Differentiation of Phoma foveata from P. exigua using a RAPD Generated PCR-RFLP Marker |
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| Authors: | Janet E Macdonald George P White Marie-José Côté |
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| Institution: | (1) Centre for Plant Quarantine Pests, Canadian Food Inspection Agency, 3851 Fallowfield Rd, Nepean, Ontario, K2H 8P9, Canada;(2) Centre for Plant Quarantine Pests, Canadian Food Inspection Agency, 3851 Fallowfield Rd, Nepean, Ontario, K2H 8P9, Canada; |
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| Abstract: | Phoma foveata and P. exigua variety exigua both infect potatoes and are morphologically very similar. P. foveata produces a pigment which allows differentiation from P. exigua in culture. Discrimination of the two species based on the production of a secondary metabolite, which is dependent on the growth conditions, is not reliable. Therefore, there is a need to develop nucleic acid based identification markers. A 482 bp random amplified polymorphic DNA (RAPD) fragment from P. foveata was isolated and sequenced. Polymerase chain reaction (PCR) primers, developed from the sequence of the RAPD product, amplified a 474bp fragment for P. foveata and P. exigua varieties exigua, diversispora, inoxydibilis and sambuci-nigrae. The similarity of the PCR fragments was demonstrated by sequence analysis and by using the restriction enzymes DdeI and DpnII. P. foveata was distinguished from the four varieties of P. exigua on the basis of the RFLP patterns of the PCR fragment. Ten isolates of P. foveata and nine of P. exigua var. exigua from different geographic locations were tested and all isolates but one showed the restriction digest pattern of the PCR fragment (PCR-RFLP) specific to each species. One isolate of P. foveata demonstrated a PCR-RFLP pattern similar to P. exigua var. exigua leading to the conclusion that the isolate had been previously misidentified as a strain of P. foveata lacking the ability to produce pigment. |
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| Keywords: | genetic marker PCR-RFLP Phoma exigua var foveata polymerase chain reaction potato gangrene random amplified polymorphic DNA |
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