Hello,
Can someone please tell me how the gene mapping in worms are being carried out?
Like what techniques or what procedures are followed?
Thanks a lot.
Check out the WormBook chapter on genetics and genomics. It has everything you need to know about mapping genes.
In addition to the classic techniques described on Wormbook, there are also new strategies available to map genes or mutations using deep sequencing technology. We recently developed a technique that negates the need to perform any SNP mapping or the creation of mapping populations. See Zuryn et al. A strategy for direct mapping and identification of mutations by whole genome sequencing, Genetics 2010.
I’m curious if anyone is doing this and can give me an idea as to the cost. We are mapping a synthetic mutation currently, and it hasn’t been easy since we have to have the second mutation in the background of all mapping crosses. Thanks for any advice!
I don’t know how much facilities are charging for the service but, if you have access to the instrument, reagent costs for a single sample are $50 for library prep and $600 for a single lane of 50bp Illumina sequencing (and the new HiSeq2000 can generate enough data for two mutants per lane). Data analysis for one sample can be done in a day on a decent desktop workstation (quad core, 12GB RAM).
Harold
I used this protocol for my undergraduate project:
Rapid single nucleotide polymorphism mapping in C. elegans, Davis et al. 2005
It’s very easy and cheap, ideal for a small lab with limited resources. Worked pretty well too – I mapped a few alleles to small intervals containing several dozen candidate genes. At that point I could just use feeding RNAi to knock down each candidate gene, looking for one that had the same phenotype as my mapped alleles. (probably won’t help medawg, but might be useful for NEMATODE)
@medawg. We have often thought about mapping a double mutant using the deep sequencing technique we developed and believe it is possible. If you can backcross your mutant whilst maintaining both mutations, you should be able to discern 2 separate peaks of EMS damage at different loci. The 2 peaks should correspond to the chromosomal positions of each mutation, and you could then study the sequences within. We have yet to put this theory into practice. However, we are currently sequencing many more single mutants with the technique, and are finding it very useful for mutants with a very low penetrance!