Assignment: using online FlyLab simulation

Instructions for Fly Lab Simulation

The assignment is performed using online FlyLab simulation at: https://www.sciencecourseware.org/FlyLabJS/

You can design a fly with any mutations you choose by clicking the Design tab. Keep in mind that some mutations may interact with each other so the program may restrict you from picking two different eye color mutations in the same fly, for example.

 

Once you have designed a fly, click “Select fly for mating”, and you will be taken to the Mating tab, where you can design the fly to mate to your first. After you click “Select fly for mating” for the second fly, you will return to the Mating tab automatically, where you can click on the “Mate Flies” button. This will take you to the Crosses tab, where you will see the parents and their progeny (usually around 1000, about 10 times more than you would get from mating a pair). They are sorted by phenotypes and sex.

 

If you are going to perform a cross with any of the progeny, just click on the “Select to mate” button under it. If you are crossing two progeny together, you can click on the second one and select it the same way. Otherwise, if you are going to do a testcross on one of the progeny, after you have selected one of the progeny to mate, click on the Mating tab and you will be able to design a fly to mate with the first progeny selected.

 

You can click on the “Mate Flies” button again and view the progeny. After you have looked at the phenotypes, you might find it easier to look at the numbers in table form by clicking on the Analyze tab. If you are sure none of the mutations are on the X chromosome, you can check the “Ignore sex of flies” box; this will condense the table by lumping all the flies of a given phenotype together, regardless of sex. (Caution! If your mutation is on the X chromosome, checking this box will make it impossible to detect the sex linkage that is happening). You can refer to previous crosses in the Cross tab by clicking on the “Select cross” menu button.

 

If you wish to do a Chi-squared analysis, click the “Include a test of hypothesis” box: you will be able to enter appropriate ratios for your hypothesis, then click the “Test your hypothesis” button to perform the analysis. The program will determine the probability for each class of progeny expected as well as the number expected. It performs the rest of the chi-squared calculations and even determines the p value (level of significance).

 

You can click the “Add results to lab notebook” button to save your results from any experiment to a page containing all your results from the session. Copying and pasting results from the Lab can be unpredictable, but if you go to the Lab notebook page, select what you want to copy, then select Copy from your browser’s Edit menu, it should work. Unfortunately, the “Export as web page” button does not seem to work.

 

 

Assignment 1: 
Segregation and Chi-Squared

Part A: Segregation of different traits

Cross a female with one mutation to a male with a different mutation. You can pick anything you want except Curly or Dichaete wings, we will use them later. Also remember not to pick two mutations that affect the same structure like two eye color mutations. ONLY ONE MUTATION WITH A WILD TYPE

 

1. In the F1, are either of the mutations you selected dominant? Why?

 

 

 

 

 

2. Does the mutation appear to be sex linked? Why?

 

 

 

 

 

 

 

Cross two of the F1 progeny and observed the ratios of the resulting progeny.

3. Does the ratio observed agree with two independently assorting genes? Why? Use a chi-squared test to support your conclusions and suggest an alternative explanation if your data do not fit independent assortment.

 

 

Part B: Test your conclusions with another experiment

 

For each mutant you selected above, we will identify its chromosome by crossing to a tester strain with known, dominant markers for Chromosomes 2 and 3. The segregation pattern will help you determine the chromosome on which your mutation resides. Chromosome 1 is the X chromosome, which would show sex linkage, so this cross will let you identify mutations on the three largest chromosomes covering most genes.

 

Step 1. Construct tester strain female. Select Curly wings (Cy) from Wing Shape and Dichaete (D) from Wing Angle. These are dominant mutations: Cy is on Chromosome 2, D is on Chromosome 3.

 

Step 2. Construct unknown mutant male.

Pick one of the mutations you used in Part A, but only one and stick with it in later crosses.

 

Step 3. Cross the P1 flies you just constructed. If you do not see your mutant phenotype in the F1, it is recessive.

 

Step 4. Perform a testcross to find your mutant. Pick one of the Cy;D males from the F1 for mating. It is carrying the dominant chromosome markers, but also is heterozygous for your recessive mutation. Construct a female who has the mutation you originally picked for the P1, but is wildtype for everything else. Mate the flies and look at the progeny.

 

You should find that your mutation reappeared. The male from step 4 carried the mutation as a heterozygote. If the mutation is on Chromosome 2, then he would pass on either the Cy chromosome or the recessive mutant chromosome, but you would not find progeny that were both Cy and mutant. Similar logic applies to Chromosome 3 and the D mutation. If there is a difference between the appearance of your mutation depending upon the sex, then the mutation may reside on the X chromosome.

 

Try to use Punnett squares to diagram the crosses you performed based on where you think your mutation is located. You can use the Analyze tab to perform a chi-squared test. Make sure the ratios you choose for you hypothesis fit the predictions from your Punnett squares.

Assignment 2: 
Sex Linkage

 

Sex Linkage

For many of the mutations that can be studied using FlyLab, it does not matter which parent carries a mutated allele because these mutations are located on autosomes. Reciprocal crosses produce identical results. When alleles are located on sex chromosomes, however, differences in the sex of the fly carrying a particular allele produce very different results in the phenotypic ratios of the offspring. Sex determination in Drosophila follows an X-Y chromosomal system that is similar to sex determination in humans. Female flies are XX and males are XY. Design and perform the following crosses to examine the inheritance of sex-linked alleles in Drosophila.

 

Cross a female fly with a tan body with a wild-type male. What phenotypes and ratios did you observe in the F1 generation?

 

Mate two F1 flies and observe the results of the F2 generation.

 

Based on what you know about Mendelian genetics, did the F2 generation demonstrate the phenotypic ratio that you expected? If not, what phenotypic ratio was obtained with this cross?

 

Now perform a reciprocal cross by crossing a tan male to a wildtype female. Do you see the same results in the F1 and F2 as before? Try diagramming your F2 results for both crosses. Use the Prediction chi-squared tool to test your hypothesis.

 

Assignment 3: 
Recombination

Part A: Recombination between to genes

 

In Drosophila, unlike most organisms, it is important to realize that crossing over occurs during gamete formation in female flies only. Because crossing over does not occur in male flies, recombination frequencies will differ when comparing female flies with male flies. Perform the following experiments to help you understand how recombination frequencies can be used to develop genetic maps.

Part 1: recombination between two genes

 

To understand how recombination frequencies can be used to determine an approximate map distance between closely linked genes, cross a female fly with the eyeless mutation for eye shape with a male fly with shaven bristles. Both of these genes are located on chromosome IV in Drosophila.

 

What are the phenotypes of the F1 flies? What do you think their genotype is? Perform a testcross by selecting one of the F1 females; we will be monitoring recombination during meiosis during her production of eggs for mating. Select the F1 female for mating but perform the testcross by designing her mate in the mating tab; design a male with both the eyeless and shaven bristle traits. The male will be homozygous recessive for both traits.

 

Click the Mate flies button. Most of the progeny have either the shaven or the eyeless mutation. The testcross progeny which have either both mutations or neither mutation (wild-type) are produced by crossing over in the double heterozygous F₁ female. The percentage of these recombinant phenotypes is an estimate of the map distance between these two genes.

 

Draw a map that shows the map distance (in map units or centimorgans) between the locus for the shaven bristle allele and the locus for the eyeless allele.

 

Part B: Recombination mapping of three genes

 

To understand how recombination frequencies can be used to determine a genetic map for three alleles, mate a female fly with a black body, purple eyes, and vestigial wing size (OR you could use a female with black body, purple eyes, and apterous wing) to a wild-type male. These loci are all located on chromosome II. What phenotypes do you see? Are the mutations in the female dominant or recessive?

 

Testcross one of the F1 females to a male with all three of the mutations you used in the original female above. After you see the progeny from the mating, you can look at the numbers on the Analyze tab and since we know the mutations are on chromosome II, you can check the “Ignore sex of flies” box. The most abundant types of flies should be nonrecombinant (parental) types. Does this make sense based on how mating that produced the F1 female was set up?

 

The flies with the least frequent phenotypes represent double crossovers. If you compare these mutants with the nonrecombinant types, which gene moved? The is the gene in the middle of the three genes. Now that you know which gene is in the middle, find the classes of progeny that you would expect from crossing over between the middle gene and with each gene on either side. Find the recombination frequency by adding the number of single crossovers between the two genes, then add the double crossover number to this and divide by the total progeny to determine the recombination frequency (map distance) between the two genes. Now do the same for the gene on the other side of the middle and construct a genetic map with all three genes in order.

 

What is the coefficient of coincidence and interference for this cross? What does is mean if you see interference (or coefficient of coincidence less than 1)?