Lab 7: Series2 Forward Genetics Project- SCORE!
Mapping: Do you need to take photos of the parental and recombinant progeny before you score? Think about future effective figure design and whether or not you might want to have a photomicrograph of these worms. This is your last chance to take pictures of worms from our Forward Genetics project.
Scoring the Test Cross: Count all adult and L4 progeny from one test cross plate, scoring as either wild type , Dpy , Unc or Dpy Unc. Also score the second plate. Remember to remove each animal after you have determined its phenotype. Record your totals on the spreadsheet on the computer in the middle in the back of the lab. The complete course data is a Google spreadsheet that will update as each lab section enters its data. You can find this spreadsheet in the DATA file in Resources in your lab section's Sakai site. You can calculate RF and map distance from your own group's and class' data before we have the course data completed, but, of course, the evidence used in your paper will be the RF calculated from the full data set.
Review the crosses that you diagrammed for this mapping project and make sure you understand how the test cross we set up differentiates, phenotypically, progeny of parental gametes from the progeny of recombinant gametes. Hint: how did you end up with either of the single mutant classes ( Unc or Dpy) from these parental genotypes d u/+ + (genotype of the male) and d u/ d u (genotype of the hermaphrodite parent)?
You will determine map distance of the dpy gene of interest from an unc gene using the formula: RF (recombinant frequency) =the number of single mutants (both dpy and unc single mutants) divided by the total number of worms counted * 100 (to obtain RF in % recombinants and thus in map units).
Congratulations! You now have calculated the location of the dpy mutation in map unit distance away from your reference linked unc gene on the a particular autosome. To check your location (and the accuracy of your recombination frequency relationship to map units), enter the linked unc gene name into the C. elegans database: | Wormbase at http://www.wormbase.org Wormbase. Scroll down and click on Location and Mapping Data and find the gene that is your calculated number of map units away from the linked unc gene. (Remember that you will have to look in both directions on the chromosome). Is the dpy gene that you found allelic in complementation analysis at one of these map locations? Yes? Terrific! If not, your next step would be to see what is known about the gene or ORF at those locations on the chromosome and see if what's known fits in at all with your observations. If it does, great and, if not, you have some thinking to do about the identity of your dpy gene of interest. (You will NOT write a paper about "sources of error" in your experimental design or your execution of the experiment!!!!)
IF you think you know the identity of your dpy gene, enter this name into the box at the top of the page in Wormbase and click Search. It will either bring you directly to that page or it will bring you to a page with multiple hits - click on the link that provides a definition for what the gene does.
On this new page should be all the known information about this particular gene. Its name, who named it, what the gene encodes - if that is known, and much more. At the bottom will be a list of references - or a link to a list of references. Find out the function of this gene.
Spend some time with Wormbase and marvel at all the hard work and years of research that went into discovering all this information about this tiny little nematode that causes us no harm (non-parasitic). Why do you think so many smart people have devoted so much of their time and energy to working out the genetics of "appearance or movement challenged" little worms? We will talk more about model organisms and the power of functional and comparative genomics in our next series.