Thread: avirulence genes and plant defence

If i have a known avirulence gene. i.e. a viral gene that triggers a hypersensitive response. How would i go about finding the corresponding host gene. Assuming gene for gene recognition? how are host resistance genes normally found?

I doubt it would be the actual viral gene triggering the response, it would most likely be the viral proteins.

If the genome of the plant has been sequenced it's fairly easy (but quite expensive) to do a microarray analysis.

This basically involves a tray with thousands of microscopic holes each containing unique complementary RNA to the genes of the organism being studied.

Using lysed cell material from a particular tissue of the plant, it's possible to detect the degree of transcription of each gene at a particular time by the degree of hybridisation of RNA in the plant cells to the complementary RNA on the microrray (it's measured by fluorescence).

So, do this first as a control, then challenge the plant with the virus and repeat the procedure. Using computer software, you can see exactly which genes have their transcription upregulated on challenge with the virus.

Amazing technology.

If you can't do a microarray, there are other techniques. You could use 2D polyacrymalide gel electrophoresis to determine which proteins increase in production when the plant is challenged with a virus. Then you could have part of the proteins sequenced (again, expensive) then search the genome (provided it's been sequenced) using software for the genes responsible. This can take a lot of time, which is why a microarray is a lot better.

This is providing the genome of the plant has been sequenced. If it hasn't, you could use the electrophoresis I mentioned above, get part of the amino acid sequence then use fluorescent markers to hunt down the gene to a particular area of a particular chromosome. This can be a right pain in the ass though, due to the presence of introns in eukaryotic DNA.

Hope that helps!