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Secreted in Xylem genes used for PCR-based diagnostics of distinct Fusarium oxysporum f. sp. cubense races and vegetative compatibility groups

Lilia Costa Carvalhais: Queensland Alliance for Agriculture and Food Innovation, The University of Queensland

<div>Bananas are in danger of being decimated worldwide by Panama disease tropical race 4. Bananas are not only a major staple food in numerous developing countries but are also one of the most consumed fruits worldwide. The soil-borne fungus <em>Fusarium oxysporum </em>f. sp.<em> cubense</em> (<em>Foc</em>) tropical race 4 is highly virulent on varieties belonging to the AAA Cavendish subgroup. Eradication is very challenging due to the fungus capacity to survive for long periods in the soil, plant debris or even in alternative plant hosts which act as pathogen reservoirs. An effective measure to avoid further losses to the banana industry and small holders is to keep areas free of the pathogen and containment of new incursions, which relies on sensitive and specific diagnostics methods. Here we report a new PCR-based method targeting <em>Secreted in Xylem</em> (<em>SIX</em>) genes which currently comprise the only known family of effectors in <em>F. oxysporum</em>. Primers were designed and tested to amplify specific <em>SIX</em> gene homologues of the different <em>Foc </em>races and within the race 4 of specific vegetative compatibility groups which cannot be detected using previously reported PCR-based methods. We validated our assay on an array of 134 <em>F. oxysporum</em> isolates comprising of 21 different VCG groups. Our method offers the advantages of being simple, robust and of requiring basic apparatus that are routinely used in laboratories equipped for molecular biology in any country.</div>