I would like to select a molecular marker to compare about 100 strains of Trichoderma harzianum. I think these isolates be too similar, so an appropriate maker need to differentiate them.
I think the most appropriate molecular marker techniques in such type of a population conaining many similar individuauls is the DNA markers absed on SNP, SSRs and or microsattelies.
well RAPD markers could be of good help> In case of trichoderma antagonism is not only due to antibiosis only it is also because of Mycoparasitism and colonizing or competing ability either we have to use SSR markers for all these cheracters or simply RAPDs which would be much easier
Since you have one species of Trichoderma only. The best marker will be SSRs. Don't do simple diversity but see the population structure which will help you in indentifying the various evolutionary forces shaping the fungus tragteroies
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