** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** THIS RESEARCH SEEKS TO UNDERSTAND THE FREQUENCY AND MECHANISMS BY WHICH PESTS OVERCOME PLANT RESISTANCE TRAITS CONFERRED BY ENGINEERED GENES (BRAG PRIORITY 5I), AND DEVELOP A MONITORING FRAMEWORK TO IMPROVE TRANSGENIC CROP DURABILITY. WE HAVE SHOWN THAT GENOMIC MONITORING CAN TRACK CHANGES IN RESISTANCE GENOTYPES OF WILD PESTS OVER TIME, AND THIS INFORMATION CAN BE LEVERAGED TO DETECT EMERGING RESISTANCE AND TRIGGER REMEDIATION. OUR PRIOR WORK FOCUSED ON SINGLE NUCLEOTIDE POLYMORPHISMS, BUT GENOMIC MONITORING CAN DETECT MULTIPLE TYPES OF GENETIC VARIANTS CONFERRING PEST RESISTANCE. WE RECENTLY FOUND THAT GENE COPY NUMBER VARIANTS (CNVS) STRONGLY CONTRIBUTE TO THE FIELD-EVOLVED TRANSGENIC CROP RESISTANCE OBSERVED IN H. ZEA, OUR PEST MODEL. UNDERSTANDING THE ROLE OF CNVS IN RESISTANCE EVOLUTION WILL BE KEY TO INSECT RESISTANCE MANAGEMENT BECAUSE CNVS OFTEN ACT TO BROADLY INCREASE DETOXIFICATION AND METABOLISM, CONFERRING CROSS RESISTANCE TO MANY COMPOUNDS (INCLUDING INSECTICIDES EXPRESSED BY TRANSGENIC CROPS). OUR PROPOSED WORK WILL GENERATE DATA AND DEVELOP ALGORITHMS TO IMPROVE DETECTION OF EMERGING RESISTANCE CAUSED BY CNVS. USING LONG READ SEQUENCING AND TARGETED HISTORICAL SEQUENCING, WE WILL CHARACTERIZE GENOME WIDE CNVS IN H. ZEA, WHICH WILL PROVIDE IMPORTANT INSIGHT INTO THEIR ROLE IN TRANSGENIC CROP RESISTANCE. TO IMPROVE CNV DETECTION FROM GENOMIC MONITORING DATA, WE WILL DEVELOP A NOVEL ALGORITHM AND BENCHMARK IT AGAINST AVAILABLE TOOLS, PROVIDING A NOVEL RESOURCE FOR AGRICULTURAL RESEARCHERS AND REGULATORS. THIS WORK WILL ADVANCE OUR UNDERSTANDING OF WHICH GENOMIC PATTERNS CORRESPOND TO RESISTANCE ASSOCIATED CNV EVOLUTION AND DEVELOP APPROACHES FOR DETECTION OF THOSE EVOLUTIONARY SIGNALS FROM GENOMIC MONITORING DATA.