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** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** THE FUNGUS FUSARIUM OXYSPORUM IS A SERIOUS THREAT TO AGRICULTURAL BIOSECURITY, GLOBALLY CAUSING WILT DISEASES THAT DESTROY >100 CROP PLANTS. BECAUSE F. OXYSPORUM PATHOGENS ON A GIVEN HOST ARE HIGHLY SPECIFIC TO THAT HOST, IT IS DIFFICULT OR IMPOSSIBLE TO DISTINGUISH PATHOGENS, AND PATHOGENS FROM NON-PATHOGENS, BY ANY MEANS OTHER THAN TIME-CONSUMING AND COSTLY PATHOGENICITY TESTING. A PROMISING APPROACH IS TO DETECT SEQUENCES IN A PATHOGEN GENOME THAT ARE NOT FOUND IN NON-TARGET MICROORGANISMS THAT MAY BE PRESENT IN A GIVEN PLANT, SOIL, WATER OR SEED SAMPLE. HAVING DEVELOPED A 845 ISOLATE GENOME DATASET FROM 66 HOSTS, INCLUDING PATHOGENS, ENDOPHYTES, AND NON-PLANT SUBSTRATES, WE HAVE BEEN SUCCESSFUL IN OUR EFFORTS TO IDENTIFY AND VALIDATE SUCH SEQUENCES IN F. OXYSPORUM PATHOGENS OF STRAWBERRY, LETTUCE AND TOMATO. HOWEVER, THE PROCESS OF DEVELOPING AND VALIDATING MARKERS HAS PROVEN TO BE SLOW AND INEFFICIENT. HERE WE PROPOSE TO DEVELOP AND APPLY A BIOINFORMATIC METHOD TO IDENTIFY AND DEVELOP MARKERS FOR F. OXYSPORUM PATHOGENS ON TEN DIFFERENT HOSTS, THAT CAN BE ADAPTED TO AMPLIFICATION- AS WELL AS NEXT GENERATION SEQUENCING-BASED DETECTION METHODS, WHICH PERMIT DETECTION OF MANY TARGETS IN ONE SAMPLE. OUR PRELIMINARY FINDINGS INDICATE THAT THIS METHOD REVEALS MORE POTENTIAL MARKERS, WHICH ARE OFTEN CLUSTERED IN THE SAME GENOME REGION, PROVIDING THE POTENTIAL FOR EVEN GREATER SPECIFICITY. TO FACILITATE F. OXYSPORUM DIAGNOSTICS IN THE USER COMMUNITY, WE WILL CREATE AND DISSEMINATE VIDEOS, WORKSHOP AND WEBINAR MODULES THAT PROVIDE BASIC INFORMATION ON F. OXYSPORUM, AND THE USE AND DEVELOPMENT OF THESE METHODS.

$1,150,000FY2025National Institute of Food and AgricultureUSDA

The Pennsylvania State University

Investigators

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** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** THE FUNGUS FUSARIUM OXYSPORUM IS A SERIOUS THREAT TO AGRICULTURAL BIOSECURITY, GLOBALLY CAUSING WILT DISEASES THAT DESTROY >100 CROP PLANTS. BECAUSE F. OXYSPORUM PATHOGENS ON A GIVEN HOST ARE HIGHLY SPECIFIC TO THAT HOST, IT IS DIFFICULT OR IMPOSSIBLE TO DISTINGUISH PATHOGENS, AND PATHOGENS FROM NON-PATHOGENS, BY ANY MEANS OTHER THAN TIME-CONSUMING AND COSTLY PATHOGENICITY TESTING. A PROMISING APPROACH IS TO DETECT SEQUENCES IN A PATHOGEN GENOME THAT ARE NOT FOUND IN NON-TARGET MICROORGANISMS THAT MAY BE PRESENT IN A GIVEN PLANT, SOIL, WATER OR SEED SAMPLE. HAVING DEVELOPED A 845 ISOLATE GENOME DATASET FROM 66 HOSTS, INCLUDING PATHOGENS, ENDOPHYTES, AND NON-PLANT SUBSTRATES, WE HAVE BEEN SUCCESSFUL IN OUR EFFORTS TO IDENTIFY AND VALIDATE SUCH SEQUENCES IN F. OXYSPORUM PATHOGENS OF STRAWBERRY, LETTUCE AND TOMATO. HOWEVER, THE PROCESS OF DEVELOPING AND VALIDATING MARKERS HAS PROVEN TO BE SLOW AND INEFFICIENT. HERE WE PROPOSE TO DEVELOP AND APPLY A BIOINFORMATIC METHOD TO IDENTIFY AND DEVELOP MARKERS FOR F. OXYSPORUM PATHOGENS ON TEN DIFFERENT HOSTS, THAT CAN BE ADAPTED TO AMPLIFICATION- AS WELL AS NEXT GENERATION SEQUENCING-BASED DETECTION METHODS, WHICH PERMIT DETECTION OF MANY TARGETS IN ONE SAMPLE. OUR PRELIMINARY FINDINGS INDICATE THAT THIS METHOD REVEALS MORE POTENTIAL MARKERS, WHICH ARE OFTEN CLUSTERED IN THE SAME GENOME REGION, PROVIDING THE POTENTIAL FOR EVEN GREATER SPECIFICITY. TO FACILITATE F. OXYSPORUM DIAGNOSTICS IN THE USER COMMUNITY, WE WILL CREATE AND DISSEMINATE VIDEOS, WORKSHOP AND WEBINAR MODULES THAT PROVIDE BASIC INFORMATION ON F. OXYSPORUM, AND THE USE AND DEVELOPMENT OF THESE METHODS. · GrantIndex