromosomes cross over each other.
Thomas Hunt Morgan suggested these were sites of chromosome breakage and change resulting in genetic recombination.
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17. Reciprocal exchanges between homologous chromosomes are the physical basis of recombination.
1931 – Genetic recombination depends on the reciprocal exchange of parts between maternal and paternal chromosomes.
Harriet Creighton and Barbara McClintock studied corn.
Curtis Stern studied fruit flies.
Physical markers to keep track of specific chromosome parts
Genetic markers were points of reference to determine if particular progeny were result of recombination.
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18. Genetic recombination between car and Bar genes on the Drosophila X chromosome
Figure 5.7
Fig. 5.6
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19. Chiasmata mark the sites of recombination.
Figure 5.8 a-c
Fig. 5.7 a-c
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20. Chiasmata mark the sites of recombination.
Figure 5.8 d-f
Fig. 5.5 d-f
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21. Recombination frequencies for pairs of genes reflect distance between them.
Alfred H. Sturtevant – Percentage of recombination, or recombination frequency (RF) reflects the physical distance separating two genes.
1 RF = 1 map unit (or 1 centiMorgan)
Figure 5.9
Fig. 5.8
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22. Summary of linkage and recombination
Genes close together on the same chromosome are linked and do not segregate independently.
Linked genes lead to a larger number of parental class than expected in double heterozygotes.
Mechanism of recombination is crossing over.
Chiasmata are the visible signs of crossing over.
The farther away genes are the greater the opportunity for chiasmata to form.
Recombination frequencies reflect physical distance between genes.
Recombination frequencies between two genes vary from 0% to 50%.
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23. Mapping: Locating genes along a chromosome
Two-point crosses: Comparisons help establish relative gene positions.
Genes are arranged in a line along a chromosome.
Figure 5.11
Fig. 5.9a
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24. Mapping: Locating genes along a chromosome
Genes are arranged in a line along a chromosome.
Figure 5.11
Fig. 5.9 b-d
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25. Limitations of two point crosses
Difficult to determine gene order if two genes are close together
Actual distances between genes do not always add up.
Pairwise crosses are time and labor consuming.
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26. Three Point Crosses: A faster more accurate method to map genes
Figure 5.12
Fig. 5.10a
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27. pr must be in the middle because longest distance is between vg and b
Three point cross
pr must be in the middle because longest distance is between vg and b
Fig. 5.10b
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28. Analyzing the results of a three point cross
Look at two genes at a time and compare to parental.
Figure 5.13 a,b
Fig a,b
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29. Analyzing the results of a three point cross
Figure 5.13 c,d
Fig c,d
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30. Correction for Double Crossovers
4197
X 100 = 17.7 m.u.
vg – b distance
X 100 = 12.3 m.u.
vg – pr distance
X 100 = 6.4 m.u.
b – pr distance
Correction for Double Crossovers
4197
vg – b distance
X 100 = 6.4 m.u.
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31. Interference: The number of double crossovers may be less than expected.
Sometimes the number of observable double crossovers is less than expected if the two exchanges are independent.
Occurrence of one crossover reduces likelihood that another crossover will occur in adjacent parts of the chromosome.
Chromosomal interference – crossovers do not occur independently.
Interference is not uniform among chromosomes or even within a chromosome.
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32. Measuring interference
Coefficient of coincidence = ratio between actual frequency of dco and expected frequency of dco.
Interference = 1 – coefficient of coincidence.
If interference = 0, observed and expected frequencies are equal.
If interference = 1, no double crossovers can occur.
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33. Double recombinants indicate order of three genes.
Figure 5.13 a, d
Fi.g 5.11 a,d
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34. Summary of three point cross analysis
Cross true breeding mutant with wild-type
Analyze F2 individuals (males if sex linked)
Parental class – most frequent
Double crossovers – least frequent
Determine order of genes based on parentals and recombinants
Determine genetic distance between each pair of recombinants
Calculate coefficient of coincidence and interference
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35. Do Genetic and Physical maps correspond?
Order of genes is correctly predicted by physical maps.
Distance between genes is not always similar on physical maps.
Double, triple, and more crossovers
Only 50% recombination frequency observable in a cross
Variation across chromosome in rate of recombination
Mapping functions compensate for inaccuracies, but are not often imprecise.
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36. Genes chained together by linkage relationships are known as linkage groups.
Figure 5.15
Fig. 5.13
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37. Are genetic maps and physical maps correlated?
The order of genes in a genetic map is the same as the order of those same genes along the DNA molecule of a chromosome.
The physical distance (amount of DNA separating genes) is not always the same as the genetic distance between genes.
Factors responsible for differences in physical and genetic map distances:
Double, triple, and even more crossovers
50% limit on recombination frequency observable in a cross
Recombination frequency is not uniform across a chromosome.
Recombination hotspots
Recombination deserts
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38. Tetrad analysis in fungi
Model organisms for understanding the mechanism of recombination because all four haploid products of meiosis are contained in ascus
Ascospores within ascus germinate into haploid individuals.
Saccharaomyces cerevisiae – bakers yeast
Neurospora crassa – bread mold
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39. Saccharaomyces cerevisiae life cycle
Figure 5.16 a
Fig a
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40. Neurospora crassa life cycle
Figure 5.16 b
Fig b
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41. Neurospora crassa tetrads
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42. Tetrads can be characterized by the number of parental and recombinant spores they contain.
Figure 5.17 a
Fig a
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43. Figure 5.17 b,c
Fig b,c
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44. Figure 5.17 d,e
Fig d,e
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45. Linkage is demonstrated by PDs outnumbering NPDs.
Figure 5.18
Fig. 5.16
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46. How crossovers between linked genes generate different tetrads
Figure 5.19
Fig a-c
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47. Figure 5.19
Fig d-f
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48. Calculating recombination frequency
NPD + ½ T
Total tetrads
RF =
 100
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49. Confirmation that recombination occurs at the four-strand stage
Figure 5.20
A mistaken Model
Recombination before four-strand stage not consistent with tetrads containing recombinant spores; would be NPDs instead of Ts
Fig. 5.18
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50. Tetrad analysis demonstrates that recombination is reciprocal.
In a cross between strains with different alleles at two genes, each tetrad contains and two of each type of recombinant
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51. Ordered tetrads allow mapping a gene in relation to the centromere.
Figure 5.22
Fig. 5.20
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52. Segregation patterns in ordered asci
Figure 5.23 a
Fig a
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53. Segregation patterns in ordered tetrads
Figure 5.23 b
Fig b
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54. Calculating distance to centromere
SDS
FDS + SDS
% SDS =
 100
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55. Example of genetic mapping by ordered tetrad analysis
Figure 5.24
Fig. 5.22
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56. Mitotic recombination can produce genetic mosaics.
Mitotic recombination is rare.
Initiated by
Mistakes in chromosome replication
Chance exposure to radiation
Curt Stern – observed “twin spots” in Drosophila – a form of genetic mosaicism.
Animals contained tissues with different genotypes.
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57. Mitotic crossing over between sn and centromere in Drosophila
Figure 5.26 a
Fig a
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58. Essential Concepts
Gene pairs that are close together on the same chromosome are linked because they are transmitted together more often than not.
The recombination frequency of pairs of genes indicate how often two genes are transmitted together. Gene pairs that assort independently exhibit a recombination frequency of 50%.
Statistical analysis helps determine whether or not two genes assort independently.
The greater the physical distance between linked genes, the higher the recombination frequency.
Genetic maps are visual representations of relative recombination frequencies.
Organisms that retain all the products of meiosis within an ascus reveal the relation between genetic recombination and segregation of chromosomes during meiosis.
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59. Crossing over between sn and y gene
Figure 5.26 b
Fig b
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60. Twin spots in Drosophila A form of genetic mosaicism – mistakes in chromosome replication or exposure to radiation that breaks DNA molecules lead to mitotic recombination
Figure 5.25
Fig. 5.23
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61. Origin of twin spots and yellow spots in Drosophila
Fig. 5.24a
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62. Origin of twin spots and yellow spots in Drosophila
Fig. 5.24b
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