Please check the following link.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247103/

This the protocol for  depigmentation and staining roots methodology for recording mycorrhizal colonization with application of heat. Quaternary roots are depigmented during 35 minutes in the autoclave at 1.4 atmospheres (atm) using 10% KOH. Roots are rinsed first with a solution of 10% H2O2 during 10 minutes, and later with tap water and acidified during 15 minutes with HCl 1N. Roots are stained using a solution of 0.05% trypan blue in lacto glycerol, and then mounted in plaques for evaluation of the grade of mycorrhizal colonization.

Hope it helps.

Carlos

yes. Carlo  mentioned right. You should follow the established protocol for root clearing. Philips and Haman (1970). and this article 

http://agris.fao.org/agris-search/search.do?recordID=US201301174565

Alkaline hydrolysis of mycorrhizal roots seems to be the most preferred method in preparation of roots for mycorrhizal staining and quantification (Check link) for it works for most root samples. My suggestion would be to try as low as 2% KOH and a time point (2-4/6hr) so that you don`t over-cook your root samples.

In my experience, It is very rare not to find any mycorrhizal roots from field samples unless an environmental unforeseen event has eradicated certain fungal spp, btw which is also a pretty rare occurence.

http://mycorrhizas.info/method.html

I often use varying concentrations of KOH and waiting time, from the protocol for root clearing by Philips and Haman (1970), according to the pigmentation of the roots to be analyzed.

Hope helps

Hugs