Vegetative compatibility assay in fungi is a time consuming process for huge numbers of isolates, so is there any alternative molecular method for these assays? I think the best method may be use of hybridization with probe. What is your opinions?
A multiplex-nested-PCR procedure is used to find variation among vegetative compatibility groups (VCGs). PCR markers are identified and assigned to V. dahliae VCGs, including: i) a 334 bp marker amplified from VCG1A or VCG2B334 isolates; ii) a 688 bp marker amplified from VCG2A or VCG4B isolates; and iii) a 688 bp and a 964 bp PCR marker amplified from VCG2B824 isolates. The infecting V. dahliae VCGs were identified in artichoke tissues according to specific patterns of amplified markers after two rounds of PCR. The PCR-based ‘molecular tool box’ was first optimized using DNA extracted from artichoke plants artificially inoculated with isolates representative of known VCGs. Thereafter, the efficiency of the molecular procedure was tested using DNA extracted from naturally-infected artichoke plants showing a range of symptom severity as well as from symptomless plants. The novel multiplex-nested-PCR assay was clearly superior in detecting the pathogen compared to conventional isolation procedures, and in addition was informative about the VCGs. Moreover, the PCR method allowed the detection and VCG identification of V. dahliae infections in symptomless but infected plants, which had yielded false negatives when checked by microbiological isolation procedures. This ‘molecular tool box’ has uncovered the presence of several V. dahliae VCGs infecting the same artichoke plants in the Comunidad Valenciana Region. In addition, it is useful for genetic and pathogenicity diversity studies of V. dahliae populations infecting artichoke, and may help in predicting the severity of verticillium wilt epidemics.
What Ravi describes (in a cut-and-paste format that I personally dislike...) is not a method for determining the vegetative compatibility of isolates, but rather a method for identifying genetic variation among isolates with vegetative compatibility groups that have already been determined. This is stated clearly in his opening sentence.
It should be possible, using sequence or marker data from a sufficiently large set of isolates with known VCGs to identify loci that are predictive of VCG.
If I remember correctly, in Phytophthora infestans (not a fungus, I know...) the mating type locus may be a sufficient marker for predicting vegetative compatibility.
Without prior knowledge (a diverse set of isolates with defined VCGs and genomic sequence or marker information, or at least this sort of information from a closely-related species), I think it would be difficult to predict VCGs using molecular techniques.
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