The the dominant marker, the determination of genotype is very simple, the variation is that you either get a band or you don't. Microsatellite markers are generally highly polymorphic which makes them very informative as genetic markers. However, the size difference between alleles tends to be small, so it can be difficult to resolve the different alleles with the equipment in the teaching labs. While testing various Brassica microsatellites, we came across one where the variation is simply that when you do PCR on a sample of an individual Fastplant's DNA, you either get a band or don't get a band. You still have to do PCR to detect this one, but any gel will work because you're not trying to make a fine distinction, just detect a band.
I'm currently breeding some strains with defined genotypes for this marker. When we are done we'll have some that are homozyous for the "Band" allele and others that are homozygous for the "No Band" alele.
I've been working to refine the molecular markers work with Fast Plants. One goal is to develop more markers for which the alleles can easily be differentiated. The other is to just work out methods for analysis that are more feasible for teaching labs or high schools.
I'm looking for people out there who are interested in trying out some of these things. I really want to know how well they work in others' hands. Are you interested?
I'm not aware of any horizontal polyacrylamide gel systems. You mention a vertical system that you use for proteins and ask if nondenaturing gels are available. Not knowing exactly what model you mean I can't say for sure, but I do know that they sell ready made nondenaturing gels that fit their Mini Protean system. I've bought 10% acrylamide nondenaturing (TBE) readygels from them and they resolve the microsatellites fine. What model do you have?
Regarding staining, we routinely use SYBR green in my lab and it works great, though we have a flourimager to get an image. I use silver staining in teaching because there is not need to photograph in order to save the results.
One new thing is that a student of mine recently found a microsatellite that has dominant inheritance. In other words the alleles of this locus are either Band or No Band. I think that this could be much better suited to schools because weak point with the polymorphic and codominant microsatellites is that separating alleles can be difficult. However, with a marker that gives a Yes / No result, even a small agarose slab gel would be able to give the answer. If you want more information about this new marker, let me know.
If you want to try any of our stuff I'd be glad to keep giving advice an assistance. The experiment works well in my own lab course, but I've really been wanting to find people "out there" who could try these things out.
Hi Kathy, I'm glad you tracked me down and reminded me about your work. I had emergency knee surgery right about when you and I were corresponding, and I lost track of our thinking! Sorry about that.
I read the draft you sent for the article aimed at ABT. It sounds like a very relevant topic and the right audience to me. I am not familiar with the specific labs included in the AP lab manual, so it may be obvious to those who are -- I was not sure how behavior fits into that framework. Perhaps a little more in the introduction about that and move the explanation about your experiences a little sooner in the introduction would help clarify the overall content of the article upfront. It will be a good contribution to share your experiences adding more inquiry to your students' experiences.
We grow Fast Plants on paper toweling in a Petri dish for genetics experiments as well as growth and development observations, and I'm sure Paul can tell you about growing them in a gel, too, though I have not done that.