** AWARDS ISSUED PRIOR TO JANUARY 20, 2025, WERE FUNDED UNDER PREVIOUS ADMINISTRATIONS AND MAY NOT REFLECT THE PRIORITIES AND POLICIES OF THE CURRENT ADMINISTRATION.** PANGENOMES, INCLUSIVE OF ALL ALTERNATIVE SEQUENCES AND ALLELES IN A POPULATION TO BE UTILIZED JOINTLY, CAN OVERCOME LIMITATIONS ASSOCIATED WITH USING A SINGLE LINEAR REFERENCE GENOME, WHICH REMAINS THE STANDARD APPROACH. CONCEPTUAL AND TECHNICAL ADVANCES IN RECENT YEARS HAVE MAKE PANGENOME CONSTRUCTION AND APPLICATIONS FEASIBLE. HOWEVER, AS A KEY AGRICULTURAL SPECIES, THERE IS NO PUBLIC EFFORT IN THE DOMESTIC PIG (SUS SCROFA) TO CREATE A REFERENCE PANGENOME THAT INCLUDES COMMERCIAL BREEDS RELEVANT TO THE SWINE INDUSTRY. WE PROPOSE TO ESTABLISH THE SWINE REFERENCE PANGENOME (SRP) PROJECT TO FILL THIS CRITICAL GAP. THE LONG-TERM GOALS ARE TO CONSTRUCT AND CONTINUALLY IMPROVE A PUBLICLY ACCESSIBLE SWINE REFERENCE PANGENOME. WE WILL SAMPLE FROM A DIVERSE POPULATION OF PIGS WITH EMPHASIS ON THE DUROC, LANDRACE, AND YORKSHIRE BREEDS. HIGH QUALITY GENOME ASSEMBLIES WILL BE OBTAINED BY THE TRIO-BINNING APPROACH AND LONG-READ SEQUENCING. THE ASSEMBLIES WILL BE USED TO CONSTRUCT THE SWINE REFERENCE PANGENOME. WE WILL DEMONSTRATE THE VALUE OF THE PANGENOME BY COMPARING PERFORMANCE OF PANGENOME-BASED AND TRADITIONAL LINEAR REFERENCE GENOME-BASED APPLICATIONS. FINALLY, WE WILL ESTIMATE DE NOVO MUTATION RATES IN PIGS FOR ALL TYPES OF MUTATIONS. THIS PROJECT WILL SIGNIFICANTLY ADVANCE SWINE GENETICS RESEARCH AND BENEFIT THE U.S. SWINE INDUSTRY.