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Isolation and identification of Oomycete species from cocoa farm soils in Nigeria based on PCR analysis

Sylvester Aigbe: Ambrose Alli University

<div>In Nigeria, <em>Phytophthora megakarya</em> and <em>P. palmivora </em>are the predominant pathogens causing black pod of cocoa (<em>Theobroma cacao </em>L.) resulting in yield losses of 10-80%. Cocoa is the most important tree crop to the Nigerian economy. Since soil is the primary source of Oomycetes infecting cocoa pods, their diversity was studied in soil around black pod-infected cocoa trees on 50 farms in the major cocoa-producing states of Southern Nigeria. Soil samples (500 total) were collected from April to June 2015. Isolations were done by baiting with young oak and <em>Rhododendron</em> leaves and plating on PARPH-V8 selective medium. DNA was extracted using a QiagenDNeasy Plant Mini Kit and PCR products were purified with a QIAquick PCR Purification Kit after electrophoresis. PCR amplifications were run using the Oomycete-specific primer pair ITS4/ITS6. DNA sequences were compared to published sequences in GenBank using BLASTn. An abundance of <em>Phytopythium</em> and <em>Pythium </em>species were found, but <em>P. megakarya</em> or <em>P. palmivora </em>were not detected. The most common species obtained were <em>Phytopythium vexans</em>, <em>Pythium cucurbitacearum</em>, <em>P. deliense</em>, <em>P. acanthicum</em>, <em>P. oligandrum </em>and <em>P. acanthophoron</em>. <em>Pythium cucurbitacearum</em>, <em>P. deliense </em>and <em>Phytopythium vexans </em>have been reported previously as damping-off and rot pathogens of many economically important crops but their impact on cocoa needs to be investigated. <em>Pythium oligandrum, P. acanthicum </em>and <em>P. acanthophoron</em> are mycoparasites of important crop pathogens, including <em>Phytophthora </em>spp. Further isolations of Oomycete pathogens directly from infected cocoa pods and stems are currently being planned.</div>