Science Buddies: "Ask an Expert"

I want to look at the phenotypic and genotypic results of a single nucleotide polymorphism in Arabidopsis. My research has lead me to the LOL6_100F7 polymorphism in the AS2 gene. The polymorphism is described at this site http://www.arabidopsis.org/servlets/Tai ... polyallele. I have ordered seeds from the site above(if you scroll down you will see that there is a place to order the seeds). Do these seeds all have the single nucleotide polymorphism? I am planning to grow these sides and compare them with the wildtype to detect phenotypic changes. Then I am planning to do PCR and RFLP to detect the presence of the genotype, thus finding the phenotype produced by the genotypic change. I do not already know the phenotype produced by the SNP. Does this seem like a plausible project? Any suggestions or comments?

Also does anyone know of a SNP (single nucleotide polymorphism) that affects the number of roots in arabidopsis.

From what I can tell, I believe that all the seeds will have the SNP. However, the information on the page you gave said that there was no obsevable phenotype for lo16_100F7, so you may or may not find observable differences between the SNP plants and the wildtypes.

Have you explored http://www.arabidopsis.org for more than ordering purposes? I found lots of information on Arabidopsis under "Arabidopsis Info," including scientific papers. There's also a link that allows you to access SNP's, but you do have to register for it.

Hope this helps,
Sonia

Hi vr819,

I think this sounds like an interesting project - do you have a list of phenotypes you are planning to test?
Do you know what you will do if you cannot detect any phenotypic difference? i.e. a negative result. Its ok to get a negative result - it happens all of the time for real scientists but then you often have to explain more about why you tested the things you did then if you got a positive result. It can be hard work but its a very valuable lesson.

Is there any hint about what phenotypes to look for differences in? Is the SNP in a particular gene? For example, if the SNP was in a gene for iron metabolism then the plants might not grow well in iron containing medium, or if its a gene that makes a root protein the SNP might change the shape of the roots.

Another thing to be aware of is if the SNP is in an "exon" - that is the part of a gene that makes a protein. And if the SNP is in the exon/protein coding region, if it causes a change in the amino acid sequence. Generally SNPs that cause changes in the amino acid sequence are more likely to have a phenotype, but SNPs in the introns (the non-exon parts of the genes) can also have phenotype, its just harder to explain why usually.

You could try emailing the curators at Tair to see if they know of a SNP that affects number or roots, or how to search the Tair database for that information. Curators are biologists who compile the information in the database and answer questions from users so they should be able to help you.

best of luck,
Caroline