Lecture: 13 Linkage and Mapping I Flashcards
Gene mapping with recombination frequencies: What did Morgan and Sturtevant hypothesise?
= 4
Morgan and Sturtevant hypothesised that:
* crossover events happen ~randomly along the chromosome
- two genes that lie far apart are more likely to undergo crossover than two genes lying close together
- therefore one could estimate and quantify the distances between genes
- recombination frequencies could be used to deduce the order of genes along the chromosome
-> Build a genetic map of chromosome
-> 1 map unit = 1 centiMorgan (cM) = 1% recombination
Gene mapping with two-point testcrosses
Learn formula
Double crossovers reduce apparent RF = 6.
- A Single crossover will switch the alleles on homologous chromosomes,…
- But a second crossover will reverse the effects of the first, restoring the original parental combination of alleles.
3… and producing only nonrecombinant genotypes in the gametes, although parts of the chromosomes have recombined.
- A second crossover reverses the effect of the first, regenerating parental homologous chromosomes
- Cannot distinguish progeny derived from a double crossover and no crossover.
- Map distances are underestimated due to fewer recombinants produced
Genetic mapping – important points = 4
independence? recombination? double crossover? test cross for two genes?
1 * Cannot distinguish between genes on different chromosomes and genes located far apart on the same chromosome – BOTH assort independently***
2 * If genes exhibit 50% recombination, we can say they belong to different groups of linked genes (linkage groups), i.e. on different chromosomes or far apart on the same chromosome
3 * A double crossover occurs when two separate events take place between two loci
4 * Testcross for two genes that are far apart underestimates true physical distance, as will not reveal double crossovers.
What does the THREE-POINT TESTCROSS mean? = 4
Example?
- A three-point testcross can be used to map three genes
- The order of three genes is established in a single set of progeny
- Double crossovers can be detected
- Produces more accurate map distances
EXAMPLE: Consider three linked genes AaBbCc Three crossover events can occur:
– Two types of single crossover (between A and B, or B and C)
– Double crossover (between A and B, and B and C)
Each crossover produces two recombinant chromosomes and
two NR chromosomes
Recombinant gametes from a three-point testcross
Sister chromatids VS, double crossover.
- Note: in this example, only two non-sister chromatids are shown, the two other chromatids do not recombine and will provide parental NR chromosomes
- Note: in the double crossover class, the other two genes remain the same as NR chr, but the middle one has swapped position. This provides an important clue about gene order.
Remember basis for testcross:
- Homozygous recessive parent, crossover has no effect on
types of gametes produced. All gametes will be (st e ss). - Heterozygous parent will have different alleles on its two
chromosomes – this allows us to detect crossovers - 23 = 8 different progeny phenotypes from 8 different gametes!
THE STEPS IN DETERMINING GENE ORDER IN A THREE-POINT CROSS
- Identify the non-recombinant progeny (2 most-numerous phenotypes)
- Indentify the DOUBLE-CROSSOVER progeny (TWO LEAST Numerous phenotypes)
- COMPARE the phenotype of the double-crossover progeny with the phenotype of nonrecombinant progeny. They should be alike in 2 characteristics and differ in one.
- The characteristic that DIFFERS between the double CROSSOVER and the nonrecombinant progeny is encoded by the MIDDLE GENE.
A three-point testcross is used to determine the order of three linked genes. The following crossover progeny result: single crossovers, double crossovers, and no crossovers. To determine the order, one needs to compare the parental progeny to what other class of progeny?
the double crossover class
In a three-point testcross the non-recombinant progeny are A B C and a b c. The double crossover progeny are A B c and a b C. Which locus (A, B or C) is in the middle?
C
determine which single crossovers took place between which loci, so that we can assign recombination frequencies to each pair?
Second problem: Determine recombination frequencies?
- To do this, compare alleles in the non-recombinant class with alleles in each single crossover class
- Remember this chr. segregate into gametes and are fertilized with gametes from homozygous recessive parent
***Second problem: Determine recombination frequencies
- Parentals (non-recombinants)
- Single crossovers
- Double crossovers
- To calculate accurate map distance, we must include both single AND double crossover events
st–ss recombination freq: (50+52+5+3)/755 x 100% = 14.6% ss–e recombination freq: (43+41+5+3)/755 x 100% = 12.2%
Mapping with three-point test crosses = 4
1 * st–e distance is inferred by summing the st–ss and ss–e distances
2 * How does this distance differ from what we would have obtained by comparing st – e directly via a two-point test cross?
– Adding up single COs only we get (50+52+43+41)/755 = 24.6 cm
3 * By extending to loci on either side, we can generate a bigger map
4 * By including loci between these three loci, we can make the map even more accurate
Explain the Coefficient of coincidence and interference: 8
1.Mathematically, the probability of a double crossover event should be the probability of each single crossover happening independently i.e. multiply single probabilities
- st–ss RF: 0.146, ss–e RF: 0.122
=> st–e double crossover RF: 0.146 x 0.122 = 0.0178 Expected number of progeny = 0.0178 x 755 = 13.4 But in the fly data, we only saw 8! Why? - Crossovers are not independent events – they interfere with one another, reducing the likelihood of adjacent crossovers
- Degree to which one crossover reduces the formation of another is called interference.
- Coefficient of coincidence: ratio of observed double COs to expected double COs:
(5+3)/(13.4) = 0.6 - Interference = 1 – coefficient of coincidence: 1 – 0.6 = 0.4
- Conclusion: 40% of all double crossover progeny expected will not be observed
- NB: sometimes crossover can actually increase, with more doubles than expected: interference will be negative.
You calculate an interference of 0.59. What does this number tell you?
You will not observe 59% of expected double crossovers
What about multiple crossovers?
1 * Loci that are far apart will have a greater number of crossovers between them
2 * Odd-numbered crossovers will result in recombinant gamete
3 * But even-numbered crossovers will result in NR gamete
4 * Therefore some crossovers are undetected in progeny and RF is underestimated, even in a three-point test cross – hence need for as many loci as possible
Single crossover between A and B
