I am working on rice root knot nematode. For identification purpose mostly second stage juveniles are used. I wonder why females or males are not used commonly for the same purpose? I am using commonly used primers like ITS, COX-II. Please give your valuable suggestions regarding this. Thanks in advance.
It's honestly a choice of convenience and availability in samples.
J2 juveniles are the mobile form and common. Adult males are short-lived and hard to find, but you could certainly use them if you have them. Adult females are full of fertilized eggs (i.e. embryos) so you would have to be certain that you are excluding those or else you have a mixed population of DNA.
DNA extractions need to be as clean as possible. In vitro hatching and cleaning of J2s before DNA extraction would allow for better purity of DNA. ITS and other eukaryotic genes are also present in fungi. Should there be fungal contaminants, that will throw your analyses. Females contain both nematode eggs as well as other soil organisms lurking inside them. In my opinion, this is one reason to pick J2s. I also agree that it is easier to extract J2s from the soil. However, if there are more than one species of RKN and one being the lesser problem, it becomes tricky. Then, extracting eggs from root galls, hatching those eggs and identifying those J2s will be the best bet.
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