Hi Serena,

The ITS is equallyinformative for detecting intra specific variability. You are right that it is present in hundreds of copies, but this is also correct that in general the rRNA gene repeat  undergo homogenization to keep the sequences homogenous across the repeat units. So any event of hybridization can be deceted in some of the repeat units because the homogenization will take some time as there is not selection pressure due to large number of copies (the rate of homogenization will vary from species to specie)...You need to sequence several clones or other such approaches to detect variability...There are several studies in plants where ITS has been used to show evidences of intraspecific heterogeneity....On the contrary the single locus sometimes may undergo gene conversion in one event due to selection pressure...so there will be no evidence left to see if the change was there or not.. so whatever region you may choose..you need to be a bit carefull for such analysis..

bye.

thanks for the suggestion...in the past, i have started to clone ITS amplicons but it was very time consuming and expensive. I was also thinking to microsatellites, but anyway....thanks :)

Hi

Microsatellites will also be a good option to look for such variability