1. Concepts and Connections
Benjamin A. Pierce
GENETICS ESSENTIALS
Concepts and Connections
SECOND EDITION
CHAPTER 5
Linkage, Recombination, and Eukaryotic Gene Mapping
© 2013 W. H. Freeman and Company

2. Chapter 5 Outline 5.1 Linked Genes Do Not Assort Independently, 114
5.2 Linked Genes Segregate Together and Crossing Over Produces Recombination Between Them, 116
5.3 A Three-Point Testcross Can Be Used To Map Three Linked Genes, 128
5.4 Genes Can Be Located with Genomewide Association Studies, 137

3. The case of male baldness
X-linked or not?
Study of linkage of a SNP and the association with male pattern baldness shows that they do not assort independently, they are transmitted together
Pattern baldness is a hereditary trait. Recent research demonstrated that a gene for pattern baldness is linked to genetic markers located on the X chromosome, leading to the discovery that pattern baldness is influenced by variation in the androgen-receptor gene. The trait is seen in John Adams, shown here.

4. 5.1 Linked Genes Do Not Assort Independently
Linked genes: genes located close together on the same chromosome
-Belong to the same linkage group

5. Recombination and alleles

6. Flower color and pollen shape
Figure 5.2 Nonindependent assortment of flower color and pollen shape in sweet peas.

7. F1 generation gives purple color and long pollen
Appears that the purple is dominant to red and long is dominant to short pollen
What with the F2, it is expected to get 9:3:3:1
BUT…
Figure 5.2 Nonindependent assortment of flower color and pollen shape in sweet peas.

8. There is no 9:3:3:1 ratio; what happened
Figure 5.2 Nonindependent assortment of flower color and pollen shape in sweet peas.

9. 5.2 Linked Genes Segregate Together and Crossing Over Produces Recombination Between Them
Fig. 5.3
Notation for crosses with linkage
Complete linkage leads to nonrecombinant Gametes and nonrecombinant progeny
Crossing over with linked genes leads to recombinant gametes and recombinant progeny
Figs. 5.4 & 5.5

10. Figure 5.3 Crossing over takes place in meiosis and is responsible for recombination.

11. Labeling alleles of two genes on a same chromosome
Cross AA BB x aa bb can be represented by
A B a b
A B x a b
The F1 will be:
A B
a b
Also it can be represented

12. The two test cross cases
Linked v.s. not linked
Linked genes give only nonrecombinant gametes
Unlinked genes give both nonrecombinant and recombinant
Figure 5.4 A testcross reveals the effects of linkage. Results of a testcross for two loci in tomatoes that determine leaf type and plant height.

13. Concept Check 1
For single crossovers, the frequency of recombinant gametes is half the frequency of crossing over because:
a. a test cross between a homozygote and heterozygote produces ½ heterozygous and ½ homozygous progeny.
b. the frequency of recombination is always 50%.
c. each crossover takes place between only two of the four chromatids of a homologous pair.
d. crossovers take place in about 50% of meiosis.

14. What happens in recombination and the gamete formation
Figure 5.5 A single crossover produces half nonrecombinant gametes and half recombinant gametes.

15. 5.2 Linked Genes Segregate Together and Crossing Over Produces Recombination Between Them
Calculating Recombination Frequency
Recombination frequency = (No. recombinant progeny/Total No. of progeny)  100%
Fig. 5.6
Coupling and Repulsion Configuration of Linked Genes
Coupling (cis configuration): wild-type alleles are found on one chromosome; mutant alleles are found on the other chromosome.

16. Calculating frequencies
Figure 5.6 Crossing over between linked genes produces nonrecombinant and recombinant offspring. In this testcross, genes are linked and there is some crossing over.

17. Calculating frequencies
# of recombinant progeny
Total # of progeny
Rec. Frequency = x100%
Rec. Frequency = x100% 15
123
Rec. Frequency = x100%
Figure 5.6 Crossing over between linked genes produces nonrecombinant and recombinant offspring. In this testcross, genes are linked and there is some crossing over.
Rec. Frequency = 12.2 % OR

18. 5.2 Linked Genes Segregate Together and Crossing Over Produces Recombination Between Them
Coupling and Repulsion Configuration of Linked Genes
Repulsion (trans configuration): wild-type allele and mutant allele are found on the same chromosome.
Fig. 5.7
Testing for Independent Assortment
Figs. 5.8 & 5.9

19. Coupling and repulsion
p b+
p b
p b
p b+
Figure 5.7 The arrangement (coupling or repulsion) of linked genes on a chromosome affects the results of a testcross. Linked loci in the Australian blowfly, Lucilia cuprina, determine the color of the thorax and that of the puparium.

20. Coupling and repulsion
Figure 5.8 The recombination frequency allows a prediction of the proportions of offspring expected for a cross entailing linked genes.

21. 5.2 Linked Genes Segregate Together and Crossing Over Produces Recombination Between Them
Gene Mapping with Recombination Frequencies:
Genetic maps are determined by recombinant frequency.
Map unit and centiMorgans
Constructing a Genetic Map with the Use of Two-Point Testcrosses
Fig. 5.10

22. Figure 5.10 A two-strand double crossover between two linked genes produces only nonrecombinant gametes.

23. Recombination frequencies and distances of genes
Based on recombination frequencies genetic maps are generated
Actual distances are on physical maps
Recombination maps are approximations and are measured in map units or cM (centiMorgans)
One map unit equals to 1% recombination frequency

24. Genetic distances measured with recombination rates are approximately additive: if the distance from gene A to gene B is 5 m.u., the distance from gene B to gene C is 10 m.u., and the distance from gene A to gene C is 15 m.u.

25. Limitations of gene mapping
If the genes are far apart and the frequency is 50% we cannot say if the genes are on different chromosomes or just to far on same chromosome
Two genes that are relatively far will give underestimate of recombination events due to possibility of multiple crosses between the genes.

26. Example: two point cross to determine map of 4 genes

27. 5.3 A Three-Point Testcross Can Be Used to Map Three Linked Genes
Constructing a Genetic Map with the Three-Point Testcross
Fig. 5.12
Determining the gene order
Determining the location of crossovers
Fig. 5.13

28. Double crossover :three genes

29. A Three-Point Testcross Can Be Used to Map Three Linked Genes
Figure Writing the results of a three-point testcross with the loci in the correct order allows the locations of crossovers to be determined. These results are from the testcross illustrated in Figure 7.14, with the loci shown in the correct order. The location of a crossover is indicated by a slash (/). The sex of the progeny flies has been designated arbitrarily.

30. 5.3 A Three-Point Testcross Can Be Used to Map Three Linked Genes
Calculating the recombination frequencies
Interference and coefficient of coincidence
Effect of multiple crossovers

31. Calculating the recombination frequencies
Based on the numbers in the fruit fly testcross for three loci calculate the distances between the loci.
Recombinant progeny with a chromosome that underwent crossing over between the eye-color locus (st) and the bristle locus (ss) include the single crossovers ( st+ / ss e  and  st / ss+ e+ ) and the two double crossovers ( st+ / ss / e+  and  st / ss+ / e ); Total of 755 progeny; so the recombination frequency between ss and st is:

32. Calculating the recombination frequencies
Based on the numbers in the fruit fly testcross for three loci calculate the distances between the loci.
The map distance between the bristle locus (ss) and the body locus (e) is determined in the same manner. The recombinant progeny that possess a crossover between ss and e are the single crossovers  st+ ss+ / e  and  st ss / e+  and the double crossovers  st+ / ss / e+  and  st / ss+ / e . The recombination frequency is:

33. Calculating the recombination frequencies
Based on the numbers in the fruit fly testcross for three loci calculate the distances between the loci.
Finally, calculate the map distance between the outer two loci, st and e. This map distance can be obtained by summing the map distances between st and ss and between ss and e (14.6 m.u m.u. = 26.8 m.u.). We can now use the map distances to draw a map of the three genes on the chromosome:

34. Interference and coefficient of coincidence
Calculate the proportion of double-recombinant gametes by using the multiplication rule of probability
Applying this rule, the proportion (probability) of gametes with double crossovers between st and e is equal to the probability of recombination between st and ss multiplied by the probability of recombination between ss and e, or × =
Multiplying this probability by the total number of progeny gives us the expected number of double-crossover progeny from the cross: × 755 = 13.4.
Only 8 double crossovers—considerably fewer than the 13 expected—were observed in the progeny of the cross

35. Interference and coefficient of coincidence
Crossovers are frequently not independent events: the occurrence of one crossover tends to inhibit additional crossovers in the same region of the chromosome, and so double crossovers are less frequent than expected.
The degree to which one crossover interferes with additional crossovers in the same region is termed the interference. To calculate the interference, we first determine the coefficient of coincidence, which is the ratio of observed double crossovers to expected double crossovers:

36. In our case
indicates that we are actually observing only 60% of the double crossovers that we expected on the basis of the single-crossover frequencies.
Calculation of interference
Interference = 1 − coefficient of coincidence
So the interference for our three-point cross is:
interference = 1 − 0.6 = 0.4
40% of recombinations are not observed due to intefrerence

37. 5.4 Genes Can Be Located with Genomewide Association Studies
Linkage analysis (genetic markers; anonymous markers)
Genome wide association studies
Haplotype
Linkage disequilibrium

38. Figure 5.17 Genomewide association studies are based on the nonrandom association of a mutation (D–) that produces a
trait and closely linked genes that constitute the haplotype.